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Angoliga
09-22-2019, 08:00 PM
PCA G25_scaled - Africans only
Users & Ancients/Modern Avgs
(09/22/2019)



https://i.imgur.com/LvXCooZ.png


Ancients = ◇
Active Users = x
Modern Samples = ē





Inviting all native Africans to participate, we can update these PCAs as we get more African users and additional Ancient/Modern samples. For the few African users found who've already posted their G25 cords on the forum, I've had them plotted as "x" on the PCAs. To get added on these PCAs, either PM me or post your G25 cords on this thread.

If you don't already have G25 cords, here's how to get them (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and how to run PCAs on your own (it's fairly simple):


How to get your G25 cords:


"send your request and autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) to eurogenesblog@gmail.com and money via PayPal to the same e-mail" (current prices are $12 USD)

Here's an explanation of G25 cords along with instructions on how to run these PCAs for free (link) (http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html)

The PAST data files when running the PCAs are here (https://drive.google.com/open?id=1xpmRwKZV8hrf_R_TpGS7acxxKek3jZun); I'll update them as we get more samples








Sub-Regional PCAs


North-Africans:

https://i.imgur.com/uHaS6jn.png

Tropical-Africans:

https://i.imgur.com/tana38g.png

South-Africans:

https://i.imgur.com/0Axg90p.png


It might've been ideal to have separate threads for these sub-regions but seeing as we're a limited bunch on the forum, one central-thread might suffice. For better resolution, sub-regional PCAs can be updated concurrently as more samples are added.




*Feel free to discuss any observations*

Angoliga
09-23-2019, 10:12 PM
"SM_blackflash16" user added:




Tropical-Africa
https://i.imgur.com/gWW0zOh.png







Africa

https://i.imgur.com/58clgVz.png

Angoliga
09-24-2019, 05:05 AM
Here's an update with Mbuti added:


*Mbuti wasn't initially included because Davidski (creator of G25) had them removed from datasheets; I happened to grab this Mbuti_avg from an old file.
Anyhow, I've reached out for confirmation, if there's nothing fundamentally faulty with the Mbuti sample data, there'd be value in keeping it plotted.





Tropical-Africa





https://i.imgur.com/FbVl8MK.png










Africa

https://i.imgur.com/B5uUxrD.png



Regarding the Ugandan Nilo-Saharans pulling towards African-Archaics, this likely reflects absorption of indigenous Great-Lake HGs. Here's an nMonte run of the UG_ARN samples showing MWI forager, KEN_LSA and Mbuti affinities:

https://i.imgur.com/bqsXIru.png




Malawi forager ancestry circled in red, illustrating the split of Hadza/Mbuti/South-African-like affinities:

https://i.imgur.com/5H1vHhT.png



Fig 1) Skoglund, 17 (https://www.sciencedirect.com/science/article/pii/S0092867417310085#fig1)








Excerpt relating to Ugandan Central-Sudanic and GL-HGs...



https://i.imgur.com/lOtxee8.png
(A New History of Tanzania (https://books.google.ca/books?id=DkyWDwAAQBAJ&pg=PA30&lpg=PA30&dq=May+have+assimilated+the+hunter-gatherers+more+rapidly+and+thoroughly+than+did+the +southern+cushites&source=bl&ots=jeyvBLAdT1&sig=ACfU3U0S2C2Cm9PQqHgWmwIkKtzLZetbHA&hl=en&sa=X&ved=2ahUKEwjVkcXp1ujkAhXnnuAKHWWtCFkQ6AEwAHoECAgQA Q#v=onepage&q=May%20have%20assimilated%20the%20hunter-gatherers%20more%20rapidly%20and%20thoroughly%20th an%20did%20the%20southern%20cushites&f=false), Kimambo 17')


If taken as a literal reflection of GL-HGs, the extra Mbuti-affinity might reflect a prehistoric West>East cline of this Mbuti affinity emanating from the adjacent Congo-basin. Perhaps this gradient also decreased south/eastward to these Malawi HGs with lower Mbuti-affinities.

Bealfire
09-24-2019, 05:08 AM
Isn't Kongo multiethnic?

Angoliga
09-24-2019, 05:17 AM
Isn't Kongo multiethnic?

By Kongo, I think this means the Bantu ethnic group of Kikongo speakers along the Atlantic coast of modern day Congo and Angola.

This is opposed to "Congo" the nation, as in the Democratic Republic of Congo -- I also didn't catch this at first

Angoliga
09-24-2019, 06:06 AM
"EGY_COPT_lifeisdandy" user added:





North-Africa




https://i.imgur.com/jUDv85U.png









Africa



https://i.imgur.com/Lg8tYrB.png

drobbah
09-24-2019, 03:41 PM
Those Somali samples are definitely Borana admixed

Angoliga
09-24-2019, 05:56 PM
Those Somali samples are definitely Borana admixed

Good catch! I think the modern average file I obtained had Ayodo's Kenyan Somalis mixed with Somalis proper.

They're actually distinguished on the individual sample description, this is where they plot:


https://i.imgur.com/lQQ6wO5.png




https://i.imgur.com/ViiM5u0.png



I've now updated the PCAs and split the two with separate avgs (KEN_Somali, SM_Somali):

https://i.imgur.com/DR8YUEq.png

Angoliga
09-30-2019, 09:29 PM
"SM_NetNomad" user added:

https://i.imgur.com/GcgS6js.png


https://i.imgur.com/E872jyv.png


Africa PCA (updated)

https://i.imgur.com/CJDh4EB.png

Sikeliot
09-30-2019, 10:43 PM
Nilotic peoples (Sudanese and the Nilotic Ethiopians like Mursi) plot very similar to West Africans and Bantu peoples. Is this what we would have expected?

NetNomad
10-01-2019, 06:29 AM
Nilotic peoples (Sudanese and the Nilotic Ethiopians like Mursi) plot very similar to West Africans and Bantu peoples. Is this what we would have expected?

On intra-SSA PCAs, especially ones without South/Central hunter-gatherers, their distinction is more clearly visible. They aren't exactly the same.

Angoliga
10-01-2019, 09:48 PM
"SM_Typic (1/4 YMN)" user added:

https://i.imgur.com/v2KB23J.png

https://i.imgur.com/zDjtpz7.png


Africa PCA (updated):

https://i.imgur.com/e0MdduQ.png

Espoir
10-03-2019, 04:44 PM
PCA G25_scaled - Africans only
Users & Ancients/Modern Avgs
(09/22/2019)



https://i.imgur.com/LvXCooZ.png


Ancients = ◇
Active Users = x
Modern Samples = ē





Inviting all native Africans to participate, we can update these PCAs as we get more African users and additional Ancient/Modern samples. For the few African users found who've already posted their G25 cords on the forum, I've had them plotted as "x" on the PCAs. To get added on these PCAs, either PM me or post your G25 cords on this thread.

If you don't already have G25 cords, here's how to get them (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and how to run PCAs on your own (it's fairly simple):


How to get your G25 cords:


"send your request and autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) to eurogenesblog@gmail.com and money via PayPal to the same e-mail" (current prices are $12 USD)

Here's an explanation of G25 cords along with instructions on how to run these PCAs for free (link) (http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html)

The PAST data files when running the PCAs are here (https://drive.google.com/open?id=1xpmRwKZV8hrf_R_TpGS7acxxKek3jZun); I'll update them as we get more samples








Sub-Regional PCAs


North-Africans:

https://i.imgur.com/uHaS6jn.png

Tropical-Africans:

https://i.imgur.com/tana38g.png

South-Africans:

https://i.imgur.com/0Axg90p.png


It might've been ideal to have separate threads for these sub-regions but seeing as we're a limited bunch on the forum, one central-thread might suffice. For better resolution, sub-regional PCAs can be updated concurrently as more samples are added.




*Feel free to discuss any observations*
I see a beautiful Cline from NiloSaharan to North Africans. That says something about Northeast Africans. Does their Eurasian has anything to do with modern North Africans, or itís simply that their Eurasian source population is shared between them(NE African and N. Africans).
Do Biaka has west African admixture or itís another Cline that exist between southern/central and west central HGs?

Angoliga
10-04-2019, 04:28 AM
I see a beautiful Cline from NiloSaharan to North Africans. That says something about Northeast Africans. Does their Eurasian has anything to do with modern North Africans, or itís simply that their Eurasian source population is shared between them(NE African and N. Africans).

I guess you could say the same for West-Africans, honestly I think Ancestral-East-Africans might appear slightly closer to Eurasians just because the sub-set of OOA pops happened to be directly derived from them -- that plus maybe a smudge of EEF-endowed Neolithic North-Africans + Natufian/Ancient-Paleolithic SW-Asian ancestry (~<5%)

It's hard to say without more ancient samples but when you combine Lazadis' model (https://anthrogenica.com/showthread.php?17561-G25-nMonte-Inferring-ANA-Eurasian-layers-in-SSA-pops&p=577101&viewfull=1#post577101), comparative Y-DNA dating (https://anthrogenica.com/showthread.php?17561-G25-nMonte-Inferring-ANA-Eurasian-layers-in-SSA-pops&p=579840&viewfull=1#post579840), and some scanty ancient nMonte runs (https://anthrogenica.com/showthread.php?17561-G25-nMonte-Inferring-ANA-Eurasian-layers-in-SSA-pops&p=576560&viewfull=1#post576560), it's plausible that W-Africans and Ancestral-East-Africans came from a common source population not too long before the last OoA migration ~50ky BP. Here's a hypothetical position of where they might plot:

https://i.imgur.com/aq7gLjj.png
Similar to our recent Neolithic Sub-pluvial, the even stronger Green-Sahara period of the Mousterian-pluvial ~50ky BP (lasting 20ky) would've also triggered mass migrations.

The common Ancient-North-African/Iberomaurusian-like affinity we're seeing among W-Africans and E-Africans like the Dinka would reflect this much older trans-saharan admixture during the Mousterian Pluvial, whereas MAR_EN would reflect trans-saharan ANA admixture during the Neolithic-Subpluvial.

Dating of W-African and archaic-SSA introgression in this (https://anthrogenica.com/showthread.php?17561-G25-nMonte-Inferring-ANA-Eurasian-layers-in-SSA-pops&p=579818&viewfull=1#post579818) Lazardis' model would reflects the western migration of this source population into West-Africa during the M-Pluvial; this might be part of the PaleoDNA in the Shum Laka samples.

Unlike modern West and East-Africans, Ancient South-Africans might lack this ANA/Iberomaurusian-like affinity because they solely inhabited Africa between the Cape and Equatorial-regions; they lack this trans-saharan ANA affinity because they were on the other side of the continent.





Do Biaka has west African admixture or itís another Cline that exist between southern/central and west central HGs?

Not sure TBH but them pulling closer to modern-SSAs does give the impression that they're a lesser "pure-variety" of archaic HGs than Mbuti:

https://i.imgur.com/AujUXGw.png

Angoliga
10-06-2019, 06:12 AM
"RW_TUTSI_Gashagaza" sample added as requested:


* Currently not an active user; indicated as a red-dot here only as a visual reference:

https://i.imgur.com/CGX4AkV.png

Africa PCA updated:
https://i.imgur.com/XWZyaf1.png

GabrielZelalem
10-07-2019, 08:08 PM
What do we have to ask in order to be placed on the maps ? did not really get it sorry

Angoliga
10-07-2019, 10:54 PM
What do we have to ask in order to be placed on the maps ? did not really get it sorry

Hi there,

It'd be interesting seeing where you plot respective to other horners -- you'd be the first of Djiboutian decent!


... here's the steps on how to get added, they're within the spoiler of the initial post (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=603318&viewfull=1#post603318):


If you don't already have G25 cords, here's how to get them (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and how to run PCAs on your own (it's fairly simple):

How to get your G25 cords:


"send your request and autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) to eurogenesblog@gmail.com and money via PayPal to the same e-mail" (current prices are $12 USD)

Here's an explanation of G25 cords along with instructions on how to run these PCAs for free (link) (http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html)

The PAST data files when running the PCAs are here (https://drive.google.com/open?id=1xpmRwKZV8hrf_R_TpGS7acxxKek3jZun); I'll update them as we get more samples


I forgot to mention in the initial post, once you've obtained your cords you'll also be able to compare your ancestry against modern/ancients using nMonte. This is explained in the creator's link above.

Feel free to private-message me if you have any questions,

Angoliga
10-11-2019, 07:33 PM
"DJB_GabrielZelalem" user added:


Our first participant of Dijboutian ancestry seen here nearly overlapping Somali users:

https://i.imgur.com/InUczRC.png

GabrielZelalem
10-11-2019, 09:35 PM
Yeah I’m mostly Isaaq which is a the main tribe in northwestern Somalia. But I expected to be closer to the Oromo/ Ethiopian as I thought I had what seems now to be non-significant arabian ancestry ?! Thank you for that !!!!

Espoir
10-12-2019, 07:26 PM
I see a beautiful Cline from NiloSaharan to North Africans. That says something about Northeast Africans. Does their Eurasian has anything to do with modern North Africans, or itís simply that their Eurasian source population is shared between them(NE African and N. Africans).
Do Biaka has west African admixture or itís another Cline that exist between southern/central and west central HGs?
@NiloSaharan or anyone who might know why,
I was looking again on this PCA, what makes Kakwa and Aringa cluster close to Nilotes despite them showing significant input from West Africans or Bantu. Is there anything else playing in that I donít know of.

NetNomad
10-12-2019, 07:32 PM
"DJB_GabrielZelalem" user added:


Our first participant of Dijboutian ancestry seen here nearly overlapping Somali users:

https://i.imgur.com/InUczRC.png




Yeah I’m mostly Isaaq which is a the main tribe in northwestern Somalia. But I expected to be closer to the Oromo/ Ethiopian as I thought I had what seems now to be non-significant arabian ancestry ?! Thank you for that !!!!

Interesting result GabrielZelalem basically the same as Somalis from North Somalia. However, I think the Ciise / Issa tribe (Somali Dir tribe from Djibouti) may have more Afar-like admixture because they lived in Djibouti for a longer time than the Isaaq (more recently from Somalia) but this may be just speculation on my part.

Angoliga
10-12-2019, 08:08 PM
Yeah Iím mostly Isaaq which is a the main tribe in northwestern Somalia. But I expected to be closer to the Oromo/ Ethiopian as I thought I had what seems now to be non-significant arabian ancestry ?! Thank you for that !!!!

My pleasure, thanks for joining us!



Here's a crude run of you along other Horners:

Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...

https://i.imgur.com/7A1KyrU.png

You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:

*Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...
https://i.imgur.com/V4tMldi.png

So there seems to be something unique in your ancestry which we currently don't have available.

Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.

Angoliga
10-12-2019, 09:49 PM
@NiloSaharan or anyone who might know why,
I was looking again on this PCA, what makes Kakwa and Aringa cluster close to Nilotes despite them showing significant input from West Africans or Bantu. Is there anything else playing in that I donít know of.

It's their East-African forager ancestry pulling them the opposite direction of West-Africans:



These indigenous Ugandans can be modeled as a cross of Hadza/San/Mbuti-like ancestry -- with a higher affinity for the latter compared to MWI HGs:

https://i.imgur.com/5GvaIaI.png


https://i.imgur.com/sHOAUt7.png



They seem closer to Dinka because E_HGs (KEN_LSA, Mota..) are in the opposite-direction of W-Africans, so they plot in an intermediate position making them seem closer to proper-Nilotes.

It's more visually clear on the Tropical-African PCA:
https://i.imgur.com/fINlIEp.png

Espoir
10-12-2019, 10:36 PM
It's their East-African forager ancestry pulling them the opposite direction of West-Africans:



These indigenous Ugandans can be modeled as a cross of Hadza/San/Mbuti-like ancestry -- with a higher affinity for the latter compared to MWI HGs:

https://i.imgur.com/5GvaIaI.png


https://i.imgur.com/sHOAUt7.png



They seem closer to Dinka because E_HGs (KEN_LSA, Mota..) are in the opposite-direction of W-Africans, so they plot in an intermediate position making them seem closer to proper-Nilotes.

It's more visually clear on the Tropical-African PCA:
https://i.imgur.com/fINlIEp.png



It makes more sense now! U guys got very significant HGs ancestry. And did u include any Bantu group? Is all your West Africa fully west african? Or there is Bantu admixture that is hidden it that Igbo( in case u didn’t include any Bantu group)?

GabrielZelalem
10-12-2019, 11:17 PM
My pleasure, thanks for joining us!



Here's a crude run of you along other Horners:

Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...

https://i.imgur.com/7A1KyrU.png

You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:

*Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...
https://i.imgur.com/V4tMldi.png

So there seems to be something unique in your ancestry which we currently don't have available.

Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.


Interesting ! Very surprised about the results;

I already noticed on gedmatch that my results were slightly slightly different in very illogical ways compared to my somali matches. On the oracle feature of GEDmatch, I always appear to have the most distant results to the "Somali typical" out of all my somali relatives (not very significant but still), but I score almost the same distance as them to every other ethnicity available on the oracles. Does it make sense ?

sum1
10-13-2019, 12:25 AM
My pleasure, thanks for joining us!



Here's a crude run of you along other Horners:

Interestingly, you appear to have the highest affinity to Mota (ETH_4500BP) compared to other Somalis...

https://i.imgur.com/7A1KyrU.png

You also have the highest distance (worst fit) among all Horners in this sample-set, even when the most optimal neolithic pastoralist "KEN_pastoral_N" and modern Yemeni are added for a better fit:

*Given the proximity of Djibouti to Arabia, your lower affinity to Yemenis is rather surprising compared to Somalis...
https://i.imgur.com/V4tMldi.png

So there seems to be something unique in your ancestry which we currently don't have available.

Something that stood out: when comparing your results with NetNomad on this second run, both of your affinities are very similar yet your fit seems unproportionately worse.

We'll ultimately know with more regional ancient samples but maybe there's a variation of SW-Asian ancestry in Somalis that's not being fully captured by Natufian or any of these neolithic pastoral samples -- perhaps you harbour a higher amount of this paleolithic SW-Asian ancestry.



I think the problem lies not with a variation of SW-Asian ancestry but rather with the African component. I think we can infer that Somalis may have some unique local hunter-gatherer admixture from somewhere that leads to the bad fits when using Dinka and Mota as the African reference populations in Somalis.

Luckily there is some ancient DNA from Somalia coming soon from the Reich lab so perhaps that may shine some light into whatever the Unique African component is in Somalis that is causing these bad fits.

Angoliga
10-13-2019, 02:45 PM
It makes more sense now! U guys got very significant HGs ancestry. And did u include any Bantu group? Is all your West Africa fully west african? Or there is Bantu admixture that is hidden it that Igbo( in case u didnít include any Bantu group)?

Good questions! Some discretion and historical context helps provide the answers:

Based on comparitive ADMIXTURE results with the Bulala, a closer-proximate to "proto" Central-Sudanic speakers, the Bantu affinity for Aringa and Kakwa would seem around ~<5% -- maybe a little lower for the latter <~2% :



These are comparitive puntDNAL K8 runs of Kakwa and Aringa family members with "proto" Central-Sudanics (CS speakers from central Chad).
I'm careful suggesting them as "proto" because the Bulala clearly have recent Afro-Asiatic ("Western_Semitic") ancestry which proto-CSs lacked -- IMO they're still the best hypothetical proxy available atm

https://i.imgur.com/jxVgfS0.png
*positive and negative delta avgs are highlighted in green and red respectively
*"E_Benue_Congo" cluster is highest among Bantu populations

For contrast, I've included the Alur here at the bottom. They're Luo speakers in the extreme southern and western-end of the Ugandan West-Nile region bordering Congo.


Since linguistic and archaeological data (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=586859&viewfull=1#post586859) suggests Central-Sudanics assimilated E_HGs and entered the Great-Lakes region before Bantu migrations, it'd be more conservative to stick with unadmixed E_HG West-African pops even though minor Bantu (~<5%) can be expected in these UG CS-related groups.

Here's (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=601674&viewfull=1#post601674) a post I replied you with more on the topic, it includes PCAs with Aringa/Kakwa, Darfurians and Bulala, commercial user results, and a crude nMonte run using Bantu

**I'd be remissed if I didn't mention the Azande as a likely source of minor Bantu for Kakwa, Aringa and adjacent South-Sudanese. They're notorious for aggressive eastward expansion from C.A.R. into the Equatoria-region of South-Sudan, interrupting a continuous line of CS-speakers from Lake-Albert to Lake Chad: the word Azande means the people who possess much land




I intend to dedicate a thread on the topic in more detail -- I think it's deserved. I'll also elaborate there on the preference for Igbo when dealing with West-Nile CS-related groups.

Angoliga
10-13-2019, 03:58 PM
"SM_Lank" and "SM_sum1" users added:


* Newly added users are only indicated here with red-X here as a visual reference:



https://i.imgur.com/uLkXZ3c.png

Angoliga
10-13-2019, 06:32 PM
Here's an ad-hoc run of Horners requested by some of our users. I've narrowed down a few pre-selected proxies and ran them against neolithic pastoralists:

(Source samples listed below)


For observational purposes, I've split and ranked Somali and Ethiopians in descending order of their distance%:

https://i.imgur.com/WrsWaA0.png

Source samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289

While removing heavy SSA-neolithic samples, it appears I must have accidentally also removed KEN_Pastoral_N_o and KEN_Pastoral_N_Elmenteitan in the previous run :\
That said, user DJB_GabrielZelalem still has the highest distance with the exception of newly added SM_sum1
KEN_Pastoral_N, followed by TZN_PN look like clear winners for neolithic pastoral ancestry among Horners





I think the problem lies not with a variation of SW-Asian ancestry but rather with the African component. I think we can infer that Somalis may have some unique local hunter-gatherer admixture from somewhere that leads to the bad fits when using Dinka and Mota as the African reference populations in Somalis.


Judging by Ethiopian samples with the highest distance%, it does look like something lacking in their higher Mota and Dinka affinities is rendering a worse fit.

However for Somalis, users with extra KEN_Pastoral_N_o and KEN_Pastoral_N_Elmenteitan have the highest distance%. Referring back to the earlier post, these wide splits of pastoral neolithics might be nMonte trying to find missing Paleolithic-like SW-Asian ancestry which modern SW-Asians now lack, in part due to their high Levantine_LN/EBA affinities.

Ultimately, paleothic samples from both Arabia and in and around Sudan will provide a clearer picture.

Espoir
10-13-2019, 07:57 PM
Good questions! Some discretion and historical context helps provide the answers:

Based on comparitive ADMIXTURE results with the Bulala, a closer-proximate to "proto" Central-Sudanic speakers, the Bantu affinity for Aringa and Kakwa would seem around ~<5% -- maybe a little lower for the latter <~2% :



These are comparitive puntDNAL K8 runs of Kakwa and Aringa family members with "proto" Central-Sudanics (CS speakers from central Chad).
I'm careful suggesting them as "proto" because the Bulala clearly have recent Afro-Asiatic ("Western_Semitic") ancestry which proto-CSs lacked -- IMO they're still the best hypothetical proxy available atm

https://i.imgur.com/jxVgfS0.png
*positive and negative delta avgs are highlighted in green and red respectively
*"E_Benue_Congo" cluster is highest among Bantu populations

For contrast, I've included the Alur here at the bottom. They're Luo speakers in the extreme southern and western-end of the Ugandan West-Nile region bordering Congo.


Since linguistic and archaeological data (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=586859&viewfull=1#post586859) suggests Central-Sudanics assimilated E_HGs and entered the Great-Lakes region before Bantu migrations, it'd be more conservative to stick with unadmixed E_HG West-African pops even though minor Bantu (~<5%) can be expected in these UG CS-related groups.

Here's (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=601674&viewfull=1#post601674) a post I replied you with more on the topic, it includes PCAs with Aringa/Kakwa, Darfurians and Bulala, commercial user results, and a crude nMonte run using Bantu

**I'd be remissed if I didn't mention the Azande as a likely source of minor Bantu for Kakwa, Aringa and adjacent South-Sudanese. They're notorious for aggressive eastward expansion from C.A.R. into the Equatoria-region of South-Sudan, interrupting a continuous line of CS-speakers from Lake-Albert to Lake Chad: the word Azande means the people who possess much land




I intend to dedicate a thread on the topic in more detail -- I think it's deserved. I'll also elaborate there on the preference for Igbo when dealing with West-Nile CS-related groups.

Useful info, thanks!
Create a thread please. I kept playing with your coords, now u fit better as NiloSaharan source population in the face of Nilotes. Seems relevant to me considering interactions in the region of Uganda.
33868

Lank
10-13-2019, 08:02 PM
https://i.imgur.com/V4tMldi.png
One very interesting result here is how well South Omotic speakers (Ari) fit as a fairly even mixture of early Cushitic speakers and aboriginal Ethiopians (Mota), with some added KEN_LSA. The fit is among the lowest of the ones you posted. This strongly implies that Afroasiatic ancestry in Omotic speakers is closely related to Cushitic ancestry. It reaches nearly 50% in the Ari.

drobbah
10-14-2019, 12:10 AM
Sent David my raw data and my mothers.I will send my father's sample (Ethio_Somali) next week.

@Gabriel You seem to have elevated Yoruba admixture.It's quite possible that your Yemeni admixture was maybe from an Afro-Arab.

Ellerbe
10-14-2019, 01:41 AM
@Gabriel You seem to have elevated Yoruba admixture.It's quite possible that your Yemeni admixture was maybe from an Afro-Arab.

he should share his eurogenes k36 results, and k15 too.

drobbah
10-14-2019, 02:05 AM
he should share his eurogenes k36 results, and k15 too.

He's K13 doesn't seem out of place for a Somali

Numidian
10-14-2019, 03:21 AM
Luckily there is some ancient DNA from Somalia coming soon from the Reich lab so perhaps that may shine some light into whatever the Unique African component is in Somalis that is causing these bad fits.

Sorry, this is the first I'm hearing about this. Anybody have more information on where in Somalia this DNA is from and what time period?

NetNomad
10-14-2019, 09:20 AM
Sorry, this is the first I'm hearing about this. Anybody have more information on where in Somalia this DNA is from and what time period?

I believe it is from this archaeological site:

https://www.tandfonline.com/doi/abs/10.1080/00438243.1988.9980055

The samples are somewhere around 8,000 years old (double the age of Mota). I will be interesting how they come out.

GabrielZelalem
10-14-2019, 09:36 AM
He's K13 doesn't seem out of place for a Somali



EUROGENES K13
# Population Percent
1 Northeast_African 54.92
2 Red_Sea 28.12
3 East_Med 9.05
4 Sub-Saharan 6.57
5 West_Med 0.77
6 North_Atlantic 0.57

Single Population Sharing:

# Population (source) Distance
1 Somali 4.06
2 Ethiopian_Oromo 8.35
3 Ethiopian_Wolayta 10.07
4 Ethiopian_Amhara 13.82
5 Ethiopian_Tigray 16.04
6 Ethiopian_Ari_cultivator 27.63
16 Mozabite_Berber 56.3
17 Tunisian 57.75
18 Bedouin 60.13
19 Jordanian 62.28
20 Saudi 62.97


1 Somali + Somali + Somali + Somali @ 4.331881
2 Ethiopian_Oromo + Somali + Somali + Somali @ 5.427871
3 Ethiopian_Amhara + Somali + Somali + Somali @ 5.590342



EUROGENES K36
# Population Percent
1. Northeast African 77.88
2. East African 16.07
3 Central African 3.19
4. West African 1.15
5. North African 0.86
6. Arabian 0.85

The only thing that might be triggering is my Red Sea score which is slightly higher than my matches (ranging from 22%-25%). Again, out of all my relatives I have the highest distance to the "Somali".
Other than that everything seems typical I guess.

NetNomad
10-14-2019, 09:41 AM
GabrielZelalem drobbah

I don't think GabrielZelalem is Afro-Arab admixed. In the previous chart he did not score any Dinka (while most HOAs did) and it looks like the algorithm then placed it all in the Yoruba category as a replacement.

However, I think Typic's Yemeni ancestor may have had elevated Ethiopian-like admixture vs most Yemenis.

GabrielZelalem
10-14-2019, 09:43 AM
Eurogenes EUtest V2 K15
# Population Percent
1 Northeast_African 58.02
2 Red_Sea 25.33
3 Sub-Saharan 7.98
4 East_Med 6.61
5 West_Med 1.62
6 Atlantic 0.41
7 Oceanian 0.04

# Population (source) Distance
1 Somali 3.55
2 Ethiopian_Oromo 8.43
3 Ethiopian_Wolayta 10.03
4 Ethiopian_Amhara 13.82
5 Ethiopian_Tigray 16.44



# Primary Population (source) Secondary Population (source) Distance
1 98.1% Somali + 1.9% Saudi @ 3.3
2 98.4% Somali + 1.6% Moroccan @ 3.44
3 98.6% Somali + 1.4% Bedouin @ 3.45
4 98.8% Somali + 1.2% Yemenite_Jewish @ 3.45

drobbah
10-14-2019, 12:22 PM
This basically confirms that I have Oromo ancestry that is most similar to the Borana.....

Drobbah
Distance: 5.1806% / 0.05180641
Aggregated
45.4 Dinka
39.8 Levant_Natufian
11.4 ETH_4500BP
3.4 Yemenite_Jew

Drobbah's mother
Distance: 5.5115% / 0.05511483
Aggregated
51.0 Dinka
38.4 Levant_Natufian
6.8 Yemenite_Jew
3.8 ETH_4500BP

Average Somali
Distance: 4.8610% / 0.04861030
Aggregated
50.0 Dinka
39.6 Levant_Natufian
5.4 Yemenite_Jew
5.0 ETH_4500BP

Angoliga
10-14-2019, 02:18 PM
"ETH_SM_drobbah" and "ETH_SM_drobbah_XX" added:


* Newly added user & sample indicated here as red X and ē for visual reference


https://i.imgur.com/Yjgw0q0.png

Updated African PCA:
https://i.imgur.com/rt8F2Ut.png

Angoliga
10-14-2019, 02:45 PM
Here's a user-requested rerun of Horners using KEN_Pastoranl_N as the sole proxy for Cushitic ancestry:

https://i.imgur.com/q5GNPzt.png
With *all neolithic pastoralists:
https://i.imgur.com/36aKAwQ.png

Again for observational purposes, I've split and ranked Somali/Ethiopians ethnicities in descending order of their distance%

drobbah
10-14-2019, 03:09 PM
My mother is scoring more Yemeni (Jew + Al Jawf) than the other Somalis except Blackflash.

Using Malay helped me in getting better fits for both myself and my mother for some odd reason.

sum1
10-14-2019, 06:52 PM
Interesting.

My fits are the worse and significantly worse than your average Somali SM samples.

I wonder what's causing this.

Ellerbe
10-14-2019, 06:58 PM
EUROGENES K13
# Population Percent
1 Northeast_African 54.92
2 Red_Sea 28.12
3 East_Med 9.05
4 Sub-Saharan 6.57
5 West_Med 0.77
6 North_Atlantic 0.57

Single Population Sharing:

# Population (source) Distance
1 Somali 4.06
2 Ethiopian_Oromo 8.35
3 Ethiopian_Wolayta 10.07
4 Ethiopian_Amhara 13.82
5 Ethiopian_Tigray 16.04
6 Ethiopian_Ari_cultivator 27.63
16 Mozabite_Berber 56.3
17 Tunisian 57.75
18 Bedouin 60.13
19 Jordanian 62.28
20 Saudi 62.97


1 Somali + Somali + Somali + Somali @ 4.331881
2 Ethiopian_Oromo + Somali + Somali + Somali @ 5.427871
3 Ethiopian_Amhara + Somali + Somali + Somali @ 5.590342



EUROGENES K36
# Population Percent
1. Northeast African 77.88
2. East African 16.07
3 Central African 3.19
4. West African 1.15
5. North African 0.86
6. Arabian 0.85

The only thing that might be triggering is my Red Sea score which is slightly higher than my matches (ranging from 22%-25%). Again, out of all my relatives I have the highest distance to the "Somali".
Other than that everything seems typical I guess.

Yea, I think I'm with NetNomad. From what I see you're not that different from the other Somali users. There will always be statistical variation among members of the same population, because of this I don't know if we can say with certainty that you have elevated Yoruba.

drobbah
10-14-2019, 07:37 PM
Yea, I think I'm with NetNomad. From what I see you're not that different from the other Somali users. There will always be statistical variation among members of the same population, because of this I don't know if we can say with certainty that you have elevated Yoruba.

Scoring West Africa in K36 isn't normal for a Somali.I suggest he runs himself on monte using Yoruba.

Ellerbe
10-14-2019, 08:04 PM
Scoring West Africa in K36 isn't normal for a Somali.I suggest he runs himself on monte using Yoruba.

Actually, it could be normal for a Somali (like =<1%). These gedmatch calculators and even the DIY Dodecad calculators are not representative of your true scores if you were to be ran through the admixture program directly. Hence, relative to an original run on ADMIXTURE, gedmatch scores represent a breaking up of your ancestral composition to similar components; which, while it doesn't represent your scores if you were originally ran through admixture, it can still be used to compare with others uploading their stuff on gedmatch. But because of this complication, nuances have to be taken into consideration (netNomad is aware of the nuances of nMonte and how you're supposed to interpret results based off of it, like he mentioned correctly about his dinka being wholly appropriated to Yoruba; however very few people are aware of the nuances of gedmatch and the diy dodecad program that it relies on to try to mimic an original admixture run; which it can't fully duplicate at all). For instance, on an original admixture run, I can safely guarantee he would score no Arabian, and therefore it is noise. If you were to still believe he has elevated west african, it would then have to be from somali bantus, and given that he is so far up north, that becomes less likely of a possibility. So yes, you are right, that he could verify with nMonte. However, since we just saw how he scores on nMonte, and with everything I've said, I'll make an educated guess that his additional nmonte runs will corroborate that there is nothing unusual about his ancestry--that in fact, it is within the statistical variation of a Somali. Just my two cents.

tl;dr it could be noise

GabrielZelalem
10-14-2019, 09:06 PM
I suggest he runs himself on monte using Yoruba.

33888
I tried with the same populations you used to get as little distance as you could+yoruba, but still score high distance. No Yoruba shows up in here too. But for some reasons, I have a lot more "kenyan somali" than you do? Being from the same clan and same sub-sub-clan (guessed you were also Jibriil Abokor, sorry if I'm wrong) I find it strange that we are this different.

drobbah
10-14-2019, 09:32 PM
33888
I tried with the same populations you used to get as little distance as you could+yoruba, but still score high distance. No Yoruba shows up in here too. But for some reasons, I have a lot more "kenyan somali" than you do? Being from the same clan and same sub-sub-clan (guessed you were also Jibriil Abokor, sorry if I'm wrong) I find it strange that we are this different.
Yes I am also Jibriil Abokor.

We did different runs that's why the results are so vastly different.I only ran Somalia Somalis,Kenyan Somalis,Yemenis,Eth_4500 and Malay.

GabrielZelalem
10-14-2019, 10:16 PM
Seems like nothing changes. 2.28% is the closest distance I'm able to get with all the populations available. 33891

Angoliga
10-14-2019, 10:18 PM
Here's a similar run using our Tutsi-related users:

https://i.imgur.com/fDeuTsM.png

*Yoruba might seem surprisingly low because it's being eaten-up by Dinka (inherently ~25-15% West-African)






Rather than the same KEN_Pastoral_N pastoral preference in Horners, there seems to be a general TZN_PN affinity for these Tutsi-related groups.

Also interesting, a good chunk of their SW-Asian ancestry is being allotted to Natufian rather than other Neolithic pastorals -- this trend doesn't seem as accentuated among Horners (*especially not for Somalis):

https://i.imgur.com/36aKAwQ.png

Since East-African pastoral ancestry is supposedly derived from the Horn, perhaps the surplus of Natufian and the rejection of other neolithic pastoral means it's a SW-Asian affinity that's not derived from the Horn -- perhaps it's more Lower Nile-Valley/Levantine (Sudan, Egypt..).

In the last spoiler, you can see the Natufian surplus happened to be highest for user "ERI_TGY_Lank" and the Agaw -- that might have to do with them being adjacent to North Sudanese pops.

This would explain the seemingly high Sudanese affinity for Tutsi-related groups on commercial tests like 23andMe (separate thread here (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=601990&viewfull=1#post601990)).

*There's no distinction between North and South-Sudan on these particular 23nMe tests, so it's uncertain how much would be Dinka or closer to Sudanese Arabs.

GabrielZelalem
10-14-2019, 10:34 PM
Seems like nothing changes. 2.28% is the closest distance I'm able to get with all the populations available. 33891

Changed the Malay with Afar and then Amhara and it sliiiiightly improved : 33892

drobbah
10-15-2019, 04:02 PM
Here's a similar run using our Tutsi-related users:

https://i.imgur.com/fDeuTsM.png

*Yoruba might seem surprisingly low because it's being eaten-up by Dinka (inherently ~25-15% West-African)






Rather than the same KEN_Pastoral_N pastoral preference in Horners, there seems to be a general TZN_PN affinity for these Tutsi-related groups.

Also interesting, a good chunk of their SW-Asian ancestry is being allotted to Natufian rather than other Neolithic pastorals -- this trend doesn't seem as accentuated among Horners (*especially not for Somalis):

https://i.imgur.com/36aKAwQ.png

Since East-African pastoral ancestry is supposedly derived from the Horn, perhaps the surplus of Natufian and the rejection of other neolithic pastoral means it's a SW-Asian affinity that's not derived from the Horn -- perhaps it's more Lower Nile-Valley/Levantine (Sudan, Egypt..).

In the last spoiler, you can see the Natufian surplus happened to be highest for user "ERI_TGY_Lank" and the Agaw -- that might have to do with them being adjacent to North Sudanese pops.

This would explain the seemingly high Sudanese affinity for Tutsi-related groups on commercial tests like 23andMe (separate thread here (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=601990&viewfull=1#post601990)).

*There's no distinction between North and South-Sudan on these particular 23nMe tests, so it's uncertain how much would be Dinka or closer to Sudanese Arabs.

The extra Natufian for Tigray and the Agaw is probably just their Ethio-Semitic admixture from Yemen expressing itself.I also don't believe there is a difference in the 'non-SSA' ancestry of Horners and of those SE African ethnicities with Cushitic ancestry.The only difference would be that the Horners received an extra layer of Eurasian ancestry from the Arabian Peninsula.

Angoliga
10-15-2019, 05:05 PM
The extra Natufian for Tigray and the Agaw is probably just their Ethio-Semitic admixture from Yemen expressing itself.I also don't believe there is a difference in the 'non-SSA' ancestry of Horners and of those SE African ethnicities with Cushitic ancestry.The only difference would be that the Horners received an extra layer of Eurasian ancestry from the Arabian Peninsula.

If the Natufian affinity is derived from Yemeni ancestry, why isn't it being allotted to the wide array of Yemeni samples included in the run:


Yemenite_Al_Jawf
Yemenite_Jew
Yemenite_Ma'rib
Yemenite_Mahra



Surely, these four samples have a closer affinity to Yemeni pops than Late Epipaleolithic ancestry.

The preference for Natufian in concurrence with the rejection of neoltihic pastorals and Yemenis means it's likely a proxy for something else entirely.

This can be demonstrated on nMonte with a deeper layer of ancestry, I'll process the run when I get home the evening (@work atm)

Stay tuned....

sum1
10-15-2019, 05:55 PM
If the Natufian affinity is derived from Yemeni ancestry, why isn't it being allotted to the wide array of Yemeni samples included in the run:


Yemenite_Al_Jawf
Yemenite_Jew
Yemenite_Ma'rib
Yemenite_Mahra



Surely, these four samples have a closer affinity to Yemeni pops than Late Epipaleolithic ancestry.

The preference for Natufian in concurrence with the rejection of neoltihic pastorals and Yemenis means it's likely a proxy for something else entirely.

This can be demonstrated on nMonte with a deeper layer of ancestry, I'll process the run when I get home the evening (@work atm)

Stay tuned....


Could it be judging by their proximity to Sudan that the extra natufian ancestry could be derived from proto-Beja?

The South Cushitic paper showed differing levels of Eurasian Ancestry in Cushitic populations , perhaps the Proto-Beja were close to or similar to the South Cushitic populations and thus contributed to higher than expected natufian ancestry compared to other Cushitic populations ?

Angoliga
10-15-2019, 10:49 PM
"KEN_SwahiliPrince" user added:


First user of Kenyan descent; compared to Bantu_Kenya he looks to be roughly drifting towards admixed Cushitic/E_African forager pops.



* Newly added user indicated here as X visual reference


https://i.imgur.com/HsBRaqb.png


Updated African PCA:

https://i.imgur.com/mSW2VpE.png

Angoliga
10-16-2019, 02:34 AM
Here's an attempt at a "deeper-layer" run of Horners and Tutsi-related users, this time replacing pastoral neolithics for Levant ancients:


(Source Samples listed here):
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534


Tutsi-related groups:

https://i.imgur.com/FjNqA3o.png

Horners:

https://i.imgur.com/hmiFPcL.png
Not as clear-cut as desired:

Tutsi-related samples appear to have a Levant_PPNC affinity that's lacking in Horners; however, the fits for Horners might be too high for this run to be taken credibly.
Also, the Eritrean Tigrinya and Agaw sample lose distinction when the neolithic pastorals are removed.

Previous runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=610801&viewfull=1#post610801) showing lower fits with pastoral neolithics seems to carry more weight for drawing distinctions in SW-Asian ancestry.

NetNomad
10-16-2019, 07:59 AM
I don't think Somalis descend from these Ancient PN South Cushitic groups while Southeast Africans and Ethiopians largely do. Likely Somalis descend from another Cushitic migration wave that carried different ratios of North African and Nilo-Saharan and subsequently Somalis have admixed with local HGs at a rate of 10-20%. That is my hypothesis.

Lank
10-16-2019, 08:32 AM
I don't think Somalis descend from these Ancient PN South Cushitic groups while Southeast Africans and Ethiopians largely do. Likely Somalis descend from another Cushitic migration wave that carried different ratios of North African and Nilo-Saharan and subsequently Somalis have admixed with local HGs at a rate of 10-20%. That is my hypothesis.
What makes you say Ethiopians but not Somalis descend from SE African pastoralists? :confused: Considering the supposed relation between East and South Cushitic languages, and the M293-related lineages (Y5919) found in Somalis, I'd guess Somalis are more likely to descend from them than Ethiopians. V32 was also reported in the Kenyan ancient DNA.

NetNomad
10-16-2019, 08:40 AM
What makes you say Ethiopians but not Somalis descend from SE African pastoralists? :confused: Considering the supposed relation between East and South Cushitic languages, and the M293-related lineages (Y5919) found in Somalis, I'd guess Somalis are more likely to descend from them than Ethiopians. V32 was also reported in the Kenyan ancient DNA.

They moved through Ethiopia to get to Southeast Africa. Additionally, they have North African/NS/Mota ratios more akin of Ethiopans than of Somalis. As for V32, there are divergent ones like E-BY8114 that could have taken a completely different migration route. Even if he was E-Z813 then there's a ~2 kya gap which is still rather significant (lots can happen in that time). These are just my guesses, nothing is set in stone.

As for E-M293 and E-M293-like lineages found in Somalis. Kenyan Somalis and Southeast Ethiopian Somalis are likely admixed with some populations (mainly South Oromos) that is not present in other Somali populations (ones from the North and East).

To provide some extra context: out of my 330 23andMe relatives (practically all Somali) only one has E-M293 (very rare) and he is from a bordertown between Ethiopia and Kenya and his paternal clan mostly lives in Kenya.

Lank
10-16-2019, 09:14 AM
They moved through Ethiopia to get to Southeast Africa. Additionally, they have North African/NS/Mota ratios more akin of Ethiopans than of Somalis. As for V32, there are divergent ones like E-BY8114 that could have taken a completely different migration route. Even if he was E-Z813 then there's a ~2 kya gap which is still rather significant (lots can happen in that time). These are just my guesses, nothing is set in stone.

As for E-M293 and E-M293-like lineages found in Somalis. Kenyan Somalis and Southeast Ethiopian Somalis are likely admixed with some populations (mainly South Oromos) that is not present in other Somali populations (ones from the North and East).

To provide some extra context: out of my 330 23andMe relatives (practically all Somali) only one has E-M293 (very rare) and he is from a bordertown between Ethiopia and Kenya and his paternal clan mostly lives in Kenya.
Possible, but I'd guess much of the Mota-like admixture in SE Africa rather represents local SE African HG admixture, whereas Ethiopians have become more Mota-admixed with time and later expansions of various groups.

I was thinking about the consistently significant presence of V2881/Y5919 in Somalis from Trombetta 2015, including Somalis from Somalia. Then again sample sizes were rather small and I'm not sure which part of Somalia the sample was from, so perhaps northern Somalis largely lack it?

NetNomad
10-16-2019, 09:27 AM
I was thinking about the consistently significant presence of V2881/Y5919 in Somalis from Trombetta 2015, including Somalis from Somalia. Then again sample sizes were rather small and I'm not sure which part of Somalia the sample was from, so perhaps northern Somalis largely lack it?

So far the non-V32s/non-Ts from the North Somali regions have been E-V16, J1, E-M123, and E-M81. Perhaps other can chime in and add some others they saw. The last two (E-M123 and E-M81) however come from a 'cosmopolitan' clan with a history of coming out of Harar and to have admixed with MENA groups. So not sure how much that says about ancient history.

sum1
10-16-2019, 12:01 PM
Mota is usually favoured in runs over the Kenyan LSA sample that they have along with Hadza and Sandawe for Southern Cushites.

I don't think Southern Cushites migrated through Ethiopia either, I think they migrated along the Red Sea reaching Northern Somalia (Based on Archaeological evidence) by 3000BCE and migrated South picking up local Somali peninsular HG admixture along the way.

NetNomad
10-16-2019, 12:07 PM
I don't think Southern Cushites migrated through Ethiopia either, I think they migrated along the Red Sea reaching Northern Somalia (Based on Archaeological evidence) by 3000BCE and migrated South picking up local Somali peninsular HG admixture along the way.

Do you mean Eastern Cushites? A bit confused. :confused:

sum1
10-16-2019, 12:26 PM
Do you mean Eastern Cushites? A bit confused. :confused:

No Southern Cushities, the ancestors of the Tanzania Luxmanda and Iraqw.

The Harvard paper has them migrating through the white Nile or Ethiopia and reaching Kenya around 3000 BCE ( Lake Turkana).

But there is clear evidence of Pastoralism in Djibouti and Northern Somalia around 3500 BCE which would either mean that there was another Cushitic group migrating that no longer exists or that it was Southern Cushities of which I favour the latter.

The reason being is that the local hunter-gatherers that the Southern Cushities mixed with while some are closely related the LSA Samples, others seem to not show the same ancestry even though it is quite clear that they have some sort of HG ancestry.

The early pastoralists one of whom had high Eurasian ancestry seem to also have some HG ancestry that is not closely related to LSA which leads me to believe that she may have had some divergent ancestry from some source which leads me to believe that it could have been from LSA Somalia.

The fact that Reich went out of his way to test 2 samples from 1980 excavations from Somalia right after the South Cushite paper leads me to think he agrees with me as well.

NetNomad
10-16-2019, 12:36 PM
But there is clear evidence of Pastoralism in Djibouti and Northern Somalia around 3500 BCE which would either mean that there was another Cushitic group migrating that no longer exists or that it was Southern Cushities of which I favour the latter.

I'm going for the hypothesis that they were proto-Eastern Cushites who currently haven't been surveyed by archaeogenetics. :biggrin1:


The fact that Reich went out of his way to test 2 samples from 1980 excavations from Somalia right after the South Cushite paper leads me to think he agrees with me as well.

Perhaps they were interested in those remains to bolster their Northeast African*-origin Pastoral Neolithic theory.

*(as in Egypt/North Sudan).

drobbah
10-16-2019, 05:53 PM
@NiloSaharan Could you add the Kenyan Iron age sample in your run of the forums Horners.It seemed it helped me get a better fit than the one you ran but for some reason my mother stayed in a similar distance range as your run 1.9% - 2.0%

Mine for example:
Distance: 1.4837% / 0.01483694

57.4 KEN_Pastoral_N
26.2 KEN_Pastoral_IA
8.2 KEN_Early_Pastoral_N
3.4 Yemenite_Dhamar
2.2 MAR_EN
0.8 Han_NChina
0.8 Yemenite_Mahra
0.6 KEN_Pastoral_N_Elmenteitan
0.2 Papuan
0.2 MAR_LN


My mother:
Distance: 2.0387% / 0.02038746

65.0 KEN_Pastoral_N
20.0 KEN_Pastoral_IA
5.8 KEN_Pastoral_N_o
4.4 Yemenite_Jew
2.0 MAR_LN
1.2 MAR_Iberomaurusian
0.6 Han_NChina
0.4 KEN_Pastoral_N_Elmenteitan
0.4 Dinka
0.2 Levant_PPNC

Angoliga
10-16-2019, 06:58 PM
@NiloSaharan Could you add the Kenyan Iron age sample in your run of the forums Horners.It seemed it helped me get a better fit than the one you ran but for some reason my mother stayed in a similar distance range as your run 1.9% - 2.0%

Mine for example:
Distance: 1.4837% / 0.01483694

57.4 KEN_Pastoral_N
26.2 KEN_Pastoral_IA
8.2 KEN_Early_Pastoral_N
3.4 Yemenite_Dhamar
2.2 MAR_EN
0.8 Han_NChina
0.8 Yemenite_Mahra
0.6 KEN_Pastoral_N_Elmenteitan
0.2 Papuan
0.2 MAR_LN
My mother:
Distance: 2.0387% / 0.02038746

65.0 KEN_Pastoral_N
20.0 KEN_Pastoral_IA
5.8 KEN_Pastoral_N_o
4.4 Yemenite_Jew
2.0 MAR_LN
1.2 MAR_Iberomaurusian
0.6 Han_NChina
0.4 KEN_Pastoral_N_Elmenteitan
0.4 Dinka
0.2 Levant_PPNC


Horner re-run + KEN_Pastoral_IA :



https://i.imgur.com/zEbCKCc.png

Source samples:
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_IA,-0.4120395,0.080227,-0.015085,-0.0437665,0.002308,-0.026913,-0.009753,0.005884,0.107068,-0.086744,-0.016807,0.0037465,-0.018954,0.0026145,0.0211725,-0.0235345,0.014994,-0.00057,0.014581,-0.011693,0.0016225,0.00915,-0.005238,-0.001627,-0.0011375
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763


*Let's try to use spoilers where we can; we'd like to save as much page-space as possible for discussion* -- very intriguing dialogue here

sum1
10-16-2019, 07:06 PM
Horner re-run + KEN_Pastoral_IA :

(source samples listed below)



https://i.imgur.com/MomWtLz.png

Source samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
KEN_Pastoral_IA,-0.4120395,0.080227,-0.015085,-0.0437665,0.002308,-0.026913,-0.009753,0.005884,0.107068,-0.086744,-0.016807,0.0037465,-0.018954,0.0026145,0.0211725,-0.0235345,0.014994,-0.00057,0.014581,-0.011693,0.0016225,0.00915,-0.005238,-0.001627,-0.0011375
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289


*Let's try to use spoilers where we can; we'd like to save as much page-space as possible for dialogue*


My fits are double the SM average samples.

What on earth could cause that.

Lank
10-16-2019, 08:55 PM
My fits are double the SM average samples.

What on earth could cause that.
Which company did you test with and do you know which chip was used?

Not sure if it makes a difference. You could also try asking Eurogenes.

GabrielZelalem
10-16-2019, 09:47 PM
My fits are double the SM average samples.

What on earth could cause that.

Same here.


Which company did you test with and do you know which chip was used?

Not sure if it makes a difference. You could also try asking Eurogenes.


I personally tested with MyHeritage. I recently shipped my 23andMe saliva sample. Waiting a few weeks now to see if it perfectly matches MyHeritage's raw data results.

sum1
10-16-2019, 09:55 PM
Which company did you test with and do you know which chip was used?

Not sure if it makes a difference. You could also try asking Eurogenes.


I used 23andme and the v5 chip.

I'll send him an email and hopefully get some clarity.

drobbah
10-16-2019, 10:25 PM
What is Chn_tianyuan?

Angoliga
10-16-2019, 11:23 PM
I don't think it has anything to do with quality-control; there's other Horner samples with worst fits, including a Somali sample from the individuals datasheet (https://drive.google.com/file/d/1FSzKKknFGcOgfyA76q9PD7B-n-MJs7L8/view?usp=sharing).

Here's the same previous run with all Horner individuals + users ( = 159 total):



*Feel free to run the samples from the Eurogenes site (https://bga101.blogspot.com/2019/07/getting-most-out-of-global25.html) using Vahaduo (https://vahaduo.github.io/vahaduo/)*




Here's a screenshot of the worst fits:

https://i.imgur.com/1QmqZJo.png


Best fits:

https://i.imgur.com/9krxeJZ.png
These Mursi and Gumuz samples being among the worse fits (159 n) does go along with your notion of an uncaptured HG/Mota-affinity.

Maybe it's more similar to the Chabu-like affinity seen in these admix runs:

https://i.imgur.com/n1zi5kz.png
(Gopalan et al, 2019 (https://www.biorxiv.org/content/10.1101/517730v1.full))
It might be revealing that you and "DJB_Gabriel.." are both Northern Somali (Issaq clan) and among the worse fits out of all 159 Horner samples.

Rather than a distinguished Horner HG-affinity, I'd still wager it's a Paleolithic/LSA Arabian affinity -- neither of you are leaking any extra Mota or Dinka (*W-African embedded) ... the higher distance% and wide affinity for outlier pastoralists is likely nMonte trying to compensate for "ghost" SW-Asian affinities.
It would go with a West-East cline of Neolithic pastoral Cushitic affinity, being highest among Highland Ethiopians and decreasing towards Ethio-Somalis before reaching the extreme northeaster-end of the Horn.

That's entirely conjecture on my part *pending ancient samples; we'd also need higher regional resolution for validation.

Angoliga
10-16-2019, 11:34 PM
Double Post

drobbah
10-16-2019, 11:42 PM
I don't think it has anything to do with quality-control; there's other Horner samples with worst fits, including a Somali sample from the individuals datasheet (https://drive.google.com/file/d/1FSzKKknFGcOgfyA76q9PD7B-n-MJs7L8/view?usp=sharing).

Here's the same previous run with all Horner individuals + users ( = 159 total):



*Feel free to run the samples from the Eurogenes site (https://bga101.blogspot.com/2019/07/getting-most-out-of-global25.html) using Vahaduo (https://vahaduo.github.io/vahaduo/)*




Here's a screenshot of the worst fits:

https://i.imgur.com/1QmqZJo.png


Best fits:

https://i.imgur.com/9krxeJZ.png
These Mursi and Gumuz samples being among the worse fits (159 n) does go along with your notion of an uncaptured HG/Mota-affinity.

Maybe it's more similar to the Chabu-like affinity seen in these admix runs:

https://i.imgur.com/n1zi5kz.png
(Gopalan et al, 2019 (https://www.biorxiv.org/content/10.1101/517730v1.full))
It might be revealing that you and "DJB_Gabriel.." are both Northern Somali (Issaq clan) and among the worse fits out of all 159 Horner samples.

Rather than a distinguished Horner HG-affinity, I'd still wager it's a Paleolithic/LSA Arabian affinity -- neither of you are leaking any extra Mota or Dinka (*W-African embedded) ... the higher distance% and wide affinity for outlier pastoralists is likely nMonte trying to compensate for "ghost" SW-Asian affinities.
It would go with a West-East cline of Neolithic pastoral Cushitic affinity, being highest among Highland Ethiopians and decreasing towards Ethio-Somalis before reaching the extreme northeaster-end of the Horn.

That's entirely conjecture *pending ancient samples, we'd also need higher regional resolution for validation.

My mother and I are both Isaaqs.I don't think Gabriel's terrible fit has anything to do with the entire Isaaq clan or the entire North.

sum1
10-17-2019, 12:08 AM
I don't think it has anything to do with quality-control; there's other Horner samples with worst fits, including a Somali sample from the individuals datasheet (https://drive.google.com/file/d/1FSzKKknFGcOgfyA76q9PD7B-n-MJs7L8/view?usp=sharing).

Here's the same previous run with all Horner individuals + users ( = 159 total):



*Feel free to run the samples from the Eurogenes site (https://bga101.blogspot.com/2019/07/getting-most-out-of-global25.html) using Vahaduo (https://vahaduo.github.io/vahaduo/)*




Here's a screenshot of the worst fits:

https://i.imgur.com/1QmqZJo.png


Best fits:

https://i.imgur.com/9krxeJZ.png
These Mursi and Gumuz samples being among the worse fits (159 n) does go along with your notion of an uncaptured HG/Mota-affinity.

Maybe it's more similar to the Chabu-like affinity seen in these admix runs:

https://i.imgur.com/n1zi5kz.png
(Gopalan et al, 2019 (https://www.biorxiv.org/content/10.1101/517730v1.full))
It might be revealing that you and "DJB_Gabriel.." are both Northern Somali (Issaq clan) and among the worse fits out of all 159 Horner samples.

Rather than a distinguished Horner HG-affinity, I'd still wager it's a Paleolithic/LSA Arabian affinity -- neither of you are leaking any extra Mota or Dinka (*W-African embedded) ... the higher distance% and wide affinity for outlier pastoralists is likely nMonte trying to compensate for "ghost" SW-Asian affinities.
It would go with a West-East cline of Neolithic pastoral Cushitic affinity, being highest among Highland Ethiopians and decreasing towards Ethio-Somalis before reaching the extreme northeaster-end of the Horn.

That's entirely conjecture on my part *pending ancient samples; we'd also need higher regional resolution for validation.

Could Somalis have assimilated those same Paleolithic/LSA Arabians that Yemenis also assimilated/absorbed thus explaining the weird affinity that the runs have towards a Yemeni sample when Somalis have no known Yemeni ancestry or vice versa?

33942

Angoliga
10-17-2019, 12:29 AM
My mother and I are both Isaaqs.I don't think Gabriel's terrible fit has anything to do with the entire Isaaq clan or the entire North.

https://2.bp.blogspot.com/-KcQg4lIQj_o/V9CPLNvIheI/AAAAAAAAMtQ/o9KNBGpJwAok3piYiw8aINz_8zi8hIRTgCLcB/s1600/Somalia%2BTribes%2BDistribution%2Bin%2BKenya%252C% 2BSomalia%252C%2BDjibouti%252C%2BEthiopia.jpg
*Please use the spoiler feature where possible to subwindow large images*


Oh, I thought you mentioned being Borana admixed?

Two samples from Northern-Somalia showing among the top 6 worse fits of 159 horner samples is still rather curious.

Anyhow, as mentioned, we'll need higher regional resolution and ancient samples for validation.



What is Chn_tianyuan?

It's a proxy I use for ancient-asian-like affinities, it pops up every now and then among modern North and East-Africans. It can appear papuan/malagasy and sometimes gets modeled with paleolithic samples:

https://i.imgur.com/hAsM4r7.png

drobbah
10-17-2019, 12:42 AM
In both your runs and my own personal ones, adding Austronesians or a combination of North Han + Papuan had resulted in greatly improved fits.I just don't know if this East Asian ancestry is historical geneflow via the Indian Ocean trade or if it's something more deep/ancient.

Even on world pca plots,I plot East of Horners slightly drifting towards the East Asians.

Espoir
10-17-2019, 03:50 AM
Here's an attempt at a "deeper-layer" run of Horners and Tutsi-related users, this time replacing pastoral neolithics for Levant ancients:


(Source Samples listed here):
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534


Tutsi-related groups:

https://i.imgur.com/FjNqA3o.png

Horners:

https://i.imgur.com/hmiFPcL.png
Not as clear-cut as desired:

Tutsi-related samples appear to have a Levant_PPNC affinity that's lacking in Horners; however, the fits for Horners might be too high for this run to be taken credibly.
Also, the Eritrean Tigrinya and Agaw sample lose distinction when the neolithic pastorals are removed.

Previous runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=610801&viewfull=1#post610801) showing lower fits with pastoral neolithics seems to carry more weight for drawing distinctions in SW-Asian ancestry.
Letís look at a broader spectrum by adding two Iraqw samples using same reference pops as the above.
33944

Iraqw seem to carry elevated Mota.

Espoir
10-17-2019, 05:10 PM
Here's a similar run using our Tutsi-related users:

https://i.imgur.com/fDeuTsM.png

*Yoruba might seem surprisingly low because it's being eaten-up by Dinka (inherently ~25-15% West-African)






Rather than the same KEN_Pastoral_N pastoral preference in Horners, there seems to be a general TZN_PN affinity for these Tutsi-related groups.

Also interesting, a good chunk of their SW-Asian ancestry is being allotted to Natufian rather than other Neolithic pastorals -- this trend doesn't seem as accentuated among Horners (*especially not for Somalis):

https://i.imgur.com/36aKAwQ.png

Since East-African pastoral ancestry is supposedly derived from the Horn, perhaps the surplus of Natufian and the rejection of other neolithic pastoral means it's a SW-Asian affinity that's not derived from the Horn -- perhaps it's more Lower Nile-Valley/Levantine (Sudan, Egypt..).

In the last spoiler, you can see the Natufian surplus happened to be highest for user "ERI_TGY_Lank" and the Agaw -- that might have to do with them being adjacent to North Sudanese pops.
Interesting, can u add both ancient&modern North African groups in presence of ancient&present SW Asian pops? To see what happens.


33948
Iraqw don’t show much of the Levantine ancestry.
Now, my question here is did ancestors of Tutsis split early on in the southward expansion? Iraqw seem to have low/lack LSA ancestry, yet in Tutsis it’s very pronounced.



This would explain the seemingly high Sudanese affinity for Tutsi-related groups on commercial tests like 23andMe (separate thread here (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=601990&viewfull=1#post601990)).
Great observation. It seems unusual. The question would be , is this Sudan including North Sudan as far as Tutsi-related groups are concerned? I score 30% Sudan and this is the lowest I’ve seen. Everyone else(Tutsis) is somewhere between me and an individual that scores 66% Sudan. Average is about 50%.

*There's no distinction between North and South-Sudan on these particular 23nMe tests, so it's uncertain how much would be Dinka or closer to Sudanese Arabs.

Angoliga
10-18-2019, 12:04 AM
Letís look at a broader spectrum by adding two Iraqw samples using same reference pops as the above.
33944

Iraqw seem to carry elevated Mota.

Yes, the Mota-like HG affinity would've already beeen embedded in these neolithic pastoralists migrating from the Horn:

https://i.imgur.com/ub3JaRG.png

*Notice the gradual chronological decrease of Natufian, and increase of Dinka from the Early-Neolithic down to the Iron-Age: would the end result be more or less your modern-day Masai/Turkana pastoralist (*prior to Bantu assimilation)?



At the other end of the Great-Lakes region, it's interesting to note these Ugandan West-Nilers have elevated Mbuti and KEN_LSA affinities lacking in these South-Cushitic speakers:

https://i.imgur.com/aMhi5BP.png
This goes along with Central-Sudanics having assimilated GL-HGs during the Kansyore Pottery culture (posted here (https://anthrogenica.com/showthread.php?17840-Great-Lakes(Africa)-peoples%92-23andme-results&p=587954&viewfull=1#post587954)).

Angoliga
10-18-2019, 12:26 AM
In both your runs and my own personal ones, adding Austronesians or a combination of North Han + Papuan had resulted in greatly improved fits.I just don't know if this East Asian ancestry is historical geneflow via the Indian Ocean trade or if it's something more deep/ancient.

Even on world pca plots,I plot East of Horners slightly drifting towards the East Asians.

Given your ancestry, I think it's more likely a relic of something more archaic -- the minor affinity towards Papuan/Oceanians might reflect affinities of earlier ~(70kya) OoAs returning home:


"We find a genetic signature in present-day Papuans suggesting that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMH) Out-of-Africa (xOoA). Together with evidence from the Western Asian fossil record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMH out of Africa earlier than 75kya....

...This favours a small presence of xOoA lineages rather than Denisova admixture alone as the likely cause of the observed deep African-Papuan split. We also show (Methods) that such a scenario is compatible with the observed mtDNA and Y chromosome lineages in Oceania, as also previously argued."(Pagani, 2016 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164938/))



Since ancestry from that earlier OoA expansion is now extinct, apart from minor traces in Papuan/Oceanians, maybe those minor Papuan-like affinities are the closest thing nMonte can find -- it might go in hand with the asian-origin hypothesis for M1 in East and North-Africa


A few of us have also noticed this minor East-Asian affinities, according to GeseDNA's older runs I'm 2.62% (https://anthrogenica.com/showthread.php?14477-From-which-island-area-is-my-Oceanian&p=602204&viewfull=1#post602204) South-Chinese! Lol



User SwahiliPrince was shown to be 2.13% (https://anthrogenica.com/showthread.php?12745-GeseDNA&p=316416&viewfull=1#post316416) -- although more plausible for him given his coastal Indian-Ocean ancestry, Hurricane of Berber Tunisian decent has also noticed the same repeatedly: From which island/area is my Oceanian? (https://anthrogenica.com/showthread.php?14477-From-which-island-area-is-my-Oceanian)

I think you've been here long enough to remember this fun thread: Ancient Eurasia K6 - Deducing Traces of Back to Africa Migrations (https://anthrogenica.com/showthread.php?9831-Ancient-Eurasia-K6-Deducing-Traces-of-Back-to-Africa-Migrations)


Respectively, maybe this minor layer is cached in our elevated Paleolithic African ancestry (Iberomaurusian, KEN_LSA, ETH_4500BP...)? -- that seems to be the one thing we all have in common.


... still waiting on Academia for confirmation

Angoliga
10-18-2019, 02:17 AM
Interesting, can u add both ancient&modern North African groups in presence of ancient&present SW Asian pops? To see what happens.


33948
Iraqw donít show much of the Levantine ancestry.
Now, my question here is did ancestors of Tutsis split early on in the southward expansion? Iraqw seem to have low/lack LSA ancestry, yet in Tutsis itís very pronounced.



Great observation. It seems unusual. The question would be , is this Sudan including North Sudan as far as Tutsi-related groups are concerned? I score 30% Sudan and this is the lowest Iíve seen. Everyone else(Tutsis) is somewhere between me and an individual that scores 66% Sudan. Average is about 50%.

Good catch -- Adding to your point, on the runs further below KEN_LSA appears higher for Sandawe (Central TZ) compared to the Iraqw (Northern TZ). Tutsi-related groups might've absorbed more KEN_LSA on their curved South>West>Northern migration of the Rift-Valley:
https://i.imgur.com/VINBGCl.png
The last extension of that migration would be the Ugandan Banyoro on the eastern-side of Lake Albert, and the Hema to the west in DRC.... and that's where our two migrations collide "so-to-speak". It's ironic we're having this discussion, the Northern Hema pastoralists actually speak a Central-Sudanic language (Lendu) -- the Lendu people are their northern neighbors.


As requested, here's a run with ancient/modern North-Africans along with SW-Asians:


Tutsi-related
Horner
Misc. Great-Lake



(Source Samples)
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
Moroccan_South,-0.1844646,0.119896,0.0007308,-0.0569288,0.0239659,-0.0268258,-0.0321962,0.0152301,0.0538154,0.0285428,0.0060591,-0.0068189,0.0227358,-0.0173318,0.0181018,-0.0153306,0.0010921,-0.0189241,-0.0407889,0.0085196,-0.0148254,-0.038456,0.0240718,-0.0034944,0.0054934
Moroccan_North,-0.0299735,0.1373221,-0.0030378,-0.0673993,0.0280564,-0.0319174,-0.0244542,0.0050512,0.0609822,0.0327317,0.0059091,-0.0065526,0.0185908,-0.0147102,0.0151403,-0.0105629,0.0012604,-0.0179828,-0.040747,0.0092961,-0.0121937,-0.0346297,0.0214382,-0.0055763,0.0043974
Algerian,-0.0680567,0.1327805,-0.0071652,-0.0677358,0.0212218,-0.0300737,-0.0221204,0.007442,0.0530313,0.0250954,0.0055076,-0.0061695,0.0208558,-0.0138598,0.0130235,-0.0101707,-0.0033574,-0.0164009,-0.0316446,0.0071597,-0.0096392,-0.0282908,0.0181892,-0.0002661,0.0012922
Moroccan,-0.0853671,0.1302133,-0.0128221,-0.0708806,0.0211321,-0.03294,-0.0277833,0.0097687,0.0554032,0.0243993,0.0095087,-0.0090252,0.0269902,-0.0144658,0.0163016,-0.0061874,-0.0027669,-0.0170326,-0.0384216,0.0094351,-0.0098438,-0.0295119,0.0209111,-0.0011248,0.0059207
Berber_MAR_ERR,-0.0923593,0.1309307,-0.0032863,-0.0711984,0.0256529,-0.0324909,-0.0312229,0.0101041,0.0673468,0.0299258,0.0098476,-0.0059732,0.021662,-0.0161411,0.0201934,-0.0141398,-0.005979,-0.0213652,-0.0461312,0.0094778,-0.0164531,-0.0416268,0.024808,-0.0020657,0.0053715
Mozabite,-0.0649782,0.135551,-0.0032793,-0.0717622,0.0260249,-0.0328364,-0.0260656,0.0108257,0.0617306,0.0303463,0.0065097,-0.006366,0.021795,-0.0165685,0.0163159,-0.016176,-0.0027097,-0.0219282,-0.0435571,0.0082757,-0.0146263,-0.0367947,0.0246817,-0.0042277,0.0056594
Tunisian,-0.048517,0.1313841,-0.0150849,-0.0751379,0.019619,-0.0306779,-0.022091,0.005019,0.0543778,0.0197954,0.0054402,-0.0080365,0.0267404,-0.0101842,0.013046,-0.0071432,-0.003716,-0.0129222,-0.0290048,0.0051745,-0.0104502,-0.0228294,0.0181174,-0.0033439,0.0002096
Berber_MAR_TIZ,-0.1025221,0.131656,-0.0023166,-0.0759511,0.0310606,-0.0356582,-0.0335058,0.012016,0.0766524,0.0315659,0.0088154,-0.0092596,0.0247308,-0.0204174,0.0203483,-0.0157212,0.0001119,-0.0288305,-0.0534217,0.0119165,-0.0208205,-0.0511129,0.0307414,-0.0051899,0.0074671
Berber_Tunisia_Chen,-0.0279499,0.1390711,-0.0080871,-0.0764792,0.0277316,-0.0352023,-0.0313867,0.0052818,0.0684246,0.0297957,0.0040057,-0.0043877,0.0196314,-0.0161248,0.0140923,-0.0169052,0.0001521,-0.0232896,-0.0467247,0.0078579,-0.0168314,-0.0404275,0.0281347,-0.0044517,0.0063666
Berber_Tunisia_Sen,-0.0391015,0.1347667,-0.0189668,-0.0779,0.0188088,-0.0355667,-0.0216624,0.005864,0.0576878,0.0205605,0.0056455,-0.0122362,0.0263216,-0.009407,0.0124783,-0.0050072,-0.0056909,-0.0131682,-0.0303375,0.0115203,-0.0085143,-0.0241851,0.0149999,-4.95E-05,0.0005494
Saharawi,-0.0954217,0.1313418,-0.0096637,-0.0806827,0.024171,-0.0353959,-0.0328818,0.00899,0.0773356,0.0288843,0.0107311,-0.0093667,0.0305622,-0.0155687,0.0234344,-0.0147728,-0.0038028,-0.0248837,-0.048598,0.0124435,-0.0150776,-0.0415525,0.0278694,-0.0028416,0.007589
Libyan,-0.0476858,0.1309498,-0.0219326,-0.080954,0.0089733,-0.0345677,-0.020953,0.0030243,0.0520675,0.0098215,0.0061365,-0.0123917,0.0292235,-0.0049978,0.0085218,-0.0005094,-0.003788,-0.0095751,-0.0201184,0.0112686,-0.0028108,-0.0132634,0.0093993,0.0007991,-0.0002963
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Egyptian,-0.01548,0.1341176,-0.042778,-0.0872208,-0.0044008,-0.0333553,-0.0137874,0.0005691,0.037605,0.0011968,0.0069772,-0.0087772,0.0229334,0.0018258,-0.0005202,-6.19E-05,-0.003303,-0.0026182,-0.0034861,0.0032432,-0.0005781,-0.0022875,0.0008381,0.0008636,-0.0004072
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
EGY_Hellenistic,0.040976,0.159438,-0.055437,-0.102068,0,-0.060798,-0.023266,-0.008307,0.048472,0.007472,0.015427,-0.019782,0.034341,-0.004129,0.00475,-0.015646,-0.024121,0.007348,-0.005028,-0.00025,-0.004617,0.008285,-0.012571,0.005302,-0.005987
EGY_Late_Period,0.050082,0.146744,-0.042426,-0.1183805,-0.0020005,-0.049782,-0.015628,-0.004731,0.0474495,0.006196,0.0090125,-0.011465,0.029732,-0.005849,-0.0008145,-0.0020555,-0.0074315,-0.0019635,-0.0035195,0.0120055,0.005615,0.0016695,0.0036355,0 .003916,-0.0005985
Palestinian,0.0455292,0.134253,-0.0473285,-0.0780045,-0.0126482,-0.0297299,-0.0062276,-0.0019845,0.0167504,-0.0003096,0.0081843,-0.0096364,0.0203072,-0.0013211,-0.00095,0.0097452,-0.0020079,-0.001761,8.81E-05,0.0025387,0.0011356,0.0052801,-0.0001603,0.0023977,0.001844
BedouinA,0.0285823,0.1335987,-0.047601,-0.0827598,-0.0138829,-0.0323513,-0.0107061,-0.0046408,0.0234522,-0.0016198,0.0081734,-0.0107237,0.0247439,0.0004741,0.0015682,0.0070567,-0.0027381,-0.0022382,-0.0034079,0.008254,0.0002081,0.002528,0.0001916,0. 0017672,-0.0015967
BedouinB,0.041925,0.1439232,-0.0598156,-0.1169808,-0.0093179,-0.0480622,-0.0141008,-0.0087432,0.05154,-0.0052038,0.0158689,-0.0305729,0.0629496,0.004855,0.0043959,0.0288529,-0.0199706,0.00366,-0.0040153,0.029,0.0109668,0.0152299,-0.0039166,0.0071025,-0.0083092
Saudi,0.0494498,0.1411588,-0.0646136,-0.1161014,-0.0115919,-0.0481242,-0.0133696,-0.008179,0.0516537,-0.0058923,0.016293,-0.0318551,0.063346,0.0021408,0.0031818,0.0271809,-0.0220493,0.0042931,-0.0003213,0.0302646,0.0130601,0.0168853,-0.0072031,0.0082741,-0.0097528
Yemenite_Al_Bayda,0.0386997,0.1386198,-0.0626647,-0.1073983,-0.0101557,-0.0484803,-0.0131608,-0.0101533,0.0541308,-0.0059835,0.0109612,-0.0287995,0.0509163,0.004106,0.0063788,0.0241973,-0.018471,0.0071578,0.0008378,0.0179253,0.0097745,0 .0161778,-0.0074358,0.0011248,-0.003752
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Amran,0.0458544,0.135428,-0.0615246,-0.1014453,-0.0148599,-0.0421523,-0.0087289,-0.0077631,0.0450098,-0.0042566,0.0117499,-0.0229617,0.0465096,0.0052591,0.003994,0.0172555,-0.0141374,0.0042531,0.0018316,0.0157038,0.0069254, 0.0095212,-0.0063297,0.0041742,-0.0047812
Yemenite_Dhamar,0.035538,0.1411586,-0.0585374,-0.1105743,-0.0095742,-0.0472254,-0.0137351,-0.0080253,0.0492449,-0.0078563,0.0137851,-0.0263932,0.0492728,0.0059482,0.0034836,0.0152478,-0.016211,0.0045749,0.0006564,0.0170358,0.010107,0. 0114172,-0.0069568,0.0042307,-0.0030601
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289



Tutsi-related:
https://i.imgur.com/enMfACd.png

Horners:
https://i.imgur.com/TO0fxtW.png

Misc. Great-Lake pops:
https://i.imgur.com/ibiIp10.png



One noticeable distinction I noticed, Tutsi-related groups show a "Bedouin B" affinity lacking among Horners -- when it does appears in the Horn, it's only evident for ETH_Tigray and user "ERI_TGY_Lank" (Tigrinya).

Could this relate to the "extra" Natufian affinity in those earlier runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=610801&viewfull=1#post610801)? Could it be a proxy for some kind of N. Sudanese ancestry?

Espoir
10-18-2019, 02:28 AM
Yes, the Mota-like HG affinity would've already beeen embedded in these neolithic pastoralists migrating from the Horn:
And it totally makes sense. Iraqw are clearly descended from those PN, judging from haplogroups and elevated Mota/like ancestry.

What doesn’t make sense is how Tutsis despite haplogroups showing a PN origin, their Mota-like is not proportionate to what you would expect from a group that descend Savannah PN. Another thing u have mentioned before is almost entirely all the Eurasian portion for Cushitic, Semitic speaking, PN and south cushitic speakers is from Levant Natufian. Yet, for Tutsis, it doesn’t seem to be the case.


https://i.imgur.com/ub3JaRG.png

*Notice the gradual chronological decrease of Natufian, and increase of Dinka from the Early-Neolithic down to the Iron-Age: would the end result be more or less your modern-day Masai/Turkana pastoralist (*prior to Bantu assimilation)?
That is from the Nilotic expansion in Southern East Africa.
One thing I’m yet to know is if this elevated Dinka-like ancestry in Tutsis is of the Iron Age or older or very recent. Judging from these (https://anthrogenica.com/showthread.php?18015-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) Mt haplogroups can anybody answer my question right

Espoir
10-18-2019, 03:12 AM
Good catch -- Adding to your point, on the runs further below KEN_LSA appears higher for Sandawe (Central TZ) compared to the Iraqw (Northern TZ). Tutsi-related groups might've absorbed more KEN_LSA on their curved South>West>Northern migration of the Rift-Valley:
https://i.imgur.com/VINBGCl.png
The last extension of that migration would be the Ugandan Banyoro on the eastern-side of Lake Albert, and the Hema to the west in DRC.... and that's where our two migrations collide "so-to-speak". It's ironic we're having this discussion, the Northern Hema pastoralists actually speak a Central-Sudanic language (Lendu) -- the Lendu people are their northern neighbors.
Since u mention that, relations btwn Tutsis and hunter-gatherers seems to have been great throughout history.
Also one guy from the ruling Luo dynasty of Bunyoro genetically is indistinguishable from Tutsis. It’s dope how he carries E-M75. Why I say this is to hypothesize that relations btwn Tutsi-related group with Luo might have been extended to the pint that MAYBE many Luos(Biito) assimilated in them.



As requested, here's a run with ancient/modern North-Africans along with SW-Asians:


Tutsi-related
Horner
Misc. Great-Lake



(Source Samples)
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
Moroccan_South,-0.1844646,0.119896,0.0007308,-0.0569288,0.0239659,-0.0268258,-0.0321962,0.0152301,0.0538154,0.0285428,0.0060591,-0.0068189,0.0227358,-0.0173318,0.0181018,-0.0153306,0.0010921,-0.0189241,-0.0407889,0.0085196,-0.0148254,-0.038456,0.0240718,-0.0034944,0.0054934
Moroccan_North,-0.0299735,0.1373221,-0.0030378,-0.0673993,0.0280564,-0.0319174,-0.0244542,0.0050512,0.0609822,0.0327317,0.0059091,-0.0065526,0.0185908,-0.0147102,0.0151403,-0.0105629,0.0012604,-0.0179828,-0.040747,0.0092961,-0.0121937,-0.0346297,0.0214382,-0.0055763,0.0043974
Algerian,-0.0680567,0.1327805,-0.0071652,-0.0677358,0.0212218,-0.0300737,-0.0221204,0.007442,0.0530313,0.0250954,0.0055076,-0.0061695,0.0208558,-0.0138598,0.0130235,-0.0101707,-0.0033574,-0.0164009,-0.0316446,0.0071597,-0.0096392,-0.0282908,0.0181892,-0.0002661,0.0012922
Moroccan,-0.0853671,0.1302133,-0.0128221,-0.0708806,0.0211321,-0.03294,-0.0277833,0.0097687,0.0554032,0.0243993,0.0095087,-0.0090252,0.0269902,-0.0144658,0.0163016,-0.0061874,-0.0027669,-0.0170326,-0.0384216,0.0094351,-0.0098438,-0.0295119,0.0209111,-0.0011248,0.0059207
Berber_MAR_ERR,-0.0923593,0.1309307,-0.0032863,-0.0711984,0.0256529,-0.0324909,-0.0312229,0.0101041,0.0673468,0.0299258,0.0098476,-0.0059732,0.021662,-0.0161411,0.0201934,-0.0141398,-0.005979,-0.0213652,-0.0461312,0.0094778,-0.0164531,-0.0416268,0.024808,-0.0020657,0.0053715
Mozabite,-0.0649782,0.135551,-0.0032793,-0.0717622,0.0260249,-0.0328364,-0.0260656,0.0108257,0.0617306,0.0303463,0.0065097,-0.006366,0.021795,-0.0165685,0.0163159,-0.016176,-0.0027097,-0.0219282,-0.0435571,0.0082757,-0.0146263,-0.0367947,0.0246817,-0.0042277,0.0056594
Tunisian,-0.048517,0.1313841,-0.0150849,-0.0751379,0.019619,-0.0306779,-0.022091,0.005019,0.0543778,0.0197954,0.0054402,-0.0080365,0.0267404,-0.0101842,0.013046,-0.0071432,-0.003716,-0.0129222,-0.0290048,0.0051745,-0.0104502,-0.0228294,0.0181174,-0.0033439,0.0002096
Berber_MAR_TIZ,-0.1025221,0.131656,-0.0023166,-0.0759511,0.0310606,-0.0356582,-0.0335058,0.012016,0.0766524,0.0315659,0.0088154,-0.0092596,0.0247308,-0.0204174,0.0203483,-0.0157212,0.0001119,-0.0288305,-0.0534217,0.0119165,-0.0208205,-0.0511129,0.0307414,-0.0051899,0.0074671
Berber_Tunisia_Chen,-0.0279499,0.1390711,-0.0080871,-0.0764792,0.0277316,-0.0352023,-0.0313867,0.0052818,0.0684246,0.0297957,0.0040057,-0.0043877,0.0196314,-0.0161248,0.0140923,-0.0169052,0.0001521,-0.0232896,-0.0467247,0.0078579,-0.0168314,-0.0404275,0.0281347,-0.0044517,0.0063666
Berber_Tunisia_Sen,-0.0391015,0.1347667,-0.0189668,-0.0779,0.0188088,-0.0355667,-0.0216624,0.005864,0.0576878,0.0205605,0.0056455,-0.0122362,0.0263216,-0.009407,0.0124783,-0.0050072,-0.0056909,-0.0131682,-0.0303375,0.0115203,-0.0085143,-0.0241851,0.0149999,-4.95E-05,0.0005494
Saharawi,-0.0954217,0.1313418,-0.0096637,-0.0806827,0.024171,-0.0353959,-0.0328818,0.00899,0.0773356,0.0288843,0.0107311,-0.0093667,0.0305622,-0.0155687,0.0234344,-0.0147728,-0.0038028,-0.0248837,-0.048598,0.0124435,-0.0150776,-0.0415525,0.0278694,-0.0028416,0.007589
Libyan,-0.0476858,0.1309498,-0.0219326,-0.080954,0.0089733,-0.0345677,-0.020953,0.0030243,0.0520675,0.0098215,0.0061365,-0.0123917,0.0292235,-0.0049978,0.0085218,-0.0005094,-0.003788,-0.0095751,-0.0201184,0.0112686,-0.0028108,-0.0132634,0.0093993,0.0007991,-0.0002963
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Egyptian,-0.01548,0.1341176,-0.042778,-0.0872208,-0.0044008,-0.0333553,-0.0137874,0.0005691,0.037605,0.0011968,0.0069772,-0.0087772,0.0229334,0.0018258,-0.0005202,-6.19E-05,-0.003303,-0.0026182,-0.0034861,0.0032432,-0.0005781,-0.0022875,0.0008381,0.0008636,-0.0004072
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
EGY_Hellenistic,0.040976,0.159438,-0.055437,-0.102068,0,-0.060798,-0.023266,-0.008307,0.048472,0.007472,0.015427,-0.019782,0.034341,-0.004129,0.00475,-0.015646,-0.024121,0.007348,-0.005028,-0.00025,-0.004617,0.008285,-0.012571,0.005302,-0.005987
EGY_Late_Period,0.050082,0.146744,-0.042426,-0.1183805,-0.0020005,-0.049782,-0.015628,-0.004731,0.0474495,0.006196,0.0090125,-0.011465,0.029732,-0.005849,-0.0008145,-0.0020555,-0.0074315,-0.0019635,-0.0035195,0.0120055,0.005615,0.0016695,0.0036355,0 .003916,-0.0005985
Palestinian,0.0455292,0.134253,-0.0473285,-0.0780045,-0.0126482,-0.0297299,-0.0062276,-0.0019845,0.0167504,-0.0003096,0.0081843,-0.0096364,0.0203072,-0.0013211,-0.00095,0.0097452,-0.0020079,-0.001761,8.81E-05,0.0025387,0.0011356,0.0052801,-0.0001603,0.0023977,0.001844
BedouinA,0.0285823,0.1335987,-0.047601,-0.0827598,-0.0138829,-0.0323513,-0.0107061,-0.0046408,0.0234522,-0.0016198,0.0081734,-0.0107237,0.0247439,0.0004741,0.0015682,0.0070567,-0.0027381,-0.0022382,-0.0034079,0.008254,0.0002081,0.002528,0.0001916,0. 0017672,-0.0015967
BedouinB,0.041925,0.1439232,-0.0598156,-0.1169808,-0.0093179,-0.0480622,-0.0141008,-0.0087432,0.05154,-0.0052038,0.0158689,-0.0305729,0.0629496,0.004855,0.0043959,0.0288529,-0.0199706,0.00366,-0.0040153,0.029,0.0109668,0.0152299,-0.0039166,0.0071025,-0.0083092
Saudi,0.0494498,0.1411588,-0.0646136,-0.1161014,-0.0115919,-0.0481242,-0.0133696,-0.008179,0.0516537,-0.0058923,0.016293,-0.0318551,0.063346,0.0021408,0.0031818,0.0271809,-0.0220493,0.0042931,-0.0003213,0.0302646,0.0130601,0.0168853,-0.0072031,0.0082741,-0.0097528
Yemenite_Al_Bayda,0.0386997,0.1386198,-0.0626647,-0.1073983,-0.0101557,-0.0484803,-0.0131608,-0.0101533,0.0541308,-0.0059835,0.0109612,-0.0287995,0.0509163,0.004106,0.0063788,0.0241973,-0.018471,0.0071578,0.0008378,0.0179253,0.0097745,0 .0161778,-0.0074358,0.0011248,-0.003752
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Amran,0.0458544,0.135428,-0.0615246,-0.1014453,-0.0148599,-0.0421523,-0.0087289,-0.0077631,0.0450098,-0.0042566,0.0117499,-0.0229617,0.0465096,0.0052591,0.003994,0.0172555,-0.0141374,0.0042531,0.0018316,0.0157038,0.0069254, 0.0095212,-0.0063297,0.0041742,-0.0047812
Yemenite_Dhamar,0.035538,0.1411586,-0.0585374,-0.1105743,-0.0095742,-0.0472254,-0.0137351,-0.0080253,0.0492449,-0.0078563,0.0137851,-0.0263932,0.0492728,0.0059482,0.0034836,0.0152478,-0.016211,0.0045749,0.0006564,0.0170358,0.010107,0. 0114172,-0.0069568,0.0042307,-0.0030601
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289



Tutsi-related:
https://i.imgur.com/enMfACd.png

Horners:
https://i.imgur.com/TO0fxtW.png

Misc. Great-Lake pops:
https://i.imgur.com/ibiIp10.png



One noticeable distinction I noticed, Tutsi-related groups show a "Bedouin B" affinity lacking among Horners -- when it does appears in the Horn, it's only evident for ETH_Tigray and user "ERI_TGY_Lank" (Tigrinya).

Could this relate to the "extra" Natufian affinity in those earlier runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=610801&viewfull=1#post610801)? Could it be a proxy for some kind of N. Sudanese ancestry?
Sorry, didn’t clarify maybe. I meant WITHOUT PN Samples. Once u do it, Bedouin goes even higher.

SWAHILLI_PRINCE16
10-18-2019, 07:54 PM
Given your ancestry, I think it's more likely a relic of something more archaic -- the minor affinity towards Papuan/Oceanians might reflect affinities of earlier ~(70kya) OoAs returning home:




Since ancestry from that earlier OoA expansion is now extinct, apart from minor traces in Papuan/Oceanians, maybe those minor Papuan-like affinities are the closest thing nMonte can find -- it might go in hand with the asian-origin hypothesis for M1 in East and North-Africa


A few of us have also noticed this minor East-Asian affinities, according to GeseDNA's older runs I'm 2.62% (https://anthrogenica.com/showthread.php?14477-From-which-island-area-is-my-Oceanian&p=602204&viewfull=1#post602204) South-Chinese! Lol



User SwahiliPrince was shown to be 2.13% (https://anthrogenica.com/showthread.php?12745-GeseDNA&p=316416&viewfull=1#post316416) -- although more plausible for him given his coastal Indian-Ocean ancestry, Hurricane of Berber Tunisian decent has also noticed the same repeatedly: From which island/area is my Oceanian? (https://anthrogenica.com/showthread.php?14477-From-which-island-area-is-my-Oceanian)

I think you've been here long enough to remember this fun thread: Ancient Eurasia K6 - Deducing Traces of Back to Africa Migrations (https://anthrogenica.com/showthread.php?9831-Ancient-Eurasia-K6-Deducing-Traces-of-Back-to-Africa-Migrations)


Respectively, maybe this minor layer is cached in our elevated Paleolithic African ancestry (Iberomaurusian, KEN_LSA, ETH_4500BP...)? -- that seems to be the one thing we all have in common.


... still waiting on Academia for confirmation

On 23andme its minor 0.3% Indonesian Thai & Khmer which I inherit all from my father I guess it's real considering the Swahili trade history. I dont trust Gese DNA it seems kind of flawed or maybe their estimates are based on something else different?

Angoliga
10-19-2019, 12:02 AM
And it totally makes sense. Iraqw are clearly descended from those PN, judging from haplogroups and elevated Mota/like ancestry.

What doesn’t make sense is how Tutsis despite haplogroups showing a PN origin, their Mota-like is not proportionate to what you would expect from a group that descend Savannah PN. Another thing u have mentioned before is almost entirely all the Eurasian portion for Cushitic, Semitic speaking, PN and south cushitic speakers is from Levant Natufian. Yet, for Tutsis, it doesn’t seem to be the case.



There's no clear-cut rule for Haplogroups and admixture having to correlate within populations.

A few candid examples would be R1b-V88 in Chadic speakers and E-V32 among the Masalit.



That is from the Nilotic expansion in Southern East Africa.
One thing I’m yet to know is if this elevated Dinka-like ancestry in Tutsis is of the Iron Age or older or very recent. Judging from these (https://anthrogenica.com/showthread.php?18015-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) Mt haplogroups can anybody answer my question right

Sorry: regarding non-levantine ancestry in Tutsi realted groups, could you quote the specific run you're referring to -- we ran a few


Regarding Nilotic expansions in Central East-Africa, it's noteworthy to distinguish earlier Southern-Nilotic expansions (Kalenjin, Datooga speakers) vs. the more recent Eastern (Maa, Teso, Kakwa..) and Western-Nilotic expansions (Luo, Acholi:


Most of the "extra" Nilotic admixture in Tutsi-related groups is more likely related to these Rift-Valley Southern-Nilotic speaking pops who would've also migrated from Sudan (supposedly south-east of Khartoum in the middle Nile-Valley).

The migration of Eastern-Nilotic speakers was too passive IMO to have contributed significant nilotic admixture to core Tutsi-related groups who would've presumably already been settled in core Great-Lake regions.

Based on admixture results of modern Luo speakers, I'm skeptical most of the nilotic contribution in core Tutsi-related groups would be Luo derived. The Luo's success in having the most rapid nilotic-expansion (>15th century) was partly due to their efficieny in assimilating local bantu populations, that's why they can appear >75% West-African in admixture.



Luo admixture in the Banoyoro is evident and historically documented; I just doubt there was any significant Nilotic contribution from these Luo-Babito relations. Moreover, I doubt it would've extended to Rwanda/Burundi pops.



Sorry, didn’t clarify maybe. I meant WITHOUT PN Samples. Once u do it, Bedouin goes even higher.

Without PNs and without ancient Levants? That might be a little too anachronistic for meaningful comparison but I can run them for you anyway for curiosity's sake.

To avoid confusion, you can private message me the list of source samples you'd like run against the target samples.

drobbah
10-19-2019, 04:00 AM
There's no clear-cut rule for Haplogroups and admixture having to correlate within populations.

A few candid examples would be R1b-V88 in Chadic speakers and E-V32 among the Masalit.
There's also a bunch of E-V32 Cameroonians although I don't know which ethnic group they specifically belong too.

Espoir
10-19-2019, 07:35 AM
There's no clear-cut rule for Haplogroups and admixture having to correlate within populations.

A few candid examples would be R1b-V88 in Chadic speakers and E-V32 among the Masalit.




Sorry: regarding non-levantine ancestry in Tutsi realted groups, could you quote the specific run you're referring to -- we ran a few
Iím very aware of that. What I meant is progenitors if Tutsis May have taken a different path, say, White Nile. In other words didnít pass through Ethiopia. That would explain why they have little to no Mota. Rather show high Dinka-like and significant LSA ancestry. The former being south Sudanese, the latter being from the Great Lakes



Regarding Nilotic expansions in Central East-Africa, it's noteworthy to distinguish earlier Southern-Nilotic expansions (Kalenjin, Datooga speakers) vs. the more recent Eastern (Maa, Teso, Kakwa..) and Western-Nilotic expansions (Luo, Acholi:


Most of the "extra" Nilotic admixture in Tutsi-related groups is more likely related to these Rift-Valley Southern-Nilotic speaking pops who would've also migrated from Sudan (supposedly south-east of Khartoum in the middle Nile-Valley).

The migration of Eastern-Nilotic speakers was too passive IMO to have contributed significant nilotic admixture to core Tutsi-related groups who would've presumably already been settled in core Great-Lake regions.

Based on admixture results of modern Luo speakers, I'm skeptical most of the nilotic contribution in core Tutsi-related groups would be Luo derived. The Luo's success in having the most rapid nilotic-expansion (>15th century) was partly due to their efficieny in assimilating local bantu populations, that's why they can appear >75% West-African in admixture.



I meant a Luo speaking population that resembled Anuaks.




Luo admixture in the Banoyoro is evident and historically documented; I just doubt there was any significant Nilotic contribution from these Luo-Babito relations. Moreover, I doubt it would've extended to Rwanda/Burundi pops.
I would be surprised and not at the same time. It might not be Luos, but I bet another pastoral NiloSaharan group may have found its way down there.





Without PNs and without ancient Levants? That might be a little too anachronistic for meaningful comparison but I can run them for you anyway for curiosity's sake.

To avoid confusion, you can private message me the list of source samples you'd like run against the target samples.
Will PM you.

mpatsibihugu89
10-20-2019, 01:25 PM
Luo admixture in the Banoyoro is evident and historically documented; I just doubt there was any significant Nilotic contribution from these Luo-Babito relations. Moreover, I doubt it would've extended to Rwanda/Burundi pops.


All I can add to this discussion is that historically many tutsi groups are known to have originated in current UG territory in the old Bunyoro. These proto-Tutsi may have been Banyoro in Origin (Tutsi is fairly recent term ~18th century if that). Oral traditions/myths of origins for Royal Clans in the region are very similar especially those who are related to Bahima groups all over the Great Lakes Region.


Based on admixture results of modern Luo speakers, I'm skeptical most of the nilotic contribution in core Tutsi-related groups would be Luo derived. The Luo's success in having the most rapid nilotic-expansion (>15th century) was partly due to their efficieny in assimilating local bantu populations, that's why they can appear >75% West-African in admixture. This time period saw many Kingdoms pop up or get fortified. Historians like Jean-Pierre Chretien who specialize on the Great Lakes, think that a major event took place (mass migration? idk)...coincidence?! I think NOT. So these Luo migrations definitely affected Tutsi groups one way or another. Banyoro armies invaded Rwanda Twice, not sure what genetic imprint they left on locals in the aftermath. JP Chretien also mentions increase of pastoral activities around 10-11th century not sure what's happening broadly around that time regarding Pastoral groups in the region.

Alfa
10-20-2019, 04:02 PM
All I can add to this discussion is that historically many tutsi groups are known to have originated in current UG territory in the old Bunyoro. These proto-Tutsi may have been Banyoro in Origin (Tutsi is fairly recent term ~18th century if that). Oral traditions/myths of origins for Royal Clans in the region are very similar especially those who are related to Bahima groups all over the Great Lakes Region.

This time period saw many Kingdoms pop up or get fortified. Historians like Jean-Pierre Chretien who specialize on the Great Lakes, think that a major event took place (mass migration? idk)...coincidence?! I think NOT. So these Luo migrations definitely affected Tutsi groups one way or another. Banyoro armies invaded Rwanda Twice, not sure what genetic imprint they left on locals in the aftermath. JP Chretien also mentions increase of pastoral activities around 10-11th century not sure what's happening broadly around that time regarding Pastoral groups in the region.

You are very wrong. Historians already confirmed that Proto-Tutsi groups or related Tutsi groups like Hima clans may have originated from Ankole/Karagwe. Historians made clear Banyoro and Hima/Tutsi were 2 different groups. But many acknowledge interactions occured between those to groups. Banyoro/Babito are descended from Luo, they are different. Nobody know when the Babito started marrying women from Hima clans, these relations probably became more frequent at the peak of Bunyoro Kingdom

Espoir
10-20-2019, 09:28 PM
One has to understand that Bunyoro-Kitara was an empire ran by Chwezi dynasty.the general concesus is that Tutsi, Hima, Banyamulenge and the like are their descendants. What happened is after the empire fell, they expanded south to form Ankole, Rwanda, Karagwe, Burundi and Busongola. If those Luo groups were there before 1000 A.D, there might have been interactions between Tutsi-like groups and Luo.

Angoliga
10-21-2019, 12:38 AM
One has to understand that Bunyoro-Kitara was an empire ran by Chwezi dynasty.the general concesus is that Tutsi, Hima, Banyamulenge and the like are their descendants. What happened is after the empire fell, they expanded south to form Ankole, Rwanda, Karagwe, Burundi and Busongola. If those Luo groups were there before 1000 A.D, there might have been interactions between Tutsi-like groups and Luo.

Can you share any references (historical, linguistic, genetic, archaeological..) suggesting Western-Nilotic speakers expanded into the Great-Lakes region >500 years prior to established dates? This would go against data collected across several fields of study, not to mention common oral tradition spanning the GL-region.




All I can add to this discussion is that historically many tutsi groups are known to have originated in current UG territory in the old Bunyoro. These proto-Tutsi may have been Banyoro in Origin (Tutsi is fairly recent term ~18th century if that). Oral traditions/myths of origins for Royal Clans in the region are very similar especially those who are related to Bahima groups all over the Great Lakes Region.

This time period saw many Kingdoms pop up or get fortified. Historians like Jean-Pierre Chretien who specialize on the Great Lakes, think that a major event took place (mass migration? idk)...coincidence?! I think NOT. So these Luo migrations definitely affected Tutsi groups one way or another. Banyoro armies invaded Rwanda Twice, not sure what genetic imprint they left on locals in the aftermath. JP Chretien also mentions increase of pastoral activities around 10-11th century not sure what's happening broadly around that time regarding Pastoral groups in the region.



*Let's keep these ancestral suggestions as objective as possible by referring to autosomal data*




These are inferred admixture results of Luo speakers including the Ugandan Alur; an adjacent Luo population to the Bunyoro (Tishkoff, 2009 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947357/)), (Scheinfeldt, 2019 (https://www.pnas.org/content/116/10/4166)):
https://i.imgur.com/c95udsc.png

Fig 4)




https://i.imgur.com/EqL0y8u.png

Fig 1) D




https://i.imgur.com/q08ARqC.png

GEDmatch Spreadsheet (puntDNAL K8 African only)
Lower nilotic affinities concurring with higher West-African/Bantu/HG/Cushitic affinities, clearly indicates the Luo's policy towards assimilation of local populations as they migrated southward into the great-lakes region. Notice the ancestral-breakdown of Alur in the puntdNAL K8 runs, their Nilo-Saharan affinity is nearly half of the more "Proto-Luo" South_Sudan_Anuak -- that's in NW-Uganda, a continued *hypothetical expansion into Rwanda/Burndi would render similar/lower nilotic-affinities as the Kenyan Luo <20%.

The dilution of their nilotic affinities became even more intensified the further south they migrated into Great-Lake pops. This was largely due to highly polygamist traditions during Luo expansion -- these traditions have even continued into the modern-era:

"Relative to other ethnic groups in Kenya, the Luo have been characterized in literature (Lesthaeghe and Eelens 1989; Caldwell, Caldwell, Orubuloye 1992) as the group with (1) the highest prevalence of polygamy.... groups with the highest polygamous tendencies are Luo (33%)..." (Hayase, 1997 (https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1746-1049.1997.tb00849.x))



Babito-Luo relations should therefore be dismissed when trying to explain the bulk of elevated Dinka affinities (46.9% avg) against PNs in modern Tutsi:
https://i.imgur.com/enMfACd.png



(Source Samples)
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
Moroccan_South,-0.1844646,0.119896,0.0007308,-0.0569288,0.0239659,-0.0268258,-0.0321962,0.0152301,0.0538154,0.0285428,0.0060591,-0.0068189,0.0227358,-0.0173318,0.0181018,-0.0153306,0.0010921,-0.0189241,-0.0407889,0.0085196,-0.0148254,-0.038456,0.0240718,-0.0034944,0.0054934
Moroccan_North,-0.0299735,0.1373221,-0.0030378,-0.0673993,0.0280564,-0.0319174,-0.0244542,0.0050512,0.0609822,0.0327317,0.0059091,-0.0065526,0.0185908,-0.0147102,0.0151403,-0.0105629,0.0012604,-0.0179828,-0.040747,0.0092961,-0.0121937,-0.0346297,0.0214382,-0.0055763,0.0043974
Algerian,-0.0680567,0.1327805,-0.0071652,-0.0677358,0.0212218,-0.0300737,-0.0221204,0.007442,0.0530313,0.0250954,0.0055076,-0.0061695,0.0208558,-0.0138598,0.0130235,-0.0101707,-0.0033574,-0.0164009,-0.0316446,0.0071597,-0.0096392,-0.0282908,0.0181892,-0.0002661,0.0012922
Moroccan,-0.0853671,0.1302133,-0.0128221,-0.0708806,0.0211321,-0.03294,-0.0277833,0.0097687,0.0554032,0.0243993,0.0095087,-0.0090252,0.0269902,-0.0144658,0.0163016,-0.0061874,-0.0027669,-0.0170326,-0.0384216,0.0094351,-0.0098438,-0.0295119,0.0209111,-0.0011248,0.0059207
Berber_MAR_ERR,-0.0923593,0.1309307,-0.0032863,-0.0711984,0.0256529,-0.0324909,-0.0312229,0.0101041,0.0673468,0.0299258,0.0098476,-0.0059732,0.021662,-0.0161411,0.0201934,-0.0141398,-0.005979,-0.0213652,-0.0461312,0.0094778,-0.0164531,-0.0416268,0.024808,-0.0020657,0.0053715
Mozabite,-0.0649782,0.135551,-0.0032793,-0.0717622,0.0260249,-0.0328364,-0.0260656,0.0108257,0.0617306,0.0303463,0.0065097,-0.006366,0.021795,-0.0165685,0.0163159,-0.016176,-0.0027097,-0.0219282,-0.0435571,0.0082757,-0.0146263,-0.0367947,0.0246817,-0.0042277,0.0056594
Tunisian,-0.048517,0.1313841,-0.0150849,-0.0751379,0.019619,-0.0306779,-0.022091,0.005019,0.0543778,0.0197954,0.0054402,-0.0080365,0.0267404,-0.0101842,0.013046,-0.0071432,-0.003716,-0.0129222,-0.0290048,0.0051745,-0.0104502,-0.0228294,0.0181174,-0.0033439,0.0002096
Berber_MAR_TIZ,-0.1025221,0.131656,-0.0023166,-0.0759511,0.0310606,-0.0356582,-0.0335058,0.012016,0.0766524,0.0315659,0.0088154,-0.0092596,0.0247308,-0.0204174,0.0203483,-0.0157212,0.0001119,-0.0288305,-0.0534217,0.0119165,-0.0208205,-0.0511129,0.0307414,-0.0051899,0.0074671
Berber_Tunisia_Chen,-0.0279499,0.1390711,-0.0080871,-0.0764792,0.0277316,-0.0352023,-0.0313867,0.0052818,0.0684246,0.0297957,0.0040057,-0.0043877,0.0196314,-0.0161248,0.0140923,-0.0169052,0.0001521,-0.0232896,-0.0467247,0.0078579,-0.0168314,-0.0404275,0.0281347,-0.0044517,0.0063666
Berber_Tunisia_Sen,-0.0391015,0.1347667,-0.0189668,-0.0779,0.0188088,-0.0355667,-0.0216624,0.005864,0.0576878,0.0205605,0.0056455,-0.0122362,0.0263216,-0.009407,0.0124783,-0.0050072,-0.0056909,-0.0131682,-0.0303375,0.0115203,-0.0085143,-0.0241851,0.0149999,-4.95E-05,0.0005494
Saharawi,-0.0954217,0.1313418,-0.0096637,-0.0806827,0.024171,-0.0353959,-0.0328818,0.00899,0.0773356,0.0288843,0.0107311,-0.0093667,0.0305622,-0.0155687,0.0234344,-0.0147728,-0.0038028,-0.0248837,-0.048598,0.0124435,-0.0150776,-0.0415525,0.0278694,-0.0028416,0.007589
Libyan,-0.0476858,0.1309498,-0.0219326,-0.080954,0.0089733,-0.0345677,-0.020953,0.0030243,0.0520675,0.0098215,0.0061365,-0.0123917,0.0292235,-0.0049978,0.0085218,-0.0005094,-0.003788,-0.0095751,-0.0201184,0.0112686,-0.0028108,-0.0132634,0.0093993,0.0007991,-0.0002963
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Egyptian,-0.01548,0.1341176,-0.042778,-0.0872208,-0.0044008,-0.0333553,-0.0137874,0.0005691,0.037605,0.0011968,0.0069772,-0.0087772,0.0229334,0.0018258,-0.0005202,-6.19E-05,-0.003303,-0.0026182,-0.0034861,0.0032432,-0.0005781,-0.0022875,0.0008381,0.0008636,-0.0004072
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
EGY_Hellenistic,0.040976,0.159438,-0.055437,-0.102068,0,-0.060798,-0.023266,-0.008307,0.048472,0.007472,0.015427,-0.019782,0.034341,-0.004129,0.00475,-0.015646,-0.024121,0.007348,-0.005028,-0.00025,-0.004617,0.008285,-0.012571,0.005302,-0.005987
EGY_Late_Period,0.050082,0.146744,-0.042426,-0.1183805,-0.0020005,-0.049782,-0.015628,-0.004731,0.0474495,0.006196,0.0090125,-0.011465,0.029732,-0.005849,-0.0008145,-0.0020555,-0.0074315,-0.0019635,-0.0035195,0.0120055,0.005615,0.0016695,0.0036355,0 .003916,-0.0005985
Palestinian,0.0455292,0.134253,-0.0473285,-0.0780045,-0.0126482,-0.0297299,-0.0062276,-0.0019845,0.0167504,-0.0003096,0.0081843,-0.0096364,0.0203072,-0.0013211,-0.00095,0.0097452,-0.0020079,-0.001761,8.81E-05,0.0025387,0.0011356,0.0052801,-0.0001603,0.0023977,0.001844
BedouinA,0.0285823,0.1335987,-0.047601,-0.0827598,-0.0138829,-0.0323513,-0.0107061,-0.0046408,0.0234522,-0.0016198,0.0081734,-0.0107237,0.0247439,0.0004741,0.0015682,0.0070567,-0.0027381,-0.0022382,-0.0034079,0.008254,0.0002081,0.002528,0.0001916,0. 0017672,-0.0015967
BedouinB,0.041925,0.1439232,-0.0598156,-0.1169808,-0.0093179,-0.0480622,-0.0141008,-0.0087432,0.05154,-0.0052038,0.0158689,-0.0305729,0.0629496,0.004855,0.0043959,0.0288529,-0.0199706,0.00366,-0.0040153,0.029,0.0109668,0.0152299,-0.0039166,0.0071025,-0.0083092
Saudi,0.0494498,0.1411588,-0.0646136,-0.1161014,-0.0115919,-0.0481242,-0.0133696,-0.008179,0.0516537,-0.0058923,0.016293,-0.0318551,0.063346,0.0021408,0.0031818,0.0271809,-0.0220493,0.0042931,-0.0003213,0.0302646,0.0130601,0.0168853,-0.0072031,0.0082741,-0.0097528
Yemenite_Al_Bayda,0.0386997,0.1386198,-0.0626647,-0.1073983,-0.0101557,-0.0484803,-0.0131608,-0.0101533,0.0541308,-0.0059835,0.0109612,-0.0287995,0.0509163,0.004106,0.0063788,0.0241973,-0.018471,0.0071578,0.0008378,0.0179253,0.0097745,0 .0161778,-0.0074358,0.0011248,-0.003752
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Amran,0.0458544,0.135428,-0.0615246,-0.1014453,-0.0148599,-0.0421523,-0.0087289,-0.0077631,0.0450098,-0.0042566,0.0117499,-0.0229617,0.0465096,0.0052591,0.003994,0.0172555,-0.0141374,0.0042531,0.0018316,0.0157038,0.0069254, 0.0095212,-0.0063297,0.0041742,-0.0047812
Yemenite_Dhamar,0.035538,0.1411586,-0.0585374,-0.1105743,-0.0095742,-0.0472254,-0.0137351,-0.0080253,0.0492449,-0.0078563,0.0137851,-0.0263932,0.0492728,0.0059482,0.0034836,0.0152478,-0.016211,0.0045749,0.0006564,0.0170358,0.010107,0. 0114172,-0.0069568,0.0042307,-0.0030601
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289





nilotic-like affinities from such interactions would've been heavily diluted if they ever gradually introgressed into Burundi and Rwanda pops
the high Dinka/Yoruba ratios here don't add up for any plausibly significant "post 16th-century Luo-connection" across modern Tutsi-groups
earlier Nilotic expansions from rift-valley Southern-Nilotic speakers is a more likely explanation for most of the elevated Dinka in "Proto-Tutsi"

Espoir
10-21-2019, 09:30 PM
Can you share any references (historical, linguistic, genetic, archaeological..) suggesting Western-Nilotic speakers expanded into the Great-Lakes region >500 years prior to established dates? This would go against data collected across several fields of study, not to mention common oral tradition spanning the GL-region.

I just cross-checked. As much as it was an IF statement, I always assumed the wrong century when Luo expanded and conquered Bunyoro. By that time,most those that became Tutsis had expanded south into what is now Rwanda.

One other thing is Burundians show is elevated Dinka-like ancestry. Look at this guy named BR_Tutsi and by the way, those labeled RW_BR are half Rwandan,half Burundian Tutsis. Two of them clearly show elevated Dinka.
All this is a mystery how those living further South would have more Nilotic ancestry compared to for example Hima living in Uganda.

Angoliga
10-22-2019, 12:50 AM
I just cross-checked. As much as it was an IF statement, I always assumed the wrong century when Luo expanded and conquered Bunyoro. By that time,most those that became Tutsis had expanded south into what is now Rwanda.

One other thing is Burundians show is elevated Dinka-like ancestry. Look at this guy named BR_Tutsi and by the way, those labeled RW_BR are half Rwandan,half Burundian Tutsis. Two of them clearly show elevated Dinka.
All this is a mystery how those living further South would have more Nilotic ancestry compared to for example Hima living in Uganda.

It's not really all that mysterious: you've already answered part of the riddle when you remarked the lower Mota affinities in Tutsi-related groups vs. Horners.

Recall the steadily increasing Dinka-affinities in PNs from the Neolithic to the IA (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611762&viewfull=1#post611762)? This was ultimately derived from continual migration of Southern-nilotic speakers entering the Western-Rift Valley.


Here's a draft visual-aid, not sure if it helps:

https://i.imgur.com/Uo88E5t.png

Elevated Dinka and lower Mota in "Proto-Tutsi" could be explained as a predominantly Southern-Nilotic pop migrating into the Rift-Valley and absorbing PNs (+ KLSA & Bantu).

Espoir
10-22-2019, 01:07 AM
It's not really all that mysterious: you've already answered part of the riddle when you remarked the lower Mota affinities in Tutsi-related groups vs. Horners.

Recall the steadily increasing Dinka-affinities in PNs from the Neolithic to the IA (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611762&viewfull=1#post611762)? This was ultimately derived from continual migration of Southern-nilotic speakers entering the Western-Rift Valley.


Here's a draft visual-aid, not sure if it helps:

https://i.imgur.com/Uo88E5t.png

Elevated Dinka and lower Mota in "Proto-Tutsi" could be explained as a predominantly Southern-Nilotic pop migrating into the Rift-Valley and absorbing PNs (+ KLSA & Bantu).
Ooookay, so if thatís how those migrations happened, then it makes more sense. Didnít know it was a U-turn migration.
My theory was right all along. I had two hypotheses:
1- migration from Kenya directly to Uganda
2- migration through Tanzania to Uganda, Rwanda and Burundi.

I favored the latter cause of general higher affinities towards TZN_PN in Tutsis.

Angoliga
10-23-2019, 02:39 AM
More taken from the Prendergast et al, 2019 (https://science.sciencemag.org/content/365/6448/eaaw6275)paper -- this is a better illustration of the AFMD elevated Dinka affinities during the pastoral iron-age (PIA):

https://i.imgur.com/s8hf2xT.png




Admixture events contributing to ancestry of ancient eastern Africans.

Results were inferred from genome-wide ancient DNA data from 41 individuals from archaeological sites in Kenya and Tanzania, analyzed together with published ancient and present-day genetic data. Black circles represent reported individuals, placed at their median calibrated radiocarbon dates (six individuals, five of whom have forager-related ancestry, had insufficient collagen for dating and thus are not represented here). Ancestry components depicted in green and gray continue to the present day (outside of eastern Africa) but are truncated for readability.


"..The remaining four individuals (who are confidently assigned to PIA contexts) are inferred to have substantially more Sudan (Dinka)-related ancestry (~60%) than is seen in the PN."

"...The Deloraine Farm childís genetic distinctiveness as compared to the PN cluster is notable in light of similarities in artifacts between Elmenteitan sites and Deloraine Farm, viewed as evidence of continuity from the Elmenteitan to the Iron Age (32, 47). By contrast, four PIA individuals spanning an ~800-year period show greater affinity to present-day Nilotic speakers and are associated with an influx of Sudan (Dinka)-related ancestry. Similarities between archaeologically and ethnographically documented material culture suggest that PIA sites may be associated with ancestors of present-day Kenyan Nilotic speakers such as the Kalenjin or Maasai (32, 47)..."

*Nilotic speakers of both Southern and Eastern linguistic branches are cited here, Kalenjin and Maasai respectively, though Southern-nilotic speakers would be a more conservative guess within a historical linguistic context -- arguably, both southern and eastern-nilotic speakers were probably genetically indistinguishable during this time-frame within and around the Rift-Valley/Turakana-basin.



Recall the "deep-layer" Horner/Tutsi runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129) showing the minor (albeit non-negligible) Levant_PPNC-affinity across Tutsi-related samples? :

Tutsi-Related Groups:
https://i.imgur.com/YJUjrzy.png

Horners:
https://i.imgur.com/iJw66lj.png


... maybe it's not coincidental that among all ancients, these runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611762&viewfull=1#post611762)show Levant_PPNC highest during the Iron-Age (KEN_IA_Deloraine) -- the period when we're receiving this influx of Sundanese migration:
https://i.imgur.com/QY7iwTN.png

Levant_PPNC has a moderate affinity among North-Africans, it might appear even more prevalent for certain North-Sudanese pops given their closer-proximity to the Levant/Red-Sea:
https://i.imgur.com/x4YMFeW.png


*Pending more ancient/modern samples, Levant_PPNC in KEN_IA_Deloraine AND Tutsi-related samples could be a signature derived from their Southern-Nilotic ancestry.

Linguists suggest the Nilotic-branch of Nilo-Saharan speakers inhabited the Middle-Nile basin (south-east of Khartoum/south of the Abbai river), this might be a Eurasian-affinity for adjacent pops in northern-adjacent regions.

These minor affinities work as a good geographic proxy for Nilo-saharan migrations during the late neolithic: Levant_PPNC would give a N/E departure for Southern-Nilotic speakers whereas Steppe and GEO_HG affinities in Central-Sudanics gives a N/W departure (separate thread here (https://anthrogenica.com/showthread.php?17945-G25-Unscaled-Traces-of-Yamnaya-in-the-West-Nile-Noise-or-Relics-of-R1b-V88&p=587882&viewfull=1#post587882))

drobbah
10-23-2019, 03:05 AM
The Tutsis that don't score as much Levant_PPNC instead score Jordan_EBA with levels similar to Semitic admixed Horners.

drobbah
10-23-2019, 04:29 AM
It seems my mother who clusters with the other Northern Somalis and I both prefer the Ancient Egyptian samples over the Yemeni/Yemenite Jews.The Iraqw is the only sample to score Levant_PPNC....

Cushitic descended Horners + Iraqw & Rendille


34079

Source Samples

KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_IA,-0.4120395,0.080227,-0.015085,-0.0437665,0.002308,-0.026913,-0.009753,0.005884,0.107068,-0.086744,-0.016807,0.0037465,-0.018954,0.0026145,0.0211725,-0.0235345,0.014994,-0.00057,0.014581,-0.011693,0.0016225,0.00915,-0.005238,-0.001627,-0.0011375
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
EGY_Hellenistic,0.040976,0.159438,-0.055437,-0.102068,0,-0.060798,-0.023266,-0.008307,0.048472,0.007472,0.015427,-0.019782,0.034341,-0.004129,0.00475,-0.015646,-0.024121,0.007348,-0.005028,-0.00025,-0.004617,0.008285,-0.012571,0.005302,-0.005987
EGY_Late_Period,0.050082,0.146744,-0.042426,-0.1183805,-0.0020005,-0.049782,-0.015628,-0.004731,0.0474495,0.006196,0.0090125,-0.011465,0.029732,-0.005849,-0.0008145,-0.0020555,-0.0074315,-0.0019635,-0.0035195,0.0120055,0.005615,0.0016695,0.0036355,0 .003916,-0.0005985
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yemenite_Al_Bayda,0.0386997,0.1386198,-0.0626647,-0.1073983,-0.0101557,-0.0484803,-0.0131608,-0.0101533,0.0541308,-0.0059835,0.0109612,-0.0287995,0.0509163,0.004106,0.0063788,0.0241973,-0.018471,0.0071578,0.0008378,0.0179253,0.0097745,0 .0161778,-0.0074358,0.0011248,-0.003752
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
KEN_IA_Deloraine,-0.537245,0.067025,0.013953,-0.00969,0.001846,-0.00502,-0.01034,0.014538,0.022089,-0.037176,-0.006658,0.008393,-0.033003,-0.009221,-0.024565,0.017237,-0.009648,0.002407,-0.010684,0.006003,0.003494,0.003215,0.004314,0.001 084,0.000838
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916

Angoliga
10-23-2019, 05:16 AM
Ooookay, so if thatís how those migrations happened, then it makes more sense. Didnít know it was a U-turn migration.

Relating to the interplay of migration patterns, tbh I'm not anywhere near knowledgeable as I'd like to be on the subject
.. but these pastoral-migrations seem clearly correlated with the topography of the Rift-Valley -- the Albertine-Rift being the extended limits of the migration (Hima, Banyoro, Toro, Muchiga, Banyarwanda...)



I favored the latter cause of general higher affinities towards TZN_PN in Tutsis.

Touching on that: It does seem strange, the preference of TZN_PN compared to KEN_Pastoral_N for Horners:

Horners:
https://i.imgur.com/6Vqi6fB.png


Tutsi-Related:
https://i.imgur.com/GZIRqxk.png

They don't seem to vary that much with these proxies (Dinka/Natufian/Mota..):
https://i.imgur.com/uAqkW5o.png
....yet the preference between the two groups is very clear



Impossible to know for certain without more data, but perhaps the preference for TZN_PN translates a generally more southern rift-valley point of introgression of PN-like ancestry into the Dinka-like pop of Proto-Tutsi groups.
Since there's a big archaeological gap in the IA, KEN_IA_Deloraine might just be a glimpse (before or after) of heavier South-Sudanese-like migrations, stretching even further south into the South/Western-Rift Valley.

NetNomad
10-23-2019, 07:53 AM
The Tutsis that don't score as much Levant_PPNC instead score Jordan_EBA with levels similar to Semitic admixed Horners.

The assignment to clusters seem a bit random with nMonte compared to the program Admixture. The latter is more consistent with assigning folks to a cluster, however, it also has its flaws (making some modern populations appear unadmixed for example).

mpatsibihugu89
10-23-2019, 02:09 PM
Relating to the interplay of migration patterns, tbh I'm not anywhere near knowledgeable as I'd like to be on the subject
.. but these pastoral-migrations seem clearly correlated with the topography of the Rift-Valley -- the Albertine-Rift being the extended limits of the migration (Hima, Banyoro, Toro, Muchiga, Banyarwanda...)



Touching on that: It does seem strange, the preference of TZN_PN compared to KEN_Pastoral_N for Horners:

Horners:
https://i.imgur.com/6Vqi6fB.png


Tutsi-Related:
https://i.imgur.com/GZIRqxk.png

They don't seem to vary that much with these proxies (Dinka/Natufian/Mota..):
https://i.imgur.com/uAqkW5o.png
....yet the preference between the two groups is very clear



Impossible to know for certain without more data, but perhaps the preference for TZN_PN translates a generally more southern rift-valley point of introgression of PN-like ancestry into the Dinka-like pop of Proto-Tutsi groups.
Since there's a big archaeological gap in the IA, KEN_IA_Deloraine might just be a glimpse (before or after) of heavier South-Sudanese-like migrations, stretching even further south into the South/Western-Rift Valley.

Throwing in these Haplogroups pie charts Tutsi Y-DNA (https://anthrogenica.com/showthread.php?18014-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) , MT-DNA (https://anthrogenica.com/showthread.php?18015-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) for potential migratory paths Y-DNA...does it help at all complementing autosomal DNA with Haplo distribution? What relevant info should we take out of this in your opinion @Angoliga? in terms proto-tutsi pops.

Angoliga
10-23-2019, 11:24 PM
Throwing in these Haplogroups pie charts Tutsi Y-DNA (http://https://anthrogenica.com/showthread.php?18014-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) MT-DNA (https://anthrogenica.com/showthread.php?18015-Tutsi-Haplogroups-(Rwanda-Burundi-DRC-amp-Uganda)) for potential migratory paths Y-DNA...does it help at all complementing autosomal DNA with Haplo distribution? What relevant info should we take out of this in your opinion @Angoliga? in terms proto-tutsi pops.

By complement do you mean positively-correlate? -- sometimes they do, sometimes they don't as mentioned previously-- sometimes the reasons are anthropologically obvious, other times they're not.

e.g.) Horner SSA/Eurasian mtDNA roughly correlates with their SSA/Eurasian admixture , whereas founder-effects from the predominately European yDNA of Mestizo Latin-Americans is more asymmetrically correlated in respects to their mtDNA.

The paternal yDNA link isn't working, can you repost it and cite the paper -- within this relatively recent time-frame (IA-present), yDNA would be generally preferred over mtDNA.

Have you made any comparisons with other regional populations? From a glance of the mtDNA chart, the highest hgs seem to be SE/East/Northern-East African at a macro-level.

mpatsibihugu89
10-24-2019, 11:30 AM
By complement do you mean positively-correlate? -- Yes


The paternal yDNA link isn't working, can you repost it and cite the paper -- within this relatively recent time-frame (IA-present), yDNA would be generally preferred over mtDNA.

Have you made any comparisons with other regional populations? From a glance of the mtDNA chart, the highest hgs seem to be SE/East/Northern-East African at a macro-level.

Just fixed the link. These pie charts were made with data from 23andme customers from Rwanda, Burundi, UG and DRC. There is no paper to cite. We collected the Haplogroups from our relatives lists.

If you are looking for a legit link to a published study, here is one with n=94 sample of Rwandese Tutsi Y-DNA Published (https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image% 20to%20zoom&p=PMC3&id=1182266_AJHGv74p532fg1.jpg). Needless to mention it seems very different than what we got. W/o Autosomal DNA it is hard to compare our sample to theirs.

Angoliga
10-25-2019, 05:56 AM
Just fixed the link. These pie charts were made with data from 23andme customers from Rwanda, Burundi, UG and DRC. There is no paper to cite. We collected the Haplogroups from our relatives lists.

That's very impressive! I commend you for your efforts.

Given past events, we can understand some of the sensitivity when it comes to releasing data -- from whichever authorities that might be academic/governmental

It's good diligence on your part collecting these private-databases. Interpretations might be somewhat skewed due to size (n) and participant-relatedness but it doesn't hurt comparing the presented-data.


If you are looking for a legit link to a published study, here is one with n=94 sample of Rwandese Tutsi Y-DNA Published (https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image% 20to%20zoom&p=PMC3&id=1182266_AJHGv74p532fg1.jpg). Needless to mention it seems very different than what we got. W/o Autosomal DNA it is hard to compare our sample to theirs.

Thanks, I see it now: (Fig 1. Luis et al., 2004 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182266/))

- This is another paper worth consideration (Hirbo, 2011 (file:///F:/Downloads/Hirbo_umd_0117E_11892%20(2).pdf))



If we're taking the Hutu/Tutsi data for face value (untainted), could this be worth considering:

*For easy following (pg. 195 - 206), I'll refer to the haplogroups using the same labeling (E3a7 = E-M191)



Perhaps the saturated Y-DNA in Tutsis (E3a7 51%, E3a* 32%) is derived from earlier IA founder-effects between Bantu/Pastoral groups in the eastern Rift-Valley; modern-day Kenya/Tanzania.

There's clear archaeological and now genetic data that demonstrates substantial interaction and cross-exchange between different Rift-Valley subsistence groups during the IA (Hunter-Gatherers, Bantu, Pasotoralists: Southern-Nilotic/Cushitic ).

The three-way split of admixture seen with KEN_IA_Deloraine (https://i.imgur.com/QY7iwTN.png), is probably just a glimpse of such "fluid" interactions between Bantu/Nilotic/HGs -- though higher Dinka-like affinities would be regionally expected given the "influx" of likely Southern-Nilotic speakers previously cited here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613126&viewfull=1#post613126) in the Prendergast et al. paper.



"A distinct PN archaeological tradition, the Elmenteitan, has been linked by some scholars to Southern Nilotic speakers (Ambrose, 1982), while traditions of the Pastoral Iron Age (PIA), in the late 1st/early 2nd millennium CE, are sometimes seen as emerging from the Elmenteitan (Ambrose et al., 1984, Lane, 2013). As this outline (summarized in Table 1) suggests, a dominant feature of life in first-millennium CE eastern Africa was diversity and probably degrees of fluidity between linguistic, social, and economic entities, whose Ďboundariesí are often made overly firm by cultural-historical divisions such as LSA, PN, and EIA, all of which actually overlapped in space and time."



Subsistence mosaics, forager-farmer interactions, and the transition to food production in eastern Africa", (Crowther, 2017) (https://www.sciencedirect.com/science/article/pii/S1040618216302890)


Evidently, the highly detected E3a7 is also common among Kenyan Southern-Nilotic speakers -- it's detected at moderate levels among the Ogiek (https://en.wikipedia.org/wiki/Ogiek_language) and Sabaot (https://en.wikipedia.org/wiki/Sabaot_language)(25%, 36.3%). The Saboat and Ogiek are subgroups of the Southern-Nilotic speaking Kalenjin; they're cited in the Prendergast et al. paper as being associated to the Pastoral-IA sites afmd here (archaeologically and ethnographically documented material culture suggest that PIA sites may be associated with ancestors of present-day Kenyan Nilotic speakers such as the Kalenjin).

This Bantu-related yDNA might've been derived from the afmd "fluid" interactions of IA Pastoralist/Bantu migrants. Apart from the Bantu Hutu, E3a7 is also moderately detected among further-eastern Bantu pops in Uganda (Ganda, 46%). So, perhaps E3a7 in these Kenyan Southern-Nilotic speakers, Ogiek/Sabaot, was inherited via interactions of a further eastern-stretch of Bantu pops (bordering Kenya/Uganda). Therefore, the Bantu-related yDNA among Tutsis wouldn't necessarily have to be 100% Hutu > Tutsi.




"....Recent commentaries have highlighted the importance of subsistence mosaics during the agricultural transition, broadly defined as landscapes of interaction between co-existing peoples with diverse (and often overlapping) ethnic, linguistic, political, economic and social backgrounds (Moore, 1985, Kusimba, 2003, Stahl, 2004, Kusimba and Kusimba, 2005, Kusimba et al., 2005, Shipton et al., 2013). Thus, rather than chronologically bounded cultural groups replacing one another in progression, as implicit in the traditional Bantu migration model, evidence suggests that there existed an ethnically and economically diverse frontier in which groups interacted at different spatial and temporal scales in relationships involving competition, conflict, exchange, symbiosis and/or assimilation. Certainly, eastern Africa's wide environmental diversity would have promoted the co-existence of different subsistence groups (Lane, 2004, Shipton et al., 2013)."

(cited from previous paper)


Following this period of interchange between different ethnic groups, correlation of linguistic groups and Y-DNA would've become less clear. This would be the case for the Datog (https://en.wikipedia.org/wiki/Datooga_people), another Southern-Nilotic pop whose forerunners ultimately migrated down the Rift-Valley into Tanzania. Previous runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=610801&viewfull=1#post610801) showed TZN_PN as the most preferable PN-affinity for Tutsi-related groups, perhaps this preference along with the Dinka-like affinities suggests Tutsi-related groups descended from an offshoot of Southern-Nilotic speakers common to the Datog.

Similar to the Tutsi, the Datog have E3a7 along with B2b* though at a lower detection (12%, 4%). Detection of different yDNA Hgs is a lot more varied for the Datog than Tutsis, it spans different E Hgs (E2a, E3B6) with even a minor detection of the typically nilotic A3b2.

Could the overly saturated Y-DNA in Tutsis be explained by founder-effects from a similar pastoral group migrating to the Great-Lakes region?

Espoir
10-25-2019, 02:29 PM
One thing I can say about Luis et al. paper is that it’s shady. By this I mean, either they sampled the wrong population(Tutsi) knowingly or unknowingly. The latter the most likely. The paper says that less than 3% of E-M35 was detected in Tutsis. Yet, online amateurs find it at 40%. This is sharp contradiction. One would say that maybe it’s sampling issue. Again, that sharp difference is unbelievably high to believe. However, sampling issue might be true if we mean that they sampled the wrong population.

From samples of “Banyarwanda”(Tutsi and Hutu)Tishkoff et al. used. They all autosomally are similar to Great Lakes Bantus such as Baganda.
Another study confirmed 2/9 sampled Burundian Tutsis and found E-M293. What’s strange is that, they don’t tell us which other haplogroups were found, no maternal haplogroups released. They simply jumped to a conclusion that their might have been assimilation of southern Cushites in Burundian Tutsis.

Almost all papers that talk about Tutsis show them similar to neighboring Bantu, have half of the information to jump to any conclusions. By half info, I mean, either show paternal haplogroups without maternal and autosomal DNA, or show autosomal without paternal and maternal.

This to me means, there is an issue when it comes to sampling Tutsis. Why all pop geneticists find Tutsis indistinguishable from Bantu and yet all Tutsis that used commercial companies come out distinct.
Only if we can get access to the Tutsi samples Luis et al. used, we can be assured that it’s the right sample. As I’m waiting, I consider that to be politically motivated. They might have been trying to push the idea on “Rwandaness” meaning that they are all sons of Kanyarwanda, no difference btwn them.

mpatsibihugu89
10-25-2019, 03:16 PM
That's very impressive! I commend you for your efforts.

It's good diligence on your part collecting these private-databases. Interpretations might be somewhat skewed due to size (n) and participant-relatedness but it doesn't hurt comparing the presented-data. We started collecting because our observations weren't matching these published studies. Now we definitely have doubts about that sample. Also autosomal data I have seen with Tishkoff and others doesn't look similar to what we have. These are distant relatives. No brothers or close relatives sharing the same paternal line. We tried our amateur-ish best lol!!!




Thanks, I see it now: (Fig 1. Luis et al., 2004 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182266/))

- This is another paper worth consideration (Hirbo, 2011 (file:///F:/Downloads/Hirbo_umd_0117E_11892%20(2).pdf))



If we're taking the Hutu/Tutsi data for face value (untainted), could this be worth considering:

*For easy following (pg. 195 - 206), I'll refer to the haplogroups using the same labeling (E3a7 = E-M191)



Perhaps the saturated Y-DNA in Tutsis (E3a7 51%, E3a* 32%) is derived from earlier IA founder-effects between Bantu/Pastoral groups in the eastern Rift-Valley; modern-day Kenya/Tanzania.

There's clear archaeological and now genetic data that demonstrates substantial interaction and cross-exchange between different Rift-Valley subsistence groups during the IA (Hunter-Gatherers, Bantu, Pasotoralists: Southern-Nilotic/Cushitic ).

The three-way split of admixture seen with KEN_IA_Deloraine (https://i.imgur.com/QY7iwTN.png), is probably just a glimpse of such "fluid" interactions between Bantu/Nilotic/HGs -- though higher Dinka-like affinities would be regionally expected given the "influx" of likely Southern-Nilotic speakers previously cited here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613126&viewfull=1#post613126) in the Prendergast et al. paper.





Evidently, the highly detected E3a7 is also common among Kenyan Southern-Nilotic speakers -- it's detected at moderate levels among the Ogiek (https://en.wikipedia.org/wiki/Ogiek_language) and Sabaot (https://en.wikipedia.org/wiki/Sabaot_language)(25%, 36.3%). The Saboat and Ogiek are subgroups of the Southern-Nilotic speaking Kalenjin; they're cited in the Prendergast et al. paper as being associated to the Pastoral-IA sites afmd here (archaeologically and ethnographically documented material culture suggest that PIA sites may be associated with ancestors of present-day Kenyan Nilotic speakers such as the Kalenjin).

This Bantu-related yDNA might've been derived from the afmd "fluid" interactions of IA Pastoralist/Bantu migrants. Apart from the Bantu Hutu, E3a7 is also moderately detected among further-eastern Bantu pops in Uganda (Ganda, 46%). So, perhaps E3a7 in these Kenyan Southern-Nilotic speakers, Ogiek/Sabaot, was inherited via interactions of a further eastern-stretch of Bantu pops (bordering Kenya/Uganda). Therefore, the Bantu-related yDNA among Tutsis wouldn't necessarily have to be 100% Hutu > Tutsi. Good stuff. Thanks for looking into this.







Similar to the Tutsi, the Datog have E3a7 along with B2b* though at a lower detection (12%, 4%). Detection of different yDNA Hgs is a lot more varied for the Datog than Tutsis, it spans different E Hgs (E2a, E3B6) with even a minor detection of the typically nilotic A3b2.

Could the overly saturated Y-DNA in Tutsis be explained by founder-effects from a similar pastoral group migrating to the Great-Lakes region? Our sample has all these haplogroups. A3b2 is actually significant. E2a and E2b are also present, more E2a though. We have 2 individuals with B as well. We even tried tying these haplos lineages to clans but it hasn't worked so far. The Nyiginya clan (Royal tutsi clan of Rwanda) so far has more people matching w/ E-M293 but also has other individuals carrying different haplos.

Angoliga
10-26-2019, 12:24 AM
We started collecting because our observations weren't matching these published studies. Now we definitely have doubts about that sample. Also autosomal data I have seen with Tishkoff and others doesn't look similar to what we have. These are distant relatives. No brothers or close relatives sharing the same paternal line. We tried our amateur-ish best lol!!!

We're all amateurs here -- this is great!




Our sample has all these haplogroups. A3b2 is actually significant. E2a and E2b are also present, more E2a though. We have 2 individuals with B as well. We even tried tying these haplos lineages to clans but it hasn't worked so far. The Nyiginya clan (Royal tutsi clan of Rwanda) so far has more people matching w/ E-M293 but also has other individuals carrying different haplos.

Interesting! Could you share a chart/table of the collected yDNA haplogroups -- out of curiosity, have any tested on FTDNA?

For those willing and interested, it'd be encouraged to have them SNP tested and preferably added onto Yfull -- they'd have their TMRCA calculated against samples from several papers and users around the world... it would collectively paint a clearer picture of migrations.

mpatsibihugu89
10-26-2019, 12:52 AM
For those willing and interested, it'd be encouraged to have them SNP tested and preferably added onto Yfull -- they'd have their TMRCA calculated against samples from several papers and users around the world... it would collectively paint a clearer picture of migrations.
This is next for sure.

Angoliga
10-26-2019, 02:13 AM
"RW_BR4" sample added:


* Newly added sample indicated here as red ē for visual reference


This half-Rwandan/Burundi sample happens to hover around the recently afmd Southern-Nilotic speaking Ogiek (https://www.youtube.com/watch?v=9KbK_ovviio)

https://i.imgur.com/fYSEqsN.png

Updated African PCA:
https://i.imgur.com/5FQXimA.png

Espoir
10-26-2019, 03:03 AM
We're all amateurs here -- this is great!




Interesting! Could you share a chart/table of the collected yDNA haplogroups -- out of curiosity, have any tested on FTDNA?
He will answer u but I think he mentioned that the link is now fixed.( the one that wasnít working and I cross-checked it works now).


For those willing and interested, it'd be encouraged to have them SNP tested and preferably added onto Yfull -- they'd have their TMRCA calculated against samples from several papers and users around the world... it would collectively paint a clearer picture of migrations.
What does it take to do that?

Espoir
10-26-2019, 03:17 AM
"RW_BR4" sample added:


* Newly added sample indicated here as red • for visual reference


This half-Rwandan/Burundi sample happens to hover around the recently afmd Southern-Nilotic speaking Ogiek (https://www.youtube.com/watch?v=9KbK_ovviio)

https://i.imgur.com/fYSEqsN.png
Actually if u look closely, those RW_BR and Burundi have significantly lower West Africa/Bantu admixture compared to other Tutsi-related groups. Maybe that would explain why they cluster close to Ogiek
It’s indeed interesting how all those so called “Nilohamites” are clustering close to each other and to Tutsi-like groups. Is there any “pure” southern/eastern Nilotic group available or they all are cushitic and/or Bantu admixed?


Updated African PCA:
https://i.imgur.com/5FQXimA.png

Angoliga
10-26-2019, 03:12 PM
He will answer u but I think he mentioned that the link is now fixed.( the one that wasnít working and I cross-checked it works now).

...oh, that's odd -- the previous (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613755&viewfull=1#post613755) quoted link showed a figure from the Luis. et al paper. I guess he updated the link a third-time?



What does it take to do that?

FTDNA's Big-Y test would be preferable, it's a bit pricey but their holiday sales are coming up.

An alternative would be getting FTDNA's less expensive Y-DNA STR test (Y-37) without subclade specification, then you could compare your STRs with other SNP-tested members within FTDNA's yDNA database via haplogroup projects to validate your subclade -- these projects are free to join (e.g. FTDNA's E-M35 hg project (https://www.familytreedna.com/public/E3b?iframe=yresults))

Maybe a combination of both methods would be most cost-effective given participants overlapping yDNA hgs.



The SNP tested participants would then submit their results to Yfull (https://www.yfull.com/)for interpretation analysis (subclade specification, formation dating, TMRCA...). They'd then be plotted onto the Ytree which has thousands of global users and increasingly more paper samples.

For a visual, here's a Ytree screenshot of current E-M293 (https://www.yfull.com/tree/E-M293/) samples/participants:

https://i.imgur.com/xBdNYLa.png


Here's more info from a helpful blogger: Why the Big Y Test? (https://dna-explained.com/2017/11/17/why-the-big-y-test/)

If you have more questions, we can discuss in more detail via PM -- wouldn't want to derail the thread too much

Angoliga
10-26-2019, 09:08 PM
Actually if u look closely, those RW_BR and Burundi have significantly lower West Africa/Bantu admixture compared to other Tutsi-related groups.

Based on the intermediate position of Tutsi-related users and more heavily admixed Eurasian samples (Horners), there's no way to visually ascertain West-African or Dinka-like ancestry -- that's because core Ancestral-East Africans (Dinka-like) and West-African pops more or less plot in the same vicinity (some musings on why that might be here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=607235&viewfull=1#post607235)).


...Maybe that would explain why they cluster close to Ogiek.


We'd need to check their ancestral affinities to validate whether it's their Dinka or West-African affinities pulling them westward; also to take note of is the northward pull towards EAn forager groups -- all this contrasted against elevated eurasian-affinities in PN and SW-Asian/N-African affinities.



...That said, lets have a run with Ogiek along with the Tutsi-related samples:

https://i.imgur.com/DjMJcq0.png

Source Samples:
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763

Interestingly, the Ogiek have negligible West-African affinities --

so, it's not strictly West-African/Bantu related ancestry that's making RW_BR/BRs cluster around this Southern-Nilotic speaking pop.

*Notice the Ogiek's non-negligible Levant_PPNC affinity (4.4%)





Itís indeed interesting how all those so called ďNilohamitesĒ are clustering close to each other and to Tutsi-like groups.


Yeah, it's pretty neat -- it's a visual representation of Rift-Valley inter-mixture spanning several millennia: Cushitic/Nilotic/Bantu/LSA_HGs and even some relatively recent SW-Asian/N-African thrown in the mix





Is there any ďpureĒ southern/eastern Nilotic group available or they all are cushitic and/or Bantu admixed?



Good question, the short-answer is no -- literally all modern Southern/Eastern Nilotic speakers are either Cushitic, Bantu or ~KEN_LSA admixed.

Judging by ADMIXTURE (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006976) from the Hollfelder 2017 paper, the Southern-Sudanese Bari would be good contenders for nilotic "purity" among modern Eastern-Niotic speakers. Unfortunately, we can't take their genetic-profile for face-value since they've only historically migrated to South-Sudan (<17th century), supposedly from a region in-and-around Lake Turkana...so initial Bari speakers might've had higher Mota/Cushitic-like affinities before assimilating local South-Sudanese pops.

So ultimately, we'd first need ancient samples (~2000 BCE) from the Middle-Nile basin to confirm that definition of "pure". According to linguists, this is presumably when and where proto-Nilotic speakers would've split.

However, if we're strictly going with a defacto Dinka-like profile for proto-Southern/Eastern nilotic speakers (i.e. without HG/Cushitic/Bantu admixture), there's only one sample from the PN paper which might give us a clue "KEN_IA_DELORAINE" :

https://i.imgur.com/jYuDwqm.png

The Levant_PPNC affinity appears only non-negligible among IA samples, noted for having an influx of Nilotic (Dinka-like) ancestry.
*The minor Levant_PPNC in the more recent sample KEN_400BP (1540 CE) is likely tied to their Levant_PPNB and Anatolia_Barcin_N.


Since KEN_IA_DELORAINE doesn't have any Cushitic-related affinities (ETH_4500BP, Levant_Natufian), we can infer the sample's Southern-Nilotic ancestry by deducting their West-African and Forager ancestry (Yoruba, KEN_LSA).

Similar to the modern Southern-Nilotic speaking Ogeik, this IA pastoralist also has a minor Levant_PPNC affinity (6.8%) -- the Levant_PPNC affinity we're also seeing among Tutsi-related samples (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129) would seem to agree with the "Southern-Nilotic Hypothesis" for Tutsi-origin.

Relating to this signature, I initially cautioned the credibility of these deep-layer runs due to the higher distance% but above, in the first run of this post, the Ogiek are getting Levant_PPNC at reasonable fits (0.0136%).

Barring the low resolution of samples, Levant_PPNC could actually be an IA signature for Southern-Nilotic migrations. Based on KEN_IA_DELORAINE's dating (~880 CE), it's affinity among Tutsis and Ogiek would translate genetic continuum spanning at least a millennium.

Angoliga
10-26-2019, 09:44 PM
"BR_TUTSI" sample added:


* Newly added sample indicated with red ē for visual reference


https://i.imgur.com/e5f5fWq.png

Updated African PCA:
https://i.imgur.com/FfxBJm3.png

Espoir
10-27-2019, 01:11 AM
Based on the intermediate position of Tutsi-related users and more heavily admixed Eurasian samples (Horners), there's no way to visually ascertain West-African or Dinka-like ancestry -- that's because core Ancestral-East Africans (Dinka-like) and West-African pops more or less plot in the same vicinity (some musings on why that might be here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=607235&viewfull=1#post607235)).




We'd need to check their ancestral affinities to validate whether it's their Dinka or West-African affinities pulling them westward; also to take note of is the northward pull towards EAn forager groups -- all this contrasted against elevated eurasian-affinities in PN and SW-Asian/N-African affinities.



...That said, lets have a run with Ogiek along with the Tutsi-related samples:

https://i.imgur.com/DjMJcq0.png

Source Samples:
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763

Interestingly, the Ogiek have negligible West-African affinities --

so, it's not strictly West-African/Bantu related ancestry that's making RW_BR/BRs cluster around this Southern-Nilotic speaking pop.

*Notice the Ogiek's non-negligible Levant_PPNC affinity (4.4%)






Yeah, it's pretty neat -- it's a visual representation of Rift-Valley inter-mixture spanning several millennia: Cushitic/Nilotic/Bantu/LSA_HGs and even some relatively recent SW-Asian/N-African thrown in the mix







Good question, the short-answer is no -- literally all modern Southern/Eastern Nilotic speakers are either Cushitic, Bantu or ~KEN_LSA admixed.

Judging by ADMIXTURE (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006976) from the Hollfelder 2017 paper, the Southern-Sudanese Bari would be good contenders for nilotic "purity" among modern Eastern-Niotic speakers. Unfortunately, we can't take their genetic-profile for face-value since they've only historically migrated to South-Sudan (<17th century), supposedly from a region in-and-around Lake Turkana...so initial Bari speakers might've had higher Mota/Cushitic-like affinities before assimilating local South-Sudanese pops.

So ultimately, we'd first need ancient samples (~2000 BCE) from the Middle-Nile basin to confirm that definition of "pure". According to linguists, this is presumably when and where proto-Nilotic speakers would've split.

However, if we're strictly going with a defacto Dinka-like profile for proto-Southern/Eastern nilotic speakers (i.e. without HG/Cushitic/Bantu admixture), there's only one sample from the PN paper which might give us a clue "KEN_IA_DELORAINE" :

https://i.imgur.com/jYuDwqm.png

The Levant_PPNC affinity appears only non-negligible among IA samples, noted for having an influx of Nilotic (Dinka-like) ancestry.
*The minor Levant_PPNC in the more recent sample KEN_400BP (1540 CE) is likely tied to their Levant_PPNB and Anatolia_Barcin_N.


Since KEN_IA_DELORAINE doesn't have any Cushitic-related affinities (ETH_4500BP, Levant_Natufian), we can infer the sample's Southern-Nilotic ancestry by deducting their West-African and Forager ancestry (Yoruba, KEN_LSA).

Similar to the modern Southern-Nilotic speaking Ogeik, this IA pastoralist also has a minor Levant_PPNC affinity (6.8%) -- the Levant_PPNC affinity we're also seeing among Tutsi-related samples (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129) would seem to agree with the "Southern-Nilotic Hypothesis" for Tutsi-origin.

Relating to this signature, I initially cautioned the credibility of these deep-layer runs due to the higher distance% but above, in the first run of this post, the Ogiek are getting Levant_PPNC at reasonable fits (0.0136%).

Barring the low resolution of samples, Levant_PPNC could actually be an IA signature for Southern-Nilotic migrations. Based on KEN_IA_DELORAINE's dating (~880 CE), it's affinity among Tutsis and Ogiek would translate genetic continuum spanning at least a millennium.

Quite an insightful detailed observation.
Now letís be more representative and add other West African groups like Mandinka and Gambian in ref pops and see how things shake up. I was playing with them and damn, almost all that Yoruba is lost to both of them.

Angoliga can U rerun these Tutsi individuals with reference below.
Iíve added both Mandenka and Gambian
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Gambian,-0.60625,0.067787,0.01994,0.011588,0.002539,0.00589 2,-0.034664,0.038595,-0.031778,0.023736,0.006374,-0.00384,0.016446,1.7e-05,0.011808,-0.013276,0.009795,-0.000269,-0.002137,-0.00308,-0.001763,-0.002241,0.004021,0.000181,0.00217
Mandenka,-0.607246,0.063471,0.01797,0.010611,-1.5e-05,0.009078,-0.038025,0.038214,-0.030781,0.025914,0.004985,-0.000959,0.019772,-0.001129,0.015825,-0.011966,0.010685,9.5e-05,-0.002049,-0.002095,-0.001897,-0.005564,0.000801,-0.001374,0.00118

Alfa
10-27-2019, 05:16 AM
Based on the intermediate position of Tutsi-related users and more heavily admixed Eurasian samples (Horners), there's no way to visually ascertain West-African or Dinka-like ancestry -- that's because core Ancestral-East Africans (Dinka-like) and West-African pops more or less plot in the same vicinity (some musings on why that might be here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=607235&viewfull=1#post607235)).




We'd need to check their ancestral affinities to validate whether it's their Dinka or West-African affinities pulling them westward; also to take note of is the northward pull towards EAn forager groups -- all this contrasted against elevated eurasian-affinities in PN and SW-Asian/N-African affinities.



...That said, lets have a run with Ogiek along with the Tutsi-related samples:

https://i.imgur.com/DjMJcq0.png

Source Samples:
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763

Interestingly, the Ogiek have negligible West-African affinities --

so, it's not strictly West-African/Bantu related ancestry that's making RW_BR/BRs cluster around this Southern-Nilotic speaking pop.

*Notice the Ogiek's non-negligible Levant_PPNC affinity (4.4%)






Yeah, it's pretty neat -- it's a visual representation of Rift-Valley inter-mixture spanning several millennia: Cushitic/Nilotic/Bantu/LSA_HGs and even some relatively recent SW-Asian/N-African thrown in the mix







Good question, the short-answer is no -- literally all modern Southern/Eastern Nilotic speakers are either Cushitic, Bantu or ~KEN_LSA admixed.

Judging by ADMIXTURE (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006976) from the Hollfelder 2017 paper, the Southern-Sudanese Bari would be good contenders for nilotic "purity" among modern Eastern-Niotic speakers. Unfortunately, we can't take their genetic-profile for face-value since they've only historically migrated to South-Sudan (<17th century), supposedly from a region in-and-around Lake Turkana...so initial Bari speakers might've had higher Mota/Cushitic-like affinities before assimilating local South-Sudanese pops.

So ultimately, we'd first need ancient samples (~2000 BCE) from the Middle-Nile basin to confirm that definition of "pure". According to linguists, this is presumably when and where proto-Nilotic speakers would've split.

However, if we're strictly going with a defacto Dinka-like profile for proto-Southern/Eastern nilotic speakers (i.e. without HG/Cushitic/Bantu admixture), there's only one sample from the PN paper which might give us a clue "KEN_IA_DELORAINE" :

https://i.imgur.com/jYuDwqm.png

The Levant_PPNC affinity appears only non-negligible among IA samples, noted for having an influx of Nilotic (Dinka-like) ancestry.
*The minor Levant_PPNC in the more recent sample KEN_400BP (1540 CE) is likely tied to their Levant_PPNB and Anatolia_Barcin_N.


Since KEN_IA_DELORAINE doesn't have any Cushitic-related affinities (ETH_4500BP, Levant_Natufian), we can infer the sample's Southern-Nilotic ancestry by deducting their West-African and Forager ancestry (Yoruba, KEN_LSA).

Similar to the modern Southern-Nilotic speaking Ogeik, this IA pastoralist also has a minor Levant_PPNC affinity (6.8%) -- the Levant_PPNC affinity we're also seeing among Tutsi-related samples (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129) would seem to agree with the "Southern-Nilotic Hypothesis" for Tutsi-origin.

Relating to this signature, I initially cautioned the credibility of these deep-layer runs due to the higher distance% but above, in the first run of this post, the Ogiek are getting Levant_PPNC at reasonable fits (0.0136%).

Barring the low resolution of samples, Levant_PPNC could actually be an IA signature for Southern-Nilotic migrations. Based on KEN_IA_DELORAINE's dating (~880 CE), it's affinity among Tutsis and Ogiek would translate genetic continuum spanning at least a millennium.

Interesting analysis. I would be careful using the word Proto_Tutsi since the word itself none knows when people started using the word Tutsi. Tutsi derivated from different clans, some were natives and other like my clans came later on to Rwanda. I agree some Tutsi clans may have been nilotic or PIA in origin as it is obvious in Burundi. There are Hima who took dna(2 people, am not allowed to share) and show little to no nilotic admixtures, with predominent Cushitic/Bantoue admixtures. It means not everything was South nilotic by origin. I suspect a nilotic pastoralist or PIA group pastoralists penetrated first to Rwanda_Burundi ,and were later joined by Hima/Nyiginya and affiliated clans of pastoralists from Ankole/Tanzania who were only predominently Cushitic with only Bantoue admixed.


You made a great point, but still not enough evidence proving Levant_PPNC could actually be Southern Nilotic based on small sample.

How would you explain what this guy Drobbah is saying (reference page 10)?

"It seems my mother who clusters with the other Northern Somalis and I both prefer the Ancient Egyptian samples over the Yemeni/Yemenite Jews.The Iraqw is the only sample to score Levant_PPNC...."

mpatsibihugu89
10-27-2019, 03:16 PM
Based on the intermediate position of Tutsi-related users and more heavily admixed Eurasian samples (Horners), there's no way to visually ascertain West-African or Dinka-like ancestry -- that's because core Ancestral-East Africans (Dinka-like) and West-African pops more or less plot in the same vicinity (some musings on why that might be here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=607235&viewfull=1#post607235)).




We'd need to check their ancestral affinities to validate whether it's their Dinka or West-African affinities pulling them westward; also to take note of is the northward pull towards EAn forager groups -- all this contrasted against elevated eurasian-affinities in PN and SW-Asian/N-African affinities.



...That said, lets have a run with Ogiek along with the Tutsi-related samples:

https://i.imgur.com/DjMJcq0.png

Source Samples:
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
TZN_PN,-0.2922976,0.1001312,-0.0287366,-0.081396,0.0041852,-0.0387658,-0.0134898,-0.0005998,0.125087,-0.0781792,-0.0068202,-0.0029074,0.000119,-0.007927,0.0258412,-0.014399,0.0226084,0.0035726,0.0030168,-0.0024762,0.0020464,0.0038828,-0.0021444,-0.0065068,-0.0057
KEN_Pastoral_N_Elmenteitan,-0.287024,0.0907208,-0.0276555,-0.0726212,0.0024618,-0.038301,-0.0101445,-0.0047307,0.1227825,-0.0826743,-0.0060355,-0.0064442,-0.0024528,0.0003442,0.021783,-0.019093,0.01695,0.0029983,0.0102862,-0.0021678,0.0041177,0.0024938,-0.0084632,-0.0035748,0.0022753
TZN_PN_o,-0.277728,0.092413,-0.015085,-0.074936,0.005847,-0.032909,0.002585,-0.013846,0.121078,-0.074717,-0.008607,-0.019033,0.014717,-0.001376,0.028773,-0.012198,0.012256,0.006968,0.001634,-0.001876,0.001497,-0.000866,-0.003821,-0.007591,-0.005389
KEN_Pastoral_N_o,-0.25724,0.103584,-0.004525,-0.068153,0.013233,-0.021753,-0.017156,-0.011999,0.130282,-0.070708,-0.008769,-0.020232,0.002973,0.006331,0.017915,-0.012066,0.002217,-0.002787,0.010559,-0.002626,0.009858,0.001978,-0.01861,0.014942,0
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
EGY_COPT_lifeisdandy,0.018212,0.14319,-0.04978,-0.108529,0.00277,-0.042391,-0.010575,-0.002308,0.044382,-0.001458,0.00682,-0.01154,0.033003,0.003028,-0.000407,0.00305,0.001825,-0.005954,-0.008673,0.006628,-0.002496,0.000742,-0.002465,0.001566,-0.001437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
Yemenite_Ma'rib,0.0448462,0.143799,-0.0612444,-0.1170562,-0.0092324,-0.0479134,-0.0110452,-0.0045692,0.053626,-0.007581,0.0147122,-0.0271256,0.0514366,0.0055874,0.0004886,0.0201534,-0.021383,0.00451,0.0025894,0.0183086,0.0114298,0.0 13132,-0.0067292,0.004651,-0.0054844
Yemenite_Al_Jawf,0.0492282,0.1414123,-0.0630735,-0.1155542,-0.0106942,-0.0473418,-0.0094002,-0.0071535,0.0581358,-0.0025965,0.0128692,-0.0314348,0.0573088,0.003888,0.0038,0.0195902,-0.0204703,0.0039908,0.0031738,0.0221358,0.0107002, 0.0147148,-0.0130642,0.0085552,-0.008562
Yemenite_Jew,0.051383,0.1447854,-0.0632486,-0.114066,-0.0118263,-0.0466941,-0.0134963,-0.0088677,0.0489689,-0.006274,0.0113209,-0.0266121,0.0539851,0.0032439,0.0035287,0.0171607,-0.0245497,0.003475,0.0064106,0.0249583,0.012888,0. 0159867,-0.0070954,0.0046479,-0.0068941
Yemenite_Mahra,0.0542556,0.1360809,-0.0682589,-0.1211978,-0.0037272,-0.056305,-0.0130301,-0.0088204,0.0628798,-0.002045,0.0167981,-0.0325711,0.0657411,0.0058413,0.0080528,0.0270778,-0.0210643,0.0028717,-0.0019133,0.0248312,0.0137259,0.0160887,-0.0087369,0.0027848,-0.0052289
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88E-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25E-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763

Interestingly, the Ogiek have negligible West-African affinities --

so, it's not strictly West-African/Bantu related ancestry that's making RW_BR/BRs cluster around this Southern-Nilotic speaking pop.

*Notice the Ogiek's non-negligible Levant_PPNC affinity (4.4%)






Yeah, it's pretty neat -- it's a visual representation of Rift-Valley inter-mixture spanning several millennia: Cushitic/Nilotic/Bantu/LSA_HGs and even some relatively recent SW-Asian/N-African thrown in the mix







Good question, the short-answer is no -- literally all modern Southern/Eastern Nilotic speakers are either Cushitic, Bantu or ~KEN_LSA admixed.

Judging by ADMIXTURE (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006976) from the Hollfelder 2017 paper, the Southern-Sudanese Bari would be good contenders for nilotic "purity" among modern Eastern-Niotic speakers. Unfortunately, we can't take their genetic-profile for face-value since they've only historically migrated to South-Sudan (<17th century), supposedly from a region in-and-around Lake Turkana...so initial Bari speakers might've had higher Mota/Cushitic-like affinities before assimilating local South-Sudanese pops.

So ultimately, we'd first need ancient samples (~2000 BCE) from the Middle-Nile basin to confirm that definition of "pure". According to linguists, this is presumably when and where proto-Nilotic speakers would've split.

However, if we're strictly going with a defacto Dinka-like profile for proto-Southern/Eastern nilotic speakers (i.e. without HG/Cushitic/Bantu admixture), there's only one sample from the PN paper which might give us a clue "KEN_IA_DELORAINE" :

https://i.imgur.com/jYuDwqm.png

The Levant_PPNC affinity appears only non-negligible among IA samples, noted for having an influx of Nilotic (Dinka-like) ancestry.
*The minor Levant_PPNC in the more recent sample KEN_400BP (1540 CE) is likely tied to their Levant_PPNB and Anatolia_Barcin_N.


Since KEN_IA_DELORAINE doesn't have any Cushitic-related affinities (ETH_4500BP, Levant_Natufian), we can infer the sample's Southern-Nilotic ancestry by deducting their West-African and Forager ancestry (Yoruba, KEN_LSA).

Similar to the modern Southern-Nilotic speaking Ogeik, this IA pastoralist also has a minor Levant_PPNC affinity (6.8%) -- the Levant_PPNC affinity we're also seeing among Tutsi-related samples (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129) would seem to agree with the "Southern-Nilotic Hypothesis" for Tutsi-origin.

Relating to this signature, I initially cautioned the credibility of these deep-layer runs due to the higher distance% but above, in the first run of this post, the Ogiek are getting Levant_PPNC at reasonable fits (0.0136%).

Barring the low resolution of samples, Levant_PPNC could actually be an IA signature for Southern-Nilotic migrations. Based on KEN_IA_DELORAINE's dating (~880 CE), it's affinity among Tutsis and Ogiek would translate genetic continuum spanning at least a millennium.

Great stuff. Thank you.

By the way is your Paternal haplogroup also downstream of A-M118 @Angoliga? Can't figure it out just by looking at the YFull tree...they don't show A-M118 anywhere , only A-M13. Would be interesting to find out if these Tutsi with A-m118 (~15%) fall under your subclade or a different one?
Have you noticed any difference between subclades of A-m118 carried by Nilotes versus Horners? What's your take on the spread of A-m118 in the Great lakes region, Horn and the broader Southern East africa region? any good theories?

Amhas
10-27-2019, 04:29 PM
I will DM you my results when I will reach 10 posts.

NetNomad
10-27-2019, 04:31 PM
I will DM you my results when I will reach 10 posts.

Your ethnicity, let me guess, Egyptian?

Amhas
10-27-2019, 04:34 PM
Your ethnicity, let me guess, Egyptian?

Moroccan.

Angoliga
10-27-2019, 07:11 PM
Interesting analysis. I would be careful using the word Proto_Tutsi since the word itself none knows when people started using the word Tutsi.

- Thank you, indeed.
Within context of conjecture, we're only using the term as a catchphrase for lack of better wording. Would you have suggestions for a more ethnically-neutral/inclusive alternative?


This is why I've initially used quotation marks when replying it's first usage:



...earlier Nilotic expansions from rift-valley Southern-Nilotic speakers is a more likely explanation for most of the elevated Dinka in "Proto-Tutsi"




..Elevated Dinka and lower Mota in "Proto-Tutsi" could be explained as a predominantly Southern-Nilotic pop migrating into the Rift-Valley and absorbing PNs (+ KLSA & Bantu).



..in cases where we haven't used quotation marks, I hope we haven't implied it to be a definitive term:


You are very wrong. Historians already confirmed that Proto-Tutsi groups or related Tutsi groups like Hima clans may have originated from Ankole/Karagwe...



.. Impossible to know for certain without more data, but perhaps the preference for TZN_PN translates a generally more southern rift-valley point of introgression of PN-like ancestry into the Dinka-like pop of Proto-Tutsi groups.



I agree some Tutsi clans may have been nilotic or PIA in origin as it is obvious in Burundi. There are Hima who took dna(2 people, am not allowed to share) and show little to no nilotic admixtures, with predominent Cushitic/Bantoue admixtures. It means not everything was South nilotic by origin. I suspect a nilotic pastoralist or PIA group pastoralists penetrated first to Rwanda_Burundi ,and were later joined by Hima/Nyiginya and affiliated clans of pastoralists from Ankole/Tanzania who were only predominently Cushitic with only Bantoue admixed.

I can't objectively comment since no reference has been provided, though I'm very interested in their results. If they do decide to share, please ask if they'd post them on the forum -- they'd add value to the discussion.





You made a great point, but still not enough evidence proving Levant_PPNC could actually be Southern Nilotic based on small sample.

- Thank you
Correct, hence the closing statement and wording used to indicate possibility:


...Barring the low resolution of samples, Levant_PPNC could actually be an IA signature for Southern-Nilotic migrations. Based on KEN_IA_DELORAINE's dating (~880 CE), it's affinity among Tutsis and Ogiek would translate genetic continuum spanning at least a millennium.





How would you explain what this guy Drobbah is saying (reference page 10)?

"It seems my mother who clusters with the other Northern Somalis and I both prefer the Ancient Egyptian samples over the Yemeni/Yemenite Jews.The Iraqw is the only sample to score Levant_PPNC...."

Regarding Levant_PPNC exclusively being detected among Iraqw (albeit minor) while not among other Cushitic-speakers, this might be explained by Iraqw's absorption of Southern-Nilotic ancestry via nieghbouring Rift-Valley pops like the SN-speaking Datoga:


"the Iraqw culture, as it developed during the nineteenth century, was mainly consolidated through the amalgamation of people from surrounding ethnic groups, including Datoga.. "

A History under Siege Intensive Agriculture in the Mbulu Highlands, Tanzania, 19th Century to the Present (BŲrjeson, 2004 (https://www.diva-portal.org/smash/get/diva2:191044/FULLTEXT01.pdf))


Here's deep-layer results for Datog, who appear to have elevated Levant_PPNC:

https://i.imgur.com/LAjXNMl.png
*Same source samples used in previous deep-layer runs (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611129&viewfull=1#post611129)

Megalophias
10-27-2019, 07:11 PM
By the way is your Paternal haplogroup also downstream of A-M118 @Angoliga? Can't figure it out just by looking at the YFull tree...they don't show A-M118 anywhere , only A-M13.
The only A-M118 sample on the Y-Full tree is a Kenyan listed as A-YP4751*. D'Atanasio et al didn't find any in the Horn (out of 425 samples, 46 of them A-M13); only Nilotic speakers from Uganda (probably Karamojong), Bantu speakers from Kampala, and Turkana from Kenya had any in that study (which unfortunately didn't cover Sudan or South Sudan).

Angoliga
10-28-2019, 01:37 AM
Great stuff. Thank you.

By the way is your Paternal haplogroup also downstream of A-M118 @Angoliga? Can't figure it out just by looking at the YFull tree...they don't show A-M118 anywhere , only A-M13. Would be interesting to find out if these Tutsi with A-m118 (~15%) fall under your subclade or a different one?


- My pleasure

As Megalophias stated, there's only one A-M118 on Y-Full at the moment.

Here's the response I received after inquiring about the user's background (Nov, 2018):


...He belongs to the Kikuyu people and was born i Nyahururu, Rift Valley district, Kenya. His father is unknown. His mother is still alive but she has not revealed who is the father. Rift Valley district is a mixture of many different ethnical gruops, common are Masaai and Kalenjin, so it might be a good guess that the father belongs to one of these groups, or a paternal ancestor comes form one of these groups.

With best wishes,

* since no names are stated, I hope I'm not infringing on any privacy here





Have you noticed any difference between subclades of A-m118 carried by Nilotes versus Horners? What's your take on the spread of A-m118 in the Great lakes region, Horn and the broader Southern East africa region? any good theories?

Unfortunately, the papers I've come across were either a mixed group of Ethiopians or general A-M13 data without any specified subclades.

If we're going along with the "Southern-Nilotic Hypothesis", I suspect we'll find higher detection of A-M118 among populations within-and-around the edges of Western-Ethiopia:


"....After ca. 2000 B. C. the proto-Nilotes diverged into three separate societies--the River-Lake or western Nilotes evolving on the north of the proto-Nilotic homeland areas, the Highland Southern Nilotes to the southwest, probably off the southern edges of the Ethiopian plateau."

Some Thoughts on the Early History of the Nile-Congo Watershed - (Ehret, 74 (https://escholarship.org/content/qt2gd85265/qt2gd85265.pdf)')


Among the unspecified A-M13s in the Ethiopian yDNA panel, the nilotic Gumuz, rich in A&B haplogrups (Pagani, 15 (https://i.imgur.com/f9DnYHV.png)'), might be ideal candidates for A-M118 detection. Some pops within the Gambela and Southern Nations, Nationalities, and Peoples' Region might also fit the bill.

Detection of A-M118 in the Yfull sample and within the great-lakes region might relate to IA Souterhn-Nilotic migrations, having an origin somewhere in-between the western edges of the Ethiopian plateau and the Middle-Nile basin (urheimat of proto-nilotic speakers).

To validate/dismiss this theory, we'd need better survey/resolution of samples throughout the Rift-Valley (KEN, TZ..), Great-Lakes region (RW,BR..) and around these more "removed" western-regions of Ethiopia.

mpatsibihugu89
10-28-2019, 03:07 PM
- My pleasure

As Megalophias stated, there's only one A-M118 on Y-Full at the moment.

Here's the response I received after inquiring about the user's background (Nov, 2018):



* since no names are stated, I hope I'm not infringing on any privacy here






Unfortunately, the papers I've come across were either a mixed group of Ethiopians or general A-M13 data without any specified subclades.

If we're going along with the "Southern-Nilotic Hypothesis", I suspect we'll find higher detection of A-M118 among populations within-and-around the edges of Western-Ethiopia:



Among the unspecified A-M13s in the Ethiopian yDNA panel, the nilotic Gumuz, rich in A&B haplogrups (Pagani, 15 (https://i.imgur.com/f9DnYHV.png)'), might be ideal candidates for A-M118 detection. Some pops within the Gambela and Southern Nations, Nationalities, and Peoples' Region might also fit the bill.

Detection of A-M118 in the Yfull sample and within the great-lakes region might relate to IA Souterhn-Nilotic migrations, having an origin somewhere in-between the western edges of the Ethiopian plateau and the Middle-Nile basin (urheimat of proto-nilotic speakers).

To validate/dismiss this theory, we'd need better survey/resolution of samples throughout the Rift-Valley (KEN, TZ..), Great-Lakes region (RW,BR..) and around these more "removed" western-regions of Ethiopia.

34242

here is the source (https://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html?m=1) So it is quite significant in these samples only the Maale don't carry A-m118 in that sample

Angoliga
10-28-2019, 04:34 PM
... alright, so after you confirmed in PM that they've tested on 23andme, I checked my own account for curiosity's sake -- it turns out A-M118 is 23andme's general designation for A-M13 :\

https://i.imgur.com/X1bWM2l.png

https://i.imgur.com/KACQPpF.png

... so the verdict's still out on the specific A-M13 subclades for those great-lake samples (RW, BR..).



34242

here is the source (https://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html?m=1) So it is quite significant in these samples only the Maale don't carry A-m118 in that sample

Wow, totally missed that reference on ethiohelix!

Judging by those Ethiopian highlanders, "A-M118" in this paper seems to be an unspecified designation for all A-M13s.

I'm curious about that "A-M171 (xM118)" subclade.

I'm not sure if this applies: from searching SNP M171 in yfull, the return is "A-Y26839* This position for SNP is not in the YTree":
https://i.imgur.com/oPYe4mM.png

A-Y26839* (https://www.yfull.com/tree/A-Y26839*/) is an A-M13 subclade which currently has a Chadian Shuwa (Baggara) Arab sample from the D’Atanasio paper:
https://i.imgur.com/JeIdOCt.png

mpatsibihugu89
10-28-2019, 09:37 PM
I was just looking at this Variation in Y chromosome mtDNA and labels of identity in Ethiopia (https://pdfs.semanticscholar.org/25d8/95f8243e0b97e20fa6dc6861f8ec5b5d06cd.pdf) by C.Plaster seems extensive

The Gambella region in Western Ethiopia (on the border with South Sudan) has the highest frequency of A3b2 according to data collected in this paper Page 81
still no specification of downstream clade though.

sum1
10-29-2019, 01:21 AM
I tried to runs with some ancient genomes in the hopes of shedding light as to why my fits are so bad.

I used @Angoliga runs that he used in another thread looking for layers of ANA/Eurasian ancestry in African populations.

Seems the runs favour adding extra Natufian like ancestry for me and removing whatever Iranian like affinity compared to other models.

Runs with Natufian+Iberomaurusian

34255

Runs with Egyptian samples

34256

Runs with Yemeni Jews. High levels of Natufian vs the average Somali

34257

Runs with my best fit vs Average Somali best fit. Natufian ancestry still preferred for me.
34258

Lank
10-30-2019, 07:01 PM
One very interesting result here is how well South Omotic speakers (Ari) fit as a fairly even mixture of early Cushitic speakers and aboriginal Ethiopians (Mota), with some added KEN_LSA. The fit is among the lowest of the ones you posted. This strongly implies that Afroasiatic ancestry in Omotic speakers is closely related to Cushitic ancestry. It reaches nearly 50% in the Ari.
Highly speculative, but I can think of 2 main scenarios to explain this:

1) Pastoral Cushites (despite having Neolithic cultures) were similar genetically to Epipaleolithic Northeast African Afroasiatics, who also influenced Omotics. The Natufian-like ancestry in Cushites might be another hint.
2) Early Omotics, despite their supposed divergence within Afroasiatic, were simply a mixture of Cushitic-like pastoral groups with native Ethiopian groups.

If we had some high-res Y-DNA on Ari and other Omotics, that would be helpful...

NetNomad
10-30-2019, 07:22 PM
Highly speculative, but I can think of 2 main scenarios to explain this:

1) Pastoral Cushites (despite having Neolithic cultures) were similar genetically to Epipaleolithic Northeast African Afroasiatics, who also influenced Omotics. The Natufian-like ancestry in Cushites might be another hint.
2) Early Omotics, despite their supposed divergence within Afroasiatic, were simply a mixture of Cushitic-like pastoral groups with native Ethiopian groups.

If we had some high-res Y-DNA on Ari and other Omotics, that would be helpful...

There are also fringe linguistic theories claiming that Omotic is actually Cushitic (so-called West Cushitic branch).

Megalophias
10-30-2019, 09:46 PM
There is another theory that Omotic isn't Afroasiatic at all, but one or more local isolate families with areal influence; or that North Omotic is Afroasiatic but South Omotic is not. Doubting Omotic is not fringe: one of the standard linguistic references, Glottolog, splits the Omotic languages into three different top level families and does not consider the Afroasiatic membership of any of them to be demonstrated satisfactorily.

Angoliga
11-02-2019, 06:20 PM
"MAR_Amhas" user added:



* Newly added user indicated as X for visual reference


https://i.imgur.com/1CtyiSd.png


Updated African PCA:

https://i.imgur.com/gjs5qVW.png

Espoir
11-02-2019, 06:54 PM
"MAR_Amhas" user added:



* Newly added user indicated as X for visual reference


https://i.imgur.com/1CtyiSd.png


Updated African PCA:

https://i.imgur.com/gjs5qVW.png


Quick question, does ‘Morrocan_South’ have SSA ancestry?

drobbah
11-02-2019, 07:00 PM
Quick question, does ‘Morrocan_South’ have SSA ancestry?

It has substantially more West African ancestry than the average coastal North African.

Ignis90
11-02-2019, 08:42 PM
Quick question, does ĎMorrocan_Southí have SSA ancestry?

Yes, many very heterogenous West African-shifted individuals. But when you only take into account more "average " individuals, they have among the highest Iberomaurusian ancestry of the whole Maghreb.

The funny thing is indigenous southern Morocco and the Souss have the least Holocene tropical African ancestry of all NW Africa , despite having among the biggest "black"/haratin and mixed community nowadays (only lower then the region of the historical slavery hub of Essaouira/Mogador) and living in the southernmost non-Saharan part of NW Africa.

Agamemnon
11-02-2019, 09:06 PM
There is another theory that Omotic isn't Afroasiatic at all, but one or more local isolate families with areal influence; or that North Omotic is Afroasiatic but South Omotic is not. Doubting Omotic is not fringe: one of the standard linguistic references, Glottolog, splits the Omotic languages into three different top level families and does not consider the Afroasiatic membership of any of them to be demonstrated satisfactorily.

Omotic is the least-studied branch of AA. The family might comprise dozens of languages, the linguistic material is limited and covers less than 1/3rd of the languages or dialects that are labeled Omotic. We're certainly in no position to reconstruct Proto-Omotic. What has really been questioned is whether some members of the Omotic branch are in fact AA languages, those most vehement when it comes to this subject are usually proponents of the old classification of Omotic as a branch of Cushitic (as well as those who are keen on lumping every poorly understood East African language into the already overburdened Nilo-Saharan family). But this is not based on shared innovations between Cushitic and Omotic, rather lexico-statistical and typological comparisons sustain this classification model. Furthermore, the fact that some of the languages that are labeled Omotic do not look AA per se is not a good reason to invalidate Omotic's existence. The recent proposals to exclude Aroid (South Omotic) are mostly based on the pronoun system, this remains to be evaluated and IMO won't really withstand close scrutiny, but even if we were to accept it that would still leave us with a very large Omotic family with dozens of languages.

To be sure, Omotic as non-AA is a minority view at best, its exact place within AA is a real matter of debate. Most follow Ehret's lead and place it at the root of the family (and it is therefore understood to be the earliest split), this seems likely when looking at the uncontroversial AA features of Omotic.

Espoir
11-03-2019, 08:10 AM
Yes, many very heterogenous West African-shifted individuals. But when you only take into account more "average " individuals, they have among the highest Iberomaurusian ancestry of the whole Maghreb.

The funny thing is indigenous southern Morocco and the Souss have the least Holocene tropical African ancestry of all NW Africa , despite having among the biggest "black"/haratin and mixed community nowadays (only lower then the region of the historical slavery hub of Essaouira/Mogador) and living in the southernmost non-Saharan part of NW Africa.
Thanks dude!
Do we know if thatís average or an individual?

I seem to have a peculiar affinity towards N/W-Africans:

Modern:

Target: Espoir_
Distance: 0.6655% / 0.00665517
17.0 Ethiopian_Mursi:T_Mursi-1.DG
16.6 Ethiopian_Oromo:OROMO1
14.2 Ethiopian_Anuak:ANUAK14
11.2 Luo:Ayodo_430C
9.6 Ethiopian_Tigray:TYGRAY18
9.0 Somali:SOMALI15
5.8 Moroccan_South:MOU17
4.6 Saharawi:SAH31
4.2 Datog:GOR067
2.4 Yakut:455_A
2.2 Luhya_Kenya:NA19019
1.8 Gambian:HG02574
1.0 Papuan:HGDP00542
0.2 Ju_hoan_North:B_Ju_hoan_North-4
0.2 Papuan:HGDP00541

Ignis90
11-05-2019, 08:15 PM
Thanks dude!
Do we know if thatís average or an individual?

I seem to have a peculiar affinity towards N/W-Africans:

Modern:

Target: Espoir_
Distance: 0.6655% / 0.00665517
17.0 Ethiopian_Mursi:T_Mursi-1.DG
16.6 Ethiopian_Oromo:OROMO1
14.2 Ethiopian_Anuak:ANUAK14
11.2 Luo:Ayodo_430C
9.6 Ethiopian_Tigray:TYGRAY18
9.0 Somali:SOMALI15
5.8 Moroccan_South:MOU17
4.6 Saharawi:SAH31
4.2 Datog:GOR067
2.4 Yakut:455_A
2.2 Luhya_Kenya:NA19019
1.8 Gambian:HG02574
1.0 Papuan:HGDP00542
0.2 Ju_hoan_North:B_Ju_hoan_North-4
0.2 Papuan:HGDP00541

It's most likely the affinity to these individuals is expressing a West African and/or Eurasian affinity you have or these individuals have recent ancestry from around your area .
I don't have the courage to check if the individuals "Moroccan_South:MOU17" and "Saharawi:SAH31" are typical North Africans or outliers: I'm too lazy! :biggrin1:

But more generally, I would avoid using any modern Maghrebi to model any African population or individual outside of Egypt and the Sahel/West Africa. Outside these regions, there is no reason to find historical Berber ancestry.

Espoir
11-05-2019, 10:14 PM
It's most likely the affinity to these individuals is expressing a West African and/or Eurasian affinity you have or these individuals have recent ancestry from around your area .
I don't have the courage to check if the individuals "Moroccan_South:MOU17" and "Saharawi:SAH31" are typical North Africans or outliers: I'm too lazy! :biggrin1:

But more generally, I would avoid using any modern Maghrebi to model any African population or individual outside of Egypt and the Sahel/West Africa. Outside these regions, there is no reason to find historical Berber ancestry.
Lol! It’s ok. I was only wondering if u knew the groups directly( not through internet).
This run was an all moderns spreadsheet. It would have picked West Africans same way it picked Gambian since there is many in the spreadsheet. Same applies for eurasian groups. I’m not an expert on how nMonte picks any given group though.

Angoliga
11-07-2019, 12:36 AM
Finally got a 3D PCA working, we're looking much sexier than anticipated: https://plot.ly/~Angoliga/3/#/

*(might take a minute to fully load)


https://i.imgur.com/aixbaR7.png


Legend when hovering over samples:
◇= Ancients
X= Active users
• = Samples/Modern Avgs



Moving forward, we can use Plotly instead of PAST -- Plotly charts are a lot easier on the eyes and much more interactive, even on smartphones (*desktop mode).

Check out the top right panel for features to Zoom in/out, Box select samples, Download screenshots etc.. :

https://i.imgur.com/MYLBGCO.png




For more traditional folk, you can still refer to this 2D PCA: https://plot.ly/~Angoliga/4/

drobbah
11-07-2019, 01:00 AM
@Sum1 I think you were right.You definitely have some unknown hunter-gatherer ancestry.I score more Mota than you (11% vs 4%) and yet you are clustering near me.
34419

Mnemonics
11-07-2019, 05:59 AM
Hey Angoliga, sorry I couldn't reply to your PM due to the post limit. Here's my coordinates.

Mnemonics_merged_scaled,-0.301631,0.092413,-0.030547,-0.072675,0.005232,-0.036535,-0.021856,0.006461,0.115965,-0.081642,-0.001299,-0.01079,0.006541,-0.001101,0.024973,-0.020684,0.012517,-0.006588,0.001006,-0.006128,-0.000624,0.003462,-0.003328,0.00482,-0.002634

Angoliga
11-07-2019, 08:18 AM
"SM_SLD_Mnemonics" user added:



https://i.imgur.com/Sdc4grC.png

Updated African PCA:

https://i.imgur.com/Dur6lh0.png




3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/

Angoliga
11-11-2019, 01:19 AM
Here's a stab at North-Africans (users, modern avgs/ancients) using a crude "deep-layer" run:

https://i.imgur.com/QQbYWMP.png


All ancient "Levant_"s included:

https://i.imgur.com/lDkLOxR.png

Source Samples (w/ all Levants):
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_RUS_Samara,0.1255849,0.089028,0.0426986,0. 1153479,-0.0287232,0.0450564,0.0036033,-0.0025642,-0.0559032,-0.0728943,0.0018222,3.32E-05,-0.0026924,-0.0233041,0.0366141,0.0157633,-0.0012316,-0.0017879,-0.0038408,0.0137704,-0.0031749,0.0007557,0.0110649,0.0186102,-0.004537
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Gambian,-0.6064875,0.0671942,0.0197362,0.0114665,0.0021028, 0.0055777,-0.0358392,0.0387677,-0.0317353,0.0241463,0.0054132,-0.0036467,0.0162287,-0.0009865,0.011016,-0.0153362,0.009692,-0.0011823,-0.002116,-0.0032307,-0.001643,-0.0018137,0.0043958,-0.0001005,0.001377
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Basque_French,0.128051,0.1520246,0.0551727,0.01282 31,0.0564104,0.0025099,-0.00141,0.0033229,0.0305968,0.0412036,-0.0092724,0.0103408,-0.0209761,-0.0140237,0.0132192,-0.0019359,-0.0119173,0.0030278,-0.0007165,-0.0044144,0.010157,0.0024855,-0.0086397,-0.0091698,7.18E-05
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

Results summarized in bar-chart form:

https://i.imgur.com/ajQHfBE.png

EUR = "French_Basque" used as a general proxy for post IA Iberian ancestry
CHG = Caucasus (GEO_CHG)
STEPPE = Yamnaya_RUS_Samara
SSA = Gambian, Dinka, Yoruba
ANA = Ancestral North African (MAR_Iberomaurusian)
EEF = Anatolia_Barcin_N




Some observations and musings:


ē As expected, there's a declining gradient of ancient North-African ancestry (MAR_Iberomaurusian) from Western to Eastern North Africa. We see the same conversely for Natufian and Iranian_N-related ancestry

ē When all Levants are used, Levant_PPNC seems to have a declining gradient from West - Eastern North African -- the clear exceptions would be Late Period Egypt and the Copt user. Is there any meaningful interpretation for this?

ē Considering ancient Guanches are descended from North African Berbers, their genetic continuity with modern Moroccan_North is pretty astounding -- their affinities are nearly identical in these runs (see first screenshot for results)
One might expect substantially higher SSA-affinities for modern Moroccan_North (primarily due to slavery) -- but the difference is very marginal compared to ancient Guanches. I wonder how much SSA in both modern and ancient pops is related to natural green-saharan introgression vs. slavery
If these proxies have any merit, the higher SSA-preference for Yoruba over Gambian among Guanches and Moroccan_North is rather surprising. Since the modern average for Moroccan_South has substantial Gambian, would the slight uptick in Moroccan_North vs. Guanches imply it's related to more modern-relations such as slavery?

ē On a separate but related-tangent, I wonder how much European ancestry in North-Africa is derived from the Barbary slave trade. It's a seldomly mentioned period in history, worse so, there's no general consensus on estimates of enslaved Europeans. Though given some of the moderate estimates ~1 million (16-18th century), there might've been some degree of genetic impact among modern North-Africans (particularly former Ottoman provinces Algeria, Tunisia, Tripolitania -- and Morocco)

ē GEO_CHG peaks among ancient and modern Egyptians. The high ratios of GEO_CHG:Levant_Natufian in Berber_Tunisia_Chen might imply most of this ancestry wasn't derived directly from Natufian rich Eastern North-Africans (Egyptians). Perhaps it was partly derived from West-Mediterranean islanders; this paper cites Iranian-like affinities among Sicilian MBA samples (Fernandes, 2019 (https://www.biorxiv.org/content/10.1101/584714v1)). Alternatively, maybe this is all just an overthought: since Caucasus ancestry is embedded in neolithic Aegeans, minor CHG in some NW Africans could just be excess Caucus affinities leaking out of the EEF-proxy (Anatolia_Barcin_N) -- by no means would Anatolia_Barcin_N in these crude runs be the de facto genetic-profile of all periodic EEF ancestry in NW-Africa

ē Steppe ancestry appears highest among Libyans, and Tunisian Berbers. Given their geographic proximity to Sicily, could this be a relic of elevated Steppe ancestry in bronze age Sicilians (noted in the afmd paper). " In Sicily, Steppe pastoralist ancestry arrived by ∼2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes." I wonder if the maritime Strait of Sicily once served as a migration corridor for R1b-V88 and Steppe-related ancestry into North Africa. It would explain the minor Sicilian, and Steppe/CHG-related affinities in certain Nilo-Saharan speakers. There's a separate thread on Central-Sudanic speakers from NW Ugandan with such affinities (G25 Unscaled: Traces of Yamnaya in the West-Nile - Noise or Relics of R1b-V88? (https://anthrogenica.com/showthread.php?17945-G25-Unscaled-Traces-of-Yamnaya-in-the-West-Nile-Noise-or-Relics-of-R1b-V88&p=588491&viewfull=1#post588491)). To validate/dismiss that theory, we'd of course need more ancient and modern samples (Chad/Libya/Tunisia)




**I'm by no means an expert when it comes to characterizing North-African ancestry, so consider these deep-layer runs highly provisional for observational purposes. More knowledgeable folk on North-African ancestry, please feel free to chime in on better proxies and interpretations of the data -- I'd appreciate it along with other members on the forum less familiarized with NA population history**

Rwaka
11-11-2019, 07:20 AM
Here's a stab at North-Africans (users, modern avgs/ancients) using a crude "deep-layer" run:

https://i.imgur.com/QQbYWMP.png


All ancient "Levant_"s included:

https://i.imgur.com/lDkLOxR.png

Source Samples (w/ all Levants):
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_RUS_Samara,0.1255849,0.089028,0.0426986,0. 1153479,-0.0287232,0.0450564,0.0036033,-0.0025642,-0.0559032,-0.0728943,0.0018222,3.32E-05,-0.0026924,-0.0233041,0.0366141,0.0157633,-0.0012316,-0.0017879,-0.0038408,0.0137704,-0.0031749,0.0007557,0.0110649,0.0186102,-0.004537
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Gambian,-0.6064875,0.0671942,0.0197362,0.0114665,0.0021028, 0.0055777,-0.0358392,0.0387677,-0.0317353,0.0241463,0.0054132,-0.0036467,0.0162287,-0.0009865,0.011016,-0.0153362,0.009692,-0.0011823,-0.002116,-0.0032307,-0.001643,-0.0018137,0.0043958,-0.0001005,0.001377
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Basque_French,0.128051,0.1520246,0.0551727,0.01282 31,0.0564104,0.0025099,-0.00141,0.0033229,0.0305968,0.0412036,-0.0092724,0.0103408,-0.0209761,-0.0140237,0.0132192,-0.0019359,-0.0119173,0.0030278,-0.0007165,-0.0044144,0.010157,0.0024855,-0.0086397,-0.0091698,7.18E-05
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

Results summarized in bar-chart form:

https://i.imgur.com/ajQHfBE.png

EUR = "French_Basque" used as a general proxy for post IA Iberian ancestry
CHG = Caucasus (GEO_CHG)
STEPPE = Yamnaya_RUS_Samara
SSA = Gambian, Dinka, Yoruba
ANA = Ancestral North African (MAR_Iberomaurusian)
EEF = Anatolia_Barcin_N




Some observations and musings:


• As expected, there's a declining gradient of ancient North-African ancestry (MAR_Iberomaurusian) from Western to Eastern North Africa. We see the same conversely for Natufian and Iranian_N-related ancestry

• When all Levants are used, Levant_PPNC seems to have a declining gradient from West - Eastern North African -- the clear exceptions would be Late Period Egypt and the Copt user. Is there any meaningful interpretation for this?

• Considering ancient Guanches are descended from North African Berbers, their genetic continuity with modern Moroccan_North is pretty astounding -- their affinities are nearly identical in these runs (see first screenshot for results)
One might expect substantially higher SSA-affinities for modern Moroccan_North (primarily due to slavery) -- but the difference is very marginal compared to ancient Guanches. I wonder how much SSA in both modern and ancient pops is related to natural green-saharan introgression vs. slavery
If these proxies have any merit, the higher SSA-preference for Yoruba over Gambian among Guanches and Moroccan_North is rather surprising. Since the modern average for Moroccan_South has substantial Gambian, would the slight uptick in Moroccan_North vs. Guanches imply it's related to more modern-relations such as slavery?

• On a separate but related-tangent, I wonder how much European ancestry in North-Africa is derived from the Barbary slave trade. It's a seldomly mentioned period in history, worse so, there's no general consensus on estimates of enslaved Europeans. Though given some of the moderate estimates ~1 million (16-18th century), there might've been some degree of genetic impact among modern North-Africans (particularly former Ottoman provinces Algeria, Tunisia, Tripolitania -- and Morocco)

• GEO_CHG peaks among ancient and modern Egyptians. The high ratios of GEO_CHG:Levant_Natufian in Berber_Tunisia_Chen might imply most of this ancestry wasn't derived directly from Natufian rich Eastern North-Africans (Egyptians). Perhaps it was partly derived from West-Mediterranean islanders; this paper cites Iranian-like affinities among Sicilian MBA samples (Fernandes, 2019 (https://www.biorxiv.org/content/10.1101/584714v1)). Alternatively, maybe this is all just an overthought: since Caucasus ancestry is embedded in neolithic Aegeans, minor CHG in some NW Africans could just be excess Caucus affinities leaking out of the EEF-proxy (Anatolia_Barcin_N) -- by no means would Anatolia_Barcin_N in these crude runs be the de facto genetic-profile of all periodic EEF ancestry in NW-Africa

• Steppe ancestry appears highest among Libyans, and Tunisian Berbers. Given their geographic proximity to Sicily, could this be a relic of elevated Steppe ancestry in bronze age Sicilians (noted in the afmd paper). " In Sicily, Steppe pastoralist ancestry arrived by ∼2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes." I wonder if the maritime Strait of Sicily once served as a migration corridor for R1b-V88 and Steppe-related ancestry into North Africa. It would explain the minor Sicilian, and Steppe/CHG-related affinities in certain Nilo-Saharan speakers. There's a separate thread on Central-Sudanic speakers from NW Ugandan with such affinities (G25 Unscaled: Traces of Yamnaya in the West-Nile - Noise or Relics of R1b-V88? (https://anthrogenica.com/showthread.php?17945-G25-Unscaled-Traces-of-Yamnaya-in-the-West-Nile-Noise-or-Relics-of-R1b-V88&p=588491&viewfull=1#post588491)). To validate/dismiss that theory, we'd of course need more ancient and modern samples (Chad/Libya/Tunisia)




**I'm by no means an expert when it comes to characterizing North-African ancestry, so consider these deep-layer runs highly provisional for observational purposes. More knowledgeable folk on North-African ancestry, please feel free to chime in on better proxies and interpretations of the data -- I'd appreciate it along with other members on the forum less familiarized with NA population history**
Very interesting as usual. Why TUR Berb hurricane has so high SSA? What's its origin?

Moderator
11-11-2019, 06:04 PM
Please keep political discussions off the forum. Thank you.

Angoliga
11-13-2019, 04:25 AM
... I seem to have missed this modern avg from G25's database (http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html)



"Berber_Algeria" sample added :



https://i.imgur.com/8HRgyRF.png

3D PCA: https://plot.ly/~Angoliga/3/ (allow a ~minute to upload)

2D PCA: https://plot.ly/~Angoliga/4/




Ancestral Comparison ("deep-layer" run):

https://i.imgur.com/zMqKjw7.png

Source Samples:

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_RUS_Samara,0.1255849,0.089028,0.0426986,0. 1153479,-0.0287232,0.0450564,0.0036033,-0.0025642,-0.0559032,-0.0728943,0.0018222,3.32E-05,-0.0026924,-0.0233041,0.0366141,0.0157633,-0.0012316,-0.0017879,-0.0038408,0.0137704,-0.0031749,0.0007557,0.0110649,0.0186102,-0.004537
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Gambian,-0.6064875,0.0671942,0.0197362,0.0114665,0.0021028, 0.0055777,-0.0358392,0.0387677,-0.0317353,0.0241463,0.0054132,-0.0036467,0.0162287,-0.0009865,0.011016,-0.0153362,0.009692,-0.0011823,-0.002116,-0.0032307,-0.001643,-0.0018137,0.0043958,-0.0001005,0.001377
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Basque_French,0.128051,0.1520246,0.0551727,0.01282 31,0.0564104,0.0025099,-0.00141,0.0033229,0.0305968,0.0412036,-0.0092724,0.0103408,-0.0209761,-0.0140237,0.0132192,-0.0019359,-0.0119173,0.0030278,-0.0007165,-0.0044144,0.010157,0.0024855,-0.0086397,-0.0091698,7.18E-05
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534




Very interesting as usual. Why TUR Berb hurricane has so high SSA? What's its origin?

"TUN_BERB" is an abbreviation for Tunisian Berber

Rwaka
11-13-2019, 08:40 AM
"TUN_BERB" is an abbreviation for Tunisian Berber

I understand but why such high SSA?

Angoliga
11-13-2019, 10:25 PM
I understand but why such high SSA?

Pardon, didn't fully understand your question -- Do you mean why do these Tunisian user samples have higher SSA affintiies relative to other North-Africans?

Affinities in Berber populations can vary quite drastically, the North-African samples used in these past runs are just population averages; there's a wider range of variability among individuals.

Here's a demonstration using all North-African individual samples from the G25 dataset (219 n) with SSA affinities in descending order (Yoruba, Gambian, Dinka):

https://i.imgur.com/7WTcg6o.png
https://i.imgur.com/CnPtGfo.png
https://i.imgur.com/NIMK85E.png

You can see some of these samples have even higher SSA affinities than the Tunisian user samples.

*If that wasn't your intended question, let me know -- but please elaborate for clarity.

Chad Rohlfsen
11-13-2019, 11:26 PM
Finally got a 3D PCA working, we're looking much sexier than anticipated: https://plot.ly/~Angoliga/3/#/

*(might take a minute to fully load)


https://i.imgur.com/aixbaR7.png


Legend when hovering over samples:
◇= Ancients
X= Active users
• = Samples/Modern Avgs



Moving forward, we can use Plotly instead of PAST -- Plotly charts are a lot easier on the eyes and much more interactive, even on smartphones (*desktop mode).

Check out the top right panel for features to Zoom in/out, Box select samples, Download screenshots etc.. :

https://i.imgur.com/MYLBGCO.png




For more traditional folk, you can still refer to this 2D PCA: https://plot.ly/~Angoliga/4/

I'm not seeing Mota here. Is he included in the 2D? I'm also working on something that is going to be important for Northern and West African ancestry.

Angoliga
11-13-2019, 11:51 PM
Chadster!! where you been man?


I'm not seeing Mota here. Is he included in the 2D?

Mota is on both PCAs as " ETH_4500BP "

https://i.imgur.com/hz32pv3.png

https://i.imgur.com/2Joj4Rq.png

I'm also working on something that is going to be important for Northern and West African ancestry.


... but will it be anything remotely sexier than this 3D PCA?

- joking, glad to hear -- looking forward to it

Chad Rohlfsen
11-14-2019, 12:08 AM
Chadster!! where you been man?



Mota is on both PCAs as " ETH_4500BP "

https://i.imgur.com/hz32pv3.png

https://i.imgur.com/2Joj4Rq.png



... but will it be anything remotely sexier than this 3D PCA?

- joking, glad to hear -- looking forward to it

Hey, Ben! Been busy working and taking care of the kids. I'm starting to get back in the swing of things here. I believe Iberomaurusians have been looked at incorrectly all along. I'm also working on a newer tree for Africa.

I like the work you're doing here. Very impressive. If you get around to getting admixtools, I'll show you how it works.

I'll have a post not too long from now. I'm not sure how sexy it will be, but I hope it is informative.

Rwaka
11-14-2019, 01:46 AM
Pardon, didn't fully understand your question -- Do you mean why do these Tunisian user samples have higher SSA affintiies relative to other North-Africans?

Affinities in Berber populations can vary quite drastically, the North-African samples used in these past runs are just population averages; there's a wider range of variability among individuals.

Here's a demonstration using all North-African individual samples from the G25 dataset (219 n) with SSA affinities in descending order (Yoruba, Gambian, Dinka):

https://i.imgur.com/7WTcg6o.png
https://i.imgur.com/CnPtGfo.png
https://i.imgur.com/NIMK85E.png

You can see some of these samples have even higher SSA affinities than the Tunisian user samples.

*If that wasn't your intended question, let me know -- but please elaborate for clarity.

Thanks. Yeah that's what I wanted to know, and I'm quite surprised. Some are not different from me in terms of SSA percentage, which I find weird. Are they from the South? Are all those samples modern?

Angoliga
11-14-2019, 03:50 PM
Hey, Ben! Been busy working and taking care of the kids. I'm starting to get back in the swing of things here. I believe Iberomaurusians have been looked at incorrectly all along. I'm also working on a newer tree for Africa.

I like the work you're doing here. Very impressive. If you get around to getting admixtools, I'll show you how it works.

I'll have a post not too long from now. I'm not sure how sexy it will be, but I hope it is informative.

Come on, AG > Child-rearing, you know that! :P


Thank you for the kind words, it means a lot coming from someone who jumped the gun on many genetic validations well before academia.

As I'm sure many others are on the forum, I'm very interested to see your new take on Iberomaurusians (needn't worry about the sexiness).

... be careful now, I will take your word on assistance with admixtools -- as an amateur-hobbyist, I think their combined usage with G25 will be extremely beneficial for inferring "unchecked" population history

Generalissimo
11-20-2019, 02:56 AM
African views have been added to the G25 PCA tool...

https://vahaduo.github.io/g25views/#

Angoliga
11-22-2019, 04:14 AM
"SM_Deftextra" user added:



https://i.imgur.com/HSn7PN7.png

Updated PCA (All Africans):

https://i.imgur.com/dnncTCi.png


◇= Ancients
X= Active users
ē = Samples/Modern Avgs


3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/

Angoliga
11-22-2019, 04:51 AM
Here's a re-run of Horners with newly added users:


Results shown in descending order of distance..

https://i.imgur.com/4uOR16c.png



With all PNs and Levants:
https://i.imgur.com/V8wQzze.png


"SM_Deftextra" is very peculiar; found near the top (4th worst fit).

blackflash16
11-22-2019, 01:15 PM
Here's a re-run of Horners with newly added users:


Results shown in descending order of distance..

https://i.imgur.com/4uOR16c.png



With all PNs and Levants:
https://i.imgur.com/V8wQzze.png


"SM_Deftextra" is very peculiar; found near the top (4th worst fit).

Makes sense. Deftextra is Benadiri/Reer-Xamar (http://anthromadness.blogspot.com/2015/12/the-reer-xamar-are-substantially-mixed.html) if I remember correctly. The significantly elevated Tinyuan and Iran_N and poor fit is probably due to the lack of South Asian + South-East Asian (?) references.

Angoliga
11-22-2019, 02:41 PM
Makes sense. Deftextra is Benadiri/Reer-Xamar (http://anthromadness.blogspot.com/2015/12/the-reer-xamar-are-substantially-mixed.html) if I remember correctly. The significantly elevated Tinyuan and Iran_N and poor fit is probably due to the lack of South Asian + South-East Asian (?) references.

Ahh, that would explain most of it.

Below is a run against all ancients; his ranking improves dramatically with better IRAN_N and South Asian references:

https://i.imgur.com/bpphUMk.png


What's still peculiar is the minor, albeit non-negligible, North-African/embedded EEF affinities -- can't recall seeing anything like this among Horners/Erythraean-related samples *maybe just an overthought on my part

drobbah
11-22-2019, 06:22 PM
Here's a re-run of Horners with newly added users:


Results shown in descending order of distance..

https://i.imgur.com/4uOR16c.png



With all PNs and Levants:
https://i.imgur.com/V8wQzze.png


"SM_Deftextra" is very peculiar; found near the top (4th worst fit).

Do those Neolithic Moroccan carry similar ancestry to the Neolithic Anatolians? It seems those with origins in the core of Somaliland (Isaaqs) seem to carry it to the exclusion of other Somalis.

Rwaka
11-28-2019, 12:20 AM
New coordinates added:
Baka:T_Baka-1.DG
Baka:T_Baka-2.DG
Bakola:T_Bakola-1.DG
Bakola:T_Bakola-2.DG
Bantu_Kenya:S_BantuKenya-1.DG
Bantu_Kenya:S_BantuKenya-2.DG
Bedzan:T_Bedzan-1.DG
Bedzan:T_Bedzan-2.DG
Bulala:T_Bulala-1.DG
Bulala:T_Bulala-2.DG
Fulani:T_Fulani-1.DG
Fulani:T_Fulani-2.DG
Kaba:T_Kaba-1.DG
Kaba:T_Kaba-2.DG
Khomani_San:S_Khomani_San-1.DG
Khomani_San:S_Khomani_San-2.DG
Laka:T_Laka-1.DG
Laka:T_Laka-2.DG
Lemande:S_Lemande-1.DG
Lemande:S_Lemande-2.DG
Mada:T_Mada-1.DG
Mada:T_Mada-2.DG
Mbuti:A_Mbuti-5.DG
Mbuti:B_Mbuti-4.DG
Mbuti:S_Mbuti-1.DG
Mbuti:S_Mbuti-2.DG
Mbuti:S_Mbuti-3.DG
Ngumba:T_Ngumba-1.DG
Ngumba:T_Ngumba-2.DG
Tikar_South:T_Tikar_South-1.DG
Tikar_South:T_Tikar_South-2.DG

Angoliga
11-28-2019, 12:23 AM
New coordinates added:
Baka:T_Baka-1.DG
Baka:T_Baka-2.DG
Bakola:T_Bakola-1.DG
Bakola:T_Bakola-2.DG
Bantu_Kenya:S_BantuKenya-1.DG
Bantu_Kenya:S_BantuKenya-2.DG
Bedzan:T_Bedzan-1.DG
Bedzan:T_Bedzan-2.DG
Bulala:T_Bulala-1.DG
Bulala:T_Bulala-2.DG
Fulani:T_Fulani-1.DG
Fulani:T_Fulani-2.DG
Kaba:T_Kaba-1.DG
Kaba:T_Kaba-2.DG
Khomani_San:S_Khomani_San-1.DG
Khomani_San:S_Khomani_San-2.DG
Laka:T_Laka-1.DG
Laka:T_Laka-2.DG
Lemande:S_Lemande-1.DG
Lemande:S_Lemande-2.DG
Mada:T_Mada-1.DG
Mada:T_Mada-2.DG
Mbuti:A_Mbuti-5.DG
Mbuti:B_Mbuti-4.DG
Mbuti:S_Mbuti-1.DG
Mbuti:S_Mbuti-2.DG
Mbuti:S_Mbuti-3.DG
Ngumba:T_Ngumba-1.DG
Ngumba:T_Ngumba-2.DG
Tikar_South:T_Tikar_South-1.DG
Tikar_South:T_Tikar_South-2.DG

There goes my evening :)

... this should be exciting -- thank you Davidski/whatever powers might be

Rwaka
11-28-2019, 12:45 AM
New coordinates to be included: a Hima from Uganda
UG Hima_scaled,-0.451878,0.080227,-0.001886,-0.037145,0.006155,-0.015339,-0.003055,0.005538,0.058085,-0.047199,-0.010555,0.005095,-0.015163,0.001376,0.004343,-0.004773,0.00326,0.00152,-0.000754,0.008879,0.003619,-0.002968,0.000739,-0.004579,0.004191

Angoliga
11-28-2019, 02:18 AM
Both PCAs are now updated:

3D PCA: https://plot.ly/~Angoliga/3/#/ *(allow a minute to fully load)
2D PCA: https://plot.ly/~Angoliga/4/


Updated PCA:

https://i.imgur.com/9WI3Ibg.png

"Deep-Layer" runs of new samples:


Rainforest Hunter-Gatherers
https://i.imgur.com/wbN4sXI.png

Fulani + Central Sudanics:
https://i.imgur.com/GaI0vlM.png
Cameroonian + new Bantu Kenya samples + new Khomani_San
https://i.imgur.com/qMlQFYl.png
Ugandan Hima + Tutsi-related GL samples
https://i.imgur.com/4dkzALa.png



Source Samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534


*Feel free to comment with observations*

drobbah
11-28-2019, 04:18 AM
Which country is the Fulani that clusters near the Horners from?

Rwaka
11-29-2019, 07:08 AM
Which country is the Fulani that clusters near the Horners from?

It's North Cameroon; that's where the samples are from. But generally, Nomadic Fulani have more Eurasian than sedentary ones: Mbororo Fulani of Cameroon, and Wodaabe from Nuger and Northern Nigeria.

Amhas
11-29-2019, 11:27 AM
Anyone knows how to extract genomes from a study (data is available online ? There are some good new samples from North Africa (including one Toubou). And 4 Moroccans from untested regions .

https://www.cell.com/current-biology/fulltext/S0960-9822(19)31241-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com %2Fretrieve%2Fpii%2FS0960982219312412%3Fshowall%3D true

Rwaka
11-29-2019, 03:15 PM
Anyone knows how to extract genomes from a study (data is available online ? There are some good new samples from North Africa (including one Toubou). And 4 Moroccans from untested regions .

https://www.cell.com/current-biology/fulltext/S0960-9822(19)31241-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com %2Fretrieve%2Fpii%2FS0960982219312412%3Fshowall%3D true

I can ask a friend who always does this for me

Amhas
11-29-2019, 03:36 PM
That would be hella good, ask him to extract the 2 Moroccans + the 2 Moroccans berbers, they are from the rif.

Samuel7312
11-30-2019, 02:07 PM
I can ask a friend who always does this for me

By chance can you please also ask your friend if he can get the samples from this study of the Belmonte Jews https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313780/ and Malgasy https://www.genomeweb.com/genetic-research/genomic-analysis-sheds-light-diversity-malagasy-people-madagascar I know LM genetics has these samples so there avaliable somewhere on the web

afbarwaaqo
12-05-2019, 09:16 AM
PCA G25_scaled - Africans only
Users & Ancients/Modern Avgs
(09/22/2019)



https://i.imgur.com/LvXCooZ.png


Ancients = ◇
Active Users = x
Modern Samples = •





Inviting all native Africans to participate, we can update these PCAs as we get more African users and additional Ancient/Modern samples. For the few African users found who've already posted their G25 cords on the forum, I've had them plotted as "x" on the PCAs. To get added on these PCAs, either PM me or post your G25 cords on this thread.

If you don't already have G25 cords, here's how to get them (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) and how to run PCAs on your own (it's fairly simple):


How to get your G25 cords:


"send your request and autosomal genotype data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) to eurogenesblog@gmail.com and money via PayPal to the same e-mail" (current prices are $12 USD)

Here's an explanation of G25 cords along with instructions on how to run these PCAs for free (link) (http://eurogenes.blogspot.com/2019/07/getting-most-out-of-global25_12.html)

The PAST data files when running the PCAs are here (https://drive.google.com/open?id=1xpmRwKZV8hrf_R_TpGS7acxxKek3jZun); I'll update them as we get more samples








Sub-Regional PCAs


North-Africans:

https://i.imgur.com/uHaS6jn.png

Tropical-Africans:

https://i.imgur.com/tana38g.png

South-Africans:

https://i.imgur.com/0Axg90p.png


It might've been ideal to have separate threads for these sub-regions but seeing as we're a limited bunch on the forum, one central-thread might suffice. For better resolution, sub-regional PCAs can be updated concurrently as more samples are added.




*Feel free to discuss any observations*

do you have any african american or afro-caribbean samples? i was wondering where the average AA/AC would plot

Samuel7312
12-05-2019, 11:28 AM
I am a African American with possible brazillian/carribean spanish ancestry heres my scaled coordinates
,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Shmuel_scaled,-0.368787,0.081242,0.035449,0.021964,0.011694,0.013 666,-0.025616,0.017307,-0.01943,0.015308,0.000487,-0.003897,0.009217,-0.005505,0.018729,0.005834,0.01017,-0.00266,-0.001383,0.003126,0.002745,-0.00136,-0.002958,0.002169,-0.001676

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Shmuel,-0.0324,0.008,0.0094,0.0068,0.0038,0.0049,-0.0109,0.0075,-0.0095,0.0084,0.0003,-0.0026,0.0062,-0.004,0.0138,0.0044,0.0078,-0.0021,-0.0011,0.0025,0.0022,-0.0011,-0.0024,0.0018,-0.0014

sum1
12-05-2019, 06:27 PM
35159

Mota and related populations seem to have some South Eurasian like Ancestry.

Generalissimo
12-06-2019, 08:27 AM
The V PCA tool has been seriously updated...

https://vahaduo.github.io/g25views/#

NetNomad
12-06-2019, 10:50 AM
35159

Mota and related populations seem to have some South Eurasian like Ancestry.

Might just be proto-OOA affinity. Mota is the closest ancient SSA sample to all Eurasians.

Nilotes and Hadzas have less of an affinity with OOA groups.

Samuel7312
12-06-2019, 01:56 PM
Does anyone have a north Sudanese g25 sample IE -Beja or Nubian???

sum1
12-07-2019, 01:17 AM
Might just be proto-OOA affinity. Mota is the closest ancient SSA sample to all Eurasians.

Nilotes and Hadzas have less of an affinity with OOA groups.

I've done some more runs and the affinity towards South and East Eurasian populations is still the case particularly in the former. The OOA affinity seems to favour these populations over Anatolia N or Iran N even though they have substantial Basal-like admixture which Mota is the closest representative.


35199

35200

35202

35203

I'm not gonna jump to conclusions but its definitely interesting and there is the mystery of Haplogroup M and how It came back into Africa. Some more ancient DNA is needed.

Wangari
12-07-2019, 07:07 AM
As requested, here's a run with ancient/modern North-Africans along with SW-Asians:


Tutsi-related
Horner
Misc. Great-Lake



Misc. Great-Lake pops:
https://i.imgur.com/ibiIp10.png



Some of these misc. Great-lake populations have some interesting BedouinB amounts such as the Sandawe @ 6.2, the Elmolo @ 4.2 and the Kikuyu @ 8.8%.

Angoliga
12-07-2019, 07:24 PM
"AFRAM_Shmuel7312" user added:



https://i.imgur.com/vJndXqq.png

Updated PCA (All Africans + *newly added North-African Jewish modern avgs):

https://i.imgur.com/94lJ4rk.png


◇= Ancients
X= Active users
ē = Samples/Modern Avgs


3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/

Angoliga
12-07-2019, 09:01 PM
Anyone knows how to extract genomes from a study (data is available online ? There are some good new samples from North Africa (including one Toubou). And 4 Moroccans from untested regions .

https://www.cell.com/current-biology/fulltext/S0960-9822(19)31241-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com %2Fretrieve%2Fpii%2FS0960982219312412%3Fshowall%3D true

I got past the pay wall ($3.99/6hrs); files are available in this archive: https://www.ebi.ac.uk/ena/data/view/PRJEB29142

The raw genome files are quite large >30gb, we'd need someone to download and convert them into a smaller genotyped format so they can be used with G25 -- alternatively, you could request the genotyped data from the authors of the paper... this was my understanding at least from a similar request to the G25 creator (Generalissimo), perhaps he can advise?



By chance can you please also ask your friend if he can get the samples from this study of the Belmonte Jews https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313780/ and Malgasy https://www.genomeweb.com/genetic-research/genomic-analysis-sheds-light-diversity-malagasy-people-madagascar I know LM genetics has these samples so there avaliable somewhere on the web

It really sucks that we lack Madagascan data:

Unfortunately, those Malagasy samples have restricted access; they're in this archive: https://www.ebi.ac.uk/ega/studies/EGAS00001002549

From skimming through the paper (Pierron, 2017 (https://www.pnas.org/content/114/32/E6498)), it looks like they did a very through survey:



...sampling of 257 villages across Madagascar to collect DNA for analysis. They analyzed the full mitochondrial genomes of 2,691 people, Y chromosomes from 1,554 male individuals, and the genome-wide SNP data of 700 people.

Fig 1)
https://i.imgur.com/qsObkt8.png

Fig 6)
https://i.imgur.com/OvKm3c8.jpg


Regarding the Belmonte Jewish samples, maybe try asking members in the Jewish Diasporian sub-forum.

There are Sephardic Jewish G25 samples available at the moment but I'm not sure from where they're derived, if they're Iberian, some could be Belmonte Jews.

Samuel7312
12-07-2019, 09:36 PM
Thank you i will look to see what i can find

Angoliga
12-08-2019, 05:14 AM
Some of these misc. Great-lake populations have some interesting BedouinB amounts such as the Sandawe @ 6.2, the Elmolo @ 4.2 and the Kikuyu @ 8.8%.

The same was noticed (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=611775&viewfull=1#post611775) with the Tutsi-related samples:
https://i.imgur.com/zJFuECb.png
When modern SW-Asian references are removed and only neolithic SW-Asians are used (Levant_Natufian/PPNC/PPNB ...), this BedouinB affinity finds a preference with Levant_PPNC:


Misc. EA-Pops:


https://i.imgur.com/THSWIy3.png




Tutsi-Related samples:


https://i.imgur.com/xYHPGqn.png


It's *likely a relic derived from Sudanese migrations during the Pastoral Iron-Age (PIA); it would've come along with the Dinka-like affinities from PIA Southern-Nilotic speakers entering the Rift-Valley:
https://i.imgur.com/JjylZUR.png
Here's a previous post (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613126&viewfull=1#post613126) with more details/references on the plausible connection between Levant_PPNC/North-African pops and Sudanese (Southern-Nilotic) migrations into the rift-valley - let me know if you have any questions on the topic.





do you have any african american or afro-caribbean samples? i was wondering where the average AA/AC would plot

Just added (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=628832&viewfull=1#post628832) user "Samuel7312"; he's the only G25 AFRAM atm.





Does anyone have a north Sudanese g25 sample IE -Beja or Nubian???

Haven't come across any, we desperately need modern/ancient Sudanese samples to validate/dismiss degrees of genetic continuity in Horner and Central-East African pops.

Please share here if you find any : )

Amhas
12-09-2019, 06:29 PM
I got past the pay wall ($3.99/6hrs); files are available in this archive: https://www.ebi.ac.uk/ena/data/view/PRJEB29142

The raw genome files are quite large >30gb, we'd need someone to download and convert them into a smaller genotyped format so they can be used with G25 -- alternatively, you could request the genotyped data from the authors of the paper... this was my understanding at least from a similar request to the G25 creator (Generalissimo), perhaps he can advise?


I'm not familiar with this, but the good thing is that there are only few samples, only 5 are new (the moroccans and one tunisian).


Haven't come across any, we desperately need modern/ancient Sudanese samples to validate/dismiss degrees of genetic continuity in Horner and Central-East African pops.

Please share here if you find any : )


I have a Sudanese friend (with a quite high North African according to FTDNA), by some luck I will convince him to do the G25 test.

Samuel7312
12-10-2019, 03:32 PM
I'm not familiar with this, but the good thing is that there are only few samples, only 5 are new (the moroccans and one tunisian).




I have a Sudanese friend (with a quite high North African according to FTDNA), by some luck I will convince him to do the G25 test.

North Sudanese??

Amhas
12-10-2019, 05:31 PM
North Sudanese??

Yes, arabic speaking from North eastern Sudan.

drobbah
12-11-2019, 02:32 AM
The two Kenyan Iron age samples are clearly of different origins.They (IA Deloraine) are of nilotic origin while the other Kenyan Iron age group is of Cushitic/Horner origin yet both are of the same time period.I think the Tutsis might be a mixture of those populations prior to interacting with the Bantu.

Target: KEN_Pastoral_IA
Distance: 3.5832% / 0.03583181
60.6 Dinka
23.6 Levant_Natufian
14.0 ETH_4500BP
1.8 EGY_Hellenistic

Target: KEN_IA_Deloraine
Distance: 10.8395% / 0.10839518
86.8 Dinka
8.0 Levant_JOR_EBA
4.8 ETH_4500BP
0.4 Levant_PPNC

Angoliga
12-11-2019, 03:52 AM
The two Kenyan Iron age samples are clearly of different origins.They (IA Deloraine) are of nilotic origin while the other Kenyan Iron age group is of Cushitic/Horner origin yet both are of the same time period.I think the Tutsis might be a mixture of those populations prior to interacting with the Bantu.

Target: KEN_Pastoral_IA
Distance: 3.5832% / 0.03583181
60.6 Dinka
23.6 Levant_Natufian
14.0 ETH_4500BP
1.8 EGY_Hellenistic

Target: KEN_IA_Deloraine
Distance: 10.8395% / 0.10839518
86.8 Dinka
8.0 Levant_JOR_EBA
4.8 ETH_4500BP
0.4 Levant_PPNC



It's a little more complicated than that:

KEN_IA_Deloraine was already admixed with Bantu, you're missing a West-African reference along with KEN_LSA for a more appropriate variety of forager-related ancestry.


Here's a screenshot from a previous run, you can ignore the red circling, it was from a post pointing out KEN_IA_Deloraine's Levant_PPNC affinity:

https://i.imgur.com/JjylZUR.png

Angoliga
12-11-2019, 05:21 AM
"BR_Hutu? " sample added:



*The provider of these cords stated the sample was of likely Hutu origin; unable to fully confirm their background

https://i.imgur.com/McU3xoG.png

Updated PCA (All Africans):

https://i.imgur.com/TK3VKcy.png


◇= Ancients
X= Active users
ē = Samples/Modern Avgs


3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/


+ Deep-layer run:
https://i.imgur.com/pvhYGXj.png

These cords were publicly provided (https://anthrogenica.com/showthread.php?17251-Ancient-DNA-reveals-a-multistep-spread-of-the-first-herders-into-sub-Saharan-Africa&p=629651&viewfull=1#post629651):

BR_Hutu?_scaled,-0.570254,0.067025,0.008297,-0.001938,0.004924,0.002231,-0.003995,0.011999,0.003272,-0.008383,-0.001299,0.005695,-0.010704,-0.00055,-0.015336,0.011668,-0.007823,0.004434,-0.004148,0.002626,-0.003119,-0.002597,0.002342,0.000843,-0.001197
BR_Hutu?,-0.0501,0.0066,0.0022,-0.0006,0.0016,0.0008,-0.0017,0.0052,0.0016,-0.0046,-0.0008,0.0038,-0.0072,-0.0004,-0.0113,0.0088,-0.006,0.0035,-0.0033,0.0021,-0.0025,-0.0021,0.0019,0.0007,-0.001



Source Samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

Espoir
12-11-2019, 06:08 AM
"BR_Hutu? " sample added:



*The provider of these cords stated the sample was of likely Hutu origin; unable to fully confirm their background

https://i.imgur.com/McU3xoG.png

Updated PCA (All Africans):

https://i.imgur.com/TK3VKcy.png


◇= Ancients
X= Active users
• = Samples/Modern Avgs


3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/


+ Deep-layer run:
https://i.imgur.com/pvhYGXj.png

These cords were publicly provided (https://anthrogenica.com/showthread.php?17251-Ancient-DNA-reveals-a-multistep-spread-of-the-first-herders-into-sub-Saharan-Africa&p=629651&viewfull=1#post629651):

BR_Hutu?_scaled,-0.570254,0.067025,0.008297,-0.001938,0.004924,0.002231,-0.003995,0.011999,0.003272,-0.008383,-0.001299,0.005695,-0.010704,-0.00055,-0.015336,0.011668,-0.007823,0.004434,-0.004148,0.002626,-0.003119,-0.002597,0.002342,0.000843,-0.001197
BR_Hutu?,-0.0501,0.0066,0.0022,-0.0006,0.0016,0.0008,-0.0017,0.0052,0.0016,-0.0046,-0.0008,0.0038,-0.0072,-0.0004,-0.0113,0.0088,-0.006,0.0035,-0.0033,0.0021,-0.0025,-0.0021,0.0019,0.0007,-0.001



Source Samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

Isn’t it relevant to add Gambian and Mandenka to even out different West Africans admixture sources? It’s always interesting to me how it plays out.

Angoliga
12-11-2019, 06:33 AM
Isnít it relevant to add Gambian and Mandenka to even out different West Africans admixture sources? Itís always interesting to me how it plays out.

I think that would be justifiable if we were running N/W-African samples but since we've only been primarily running East-Africans, and the only primary West-African contribution in the Great-Lakes region is Bantu-related (~Niger-Delta/Cameroonian), there's no need to have much further Atlantic West-Africans added at the expense of complicating/bifurcating results for the majority of others.

I recall mentioning to you I'd do a post on West-African related ancestry, it's an add-on to this thread (https://anthrogenica.com/showthread.php?19046-Blame-it-on-the-Rain-Paleohydrologic-considerations-for-Shaping-African-Substructure&p=624361&viewfull=1#post624361), the draft is already completed. I'm just a little shy to post it since the content is very esoteric -- regardless, I'll post it tomorrow *latest

- it delves into the West-African split of West-Atlantic and more Niger-Delta-like ancestry with some 3rd party references, I think you'll find it interesting




.... **That said, don't let this stop you from posting findings here with your own runs using additional sources; West-African or not

Espoir
12-11-2019, 07:31 AM
This is what I observed. Gambian is favored for most Tutsi-related Samples. A few showing Yoruba and one Mandenka.
Captured as much as I could from a run of all Tutsi-related samples using same source population Angoliga used with addition of Mandenka and Gambian.

*Last column is Yoruba.
35258

ēSource pops

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Gambian,-0.60625,0.067787,0.01994,0.011588,0.002539,0.00589 2,-0.034664,0.038595,-0.031778,0.023736,0.006374,-0.00384,0.016446,1.7e-05,0.011808,-0.013276,0.009795,-0.000269,-0.002137,-0.00308,-0.001763,-0.002241,0.004021,0.000181,0.00217
Mandenka,-0.607246,0.063471,0.01797,0.010611,-1.5e-05,0.009078,-0.038025,0.038214,-0.030781,0.025914,0.004985,-0.000959,0.019772,-0.001129,0.015825,-0.011966,0.010685,9.5e-05,-0.002049,-0.002095,-0.001897,-0.005564,0.000801,-0.001374,0.00118

Amhas
12-11-2019, 10:36 AM
I got past the pay wall ($3.99/6hrs); files are available in this archive: https://www.ebi.ac.uk/ena/data/view/PRJEB29142

The raw genome files are quite large >30gb, we'd need someone to download and convert them into a smaller genotyped format so they can be used with G25 -- alternatively, you could request the genotyped data from the authors of the paper... this was my understanding at least from a similar request to the G25 creator (Generalissimo), perhaps he can advise?


I just got an answer from the author, he told me they haven't genotyped they just performed the complete sequence.

Angoliga
12-11-2019, 02:52 PM
This is what I observed. Gambian is favored for most Tutsi-related Samples. A few showing Yoruba and one Mandenka.
Captured as much as I could from a run of all Tutsi-related samples using same source population Angoliga used with addition of Mandenka and Gambian.

*Last column is Yoruba.
35258

•Source pops

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
Levant_Canaanite_MBA,0.0812696,0.1468454,-0.0613196,-0.0979336,-0.0105248,-0.0389334,-0.0047942,-0.0065998,0.0114534,0.0101686,0.0104904,-0.0097712,0.0215854,0.005505,-0.0075734,0.0065234,-0.0001562,-0.0011906,0.0015086,0.004252,0.0042674,0.007543,-0.0012572,0.0015906,-0.0005028
Levant_ISR_C,0.0886623,0.1666536,-0.046763,-0.135219,0.0157761,-0.0622661,-0.0120351,-0.0113436,0.0529071,0.0342603,0.0145636,-0.0154914,0.0330965,0.0045705,-0.0154936,0.0029309,-0.0032528,0.0040806,0.0034931,0.0089778,0.0023839, 0.0086492,-0.0027244,-0.0019723,-0.0039579
Levant_ISR_MLBA,0.080814,0.149283,-0.046009,-0.103683,-0.012618,-0.036256,-0.00564,-0.008769,0.00859,0.014579,0.01088,-0.007044,0.01665,0.004542,-0.012215,0.012198,0.002477,0.008742,0.006285,0.013 506,0.015348,0.013973,-0.013557,-0.001205,-0.004431
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_LBN_MA_Euro,0.1248263,0.1391273,0.0551857,0 .0273473,0.0379557,0.0087387,-0.0031333,0.006461,0.0126123,0.012453,-0.0053587,0.010191,-0.0110503,-0.011239,0.0116267,-0.0011493,-0.002955,0.0013513,0.0011733,0.0042103,0.0083187,0 .005523,-0.000616,-0.0008837,0.0018763
Levant_LBN_MA_Mixed,0.093904,0.148775,0.0052795,-0.027455,0.0238505,-0.0124105,-0.0030555,0.002769,0.008283,0.0190435,0.002923,0.0 062195,-0.0080275,-0.010666,-0.0010855,-0.0026515,0.002673,-0.0018365,-0.0022625,6.25e-05,0.0009355,-0.002102,0.005238,0.005362,0.003353
Levant_LBN_MA_NE,0.085652,0.150552,-0.0499688,-0.0856758,-0.0080785,-0.0284468,-0.0062278,-0.0122302,0.0030168,0.0139868,0.0088098,-0.0060698,0.009923,6.88e-05,-0.0090595,0.0023203,-0.0001955,-0.001869,0.004431,-0.0074722,-0.0028075,0.0007108,-0.0050838,0.0027112,0.0041315
Levant_LBN_Roman,0.0873592,0.1459822,-0.057605,-0.0873715,-0.0110788,-0.0278195,-0.007814,-0.0074422,0.0077718,0.0132578,0.0027202,-0.009704,0.012859,-0.0026492,-0.0096022,0.0102428,0.001695,-0.001172,0.0026085,0.0033142,-0.0002497,0.0044825,-0.003574,-0.0008438,-0.00479
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
Gambian,-0.60625,0.067787,0.01994,0.011588,0.002539,0.00589 2,-0.034664,0.038595,-0.031778,0.023736,0.006374,-0.00384,0.016446,1.7e-05,0.011808,-0.013276,0.009795,-0.000269,-0.002137,-0.00308,-0.001763,-0.002241,0.004021,0.000181,0.00217
Mandenka,-0.607246,0.063471,0.01797,0.010611,-1.5e-05,0.009078,-0.038025,0.038214,-0.030781,0.025914,0.004985,-0.000959,0.019772,-0.001129,0.015825,-0.011966,0.010685,9.5e-05,-0.002049,-0.002095,-0.001897,-0.005564,0.000801,-0.001374,0.00118

It's a bit deceiving, sahelian West-Africans have elevated Dinka and North-African affinities relative to Yoruba:
https://i.imgur.com/yBM8A19.png
So, since the Tutsi-related samples have ample Dinka and NA affinities, it's rendering Gambians/Mandenka as the overwhelming preference over Yoruba. It'll provide a better fit but the overall West-African ratios and canceling of Yoruba (Bantu-proxy), aren't intelligible for West-African contribution into Great-Lake pops.




I just got an answer from the author, he told me they haven't genotyped they just performed the complete sequence.

- Nice, good on you for reaching out

Did they mention if they'll eventually have them genotyped?

Alfa
12-11-2019, 04:29 PM
It's a bit deceiving, sahelian West-Africans have elevated Dinka and North-African affinities relative to Yoruba:
https://i.imgur.com/yBM8A19.png
So, since the Tutsi-related samples have ample Dinka and NA affinities, it's rendering Gambians/Mandenka as the overwhelming preference over Yoruba. It'll provide a better fit but the overall ratios and canceling of Yoruba (Bantu-proxy), aren't ineligible for West-African contribution into the Great-Lakes region.





- Nice, good on you for reaching out

Did they mention if they'll eventually have them genotyped?

Interesting. West africa source for Great Lakes pop is complicated. Same thing applies for our cushitic, dinka, great lakes huntergatherers admixtures. It is always gonna be difficult to determine the origin of our admixtures for a very mixed pop like Tutsi and Hima. Like in some runs some Tutsi have Mota, other don't. How sure are we that our Dinka is really nilotic or modern dinka, not other huntergatherers related like Mota or other usampled huntergatherers. These genetic tools could be giving us wrong us admixtures due to the fact that we have nilotic, west africa, huntergatherers. It is too early to make any conclusion.

Megalophias
12-11-2019, 05:21 PM
Yoruba seem pretty far from everyone in G25, maybe being close to a pole of variation in the PCA? Only other south Nigerians are close to Yoruba. Even Igbo, who are not far east of Yoruba geographically, are almost equidistant to Mende far to the west in Sierra Leone: Yoruba-Igbo 2.0252%, Mende-Igbo 2.2197%. Everyone else is closer to Mende, Mandenka, and Gambian than to Yoruba. East African ancestry in Bantu may have something to do with it but I don't think that's the whole story, because in ADMIXTURE graphs you commonly see Yoruba as intermediate between Mandenka and Bantu. Not sure about what formal stats say.

Mende seems to work as generic West African for G25. A mix of Igbo, Kaba, and Biaka seems to work for ancestral Bantu (though fit doesn't change much using other sources). If using ancients to model East Africans then Pemba 600BP, or do you guys find something wrong with it?

Angoliga
12-11-2019, 07:31 PM
The issue with Mende is their embedded Archaic_HG which might offset East-African HG affinities.

The Kaba are Nilo-Saharan C-S speakers; they have relatively high West-African affinities (~75%) but their elevated Dinka (~18%) would be too high for consideration.

Pemba's forager ancestry would cancel-out KEN_LSA from Great-Lake samples -- but you would provide a better fit as a Bantu proxy since a lot of the E-HG package is already included.




https://i.imgur.com/9tchtlL.png
Overall, I guess it all depends what you're trying to get out of the results:

If it's strictly a better fit that's desired, then you one could opt for modern Bantu samples and perhaps even toss in Sahelian pops as a cross-check for actual afmd West-Atlanic affinities (Mandenka/Gambians). The more western West-African affinity would be run against the same W/W-African affinity(~20%) already embedded in your Dinka reference.

Overall, I tend to favor YRI because I consider it a more conservative W-African source of Bantu, without as much HG/Dinka-like ancestry.
It allows me to tease out other affinities in a somewhat-similar way to ADMIXTURE -- when these affinities are isolated, it paints a higher-resolution of ancestral-patterns within different sample groups.

Megalophias
12-11-2019, 08:16 PM
I don't think G25 cares about the West African archaic, because it has the opposite pattern to f stats. In the f stats from "Reconstructing Prehistoric African Population Structure", it's Yoruba who are closer to everyone else than Mende are. But G25 Mende vs Yoruba distances: Mota 24.38% vs 27.01%, Dinka 20.01% vs 21.37%; Onge 70.63% vs 71.53%; Mbuti 56.99% vs 59.35%; Ju|'hoan 57.18% vs 59.88%.

I have no objection to using Yoruba at all, I am just saying I think worse fits using it are illusory, and I don't think there's some hidden East African affinity in other West Africans (or at least G25 doesn't prove that). There may well be some route of West African ancestry arriving north of the rainforest, but we don't have the samples to distinguish anything like that, more's the pity. And yeah, Kaba have East African affinity and don't remain distinct from Dinka in East African models.

PS for maximum confusion we could combine the two models in Skoglund et al and have Yoruba having more archaic ghost ancestry than Mende, but also having more East African ghost ancestry. :)

Generalissimo
12-11-2019, 09:03 PM
Yeah, the Yoruba have some recent drift that distinguishes them from other West Africans, and that's what the Global25 is picking up. It wasn't designed for measuring deep ancestry from unsampled ancient sources.

On the other hand, f-stats have a certain property that needs to be taken into account. They tend to favor populations from extremes of mixture clines. That's why, for instance, Sardinians are so sticky in f-stats analyses, and end up looking like they're the West Eurasian group most similar to the West Eurasian ancestry in Africans, usually well ahead of all Near Eastern populations.

That's why I keep saying f-stat output shouldn't be taken too literally. You always need to take into account potential confounding factors.

Angoliga
12-11-2019, 11:14 PM
Very engaging dialogue here :)


I can't speak directly to fstats but G25 actually does take the West-African Archaic into account. On both scaled and unscaled runs, archaic is being teased with these HG-proxies (KEN_LSA, Ju_hoan_north, Mbuti). KEN_LSA here shouldn't be taken as literal East-African contribution, in the context of West-African substructure for these runs, it's just an archaic proxy:



Scaled runs:
https://i.imgur.com/DGNm2GF.png



This trio of HG affinity is similar to the 3/way split of E_HG ancestry in the Skoglund paper (Mbuti/SA/Hadza-like):

https://i.imgur.com/2ESGXIU.png



There's a screenshot of more West-African runs in the previous post.


With deep-layer unscaled runs, this mirrors Mende here again as having the highest archaic affinity of West-African pops (MWI_Fingira used as a proxy):

[1] "distance%=28.0652"

Mende_Sierra_Leone

MWI_Fingira_6100BP,63.7
MWI_Fingira_2500BP,16.3
MAR_Iberomaurusian,15.2
MAR_EN,3.8
Anatolia_N_Kumtepe_low_res,0.4
RUS_Ust_Ishim,0.3
CHN_Tianyuan,0.1
Jarawa,0.1
VNM_BA_all,0.1

1] "distance%=31.1751"

Esan_Nigeria

MWI_Fingira_6100BP,67.1
MAR_Iberomaurusian,15.5
MWI_Fingira_2500BP,12.4
MAR_EN,4.1
RUS_Ust_Ishim,0.4
Anatolia_N_Kumtepe_low_res,0.4

[1] "distance%=29.943"

Igbo

MWI_Fingira_6100BP,69.5
MAR_Iberomaurusian,16
MWI_Fingira_2500BP,10.9
MAR_EN,3.3
Anatolia_N_Kumtepe_low_res,0.3

[1] "distance%=31.2193"

Yoruba

MWI_Fingira_6100BP,70.6
MAR_Iberomaurusian,15.8
MWI_Fingira_2500BP,8.5
MAR_EN,4.7
BLZ_SakiTzul_7400BP,0.2
CHL_LosRieles_5100BP,0.1
Anatolia_N_Kumtepe_low_res,0.1



[1] "distance%=28.1667"

Gambian

MWI_Fingira_6100BP,68.7
MAR_Iberomaurusian,19
MWI_Fingira_2500BP,7.3
MAR_EN,4.6
Anatolia_N_Kumtepe_low_res,0.3

[1] "distance%=28.2958"

Mandenka

MWI_Fingira_6100BP,69.6
MAR_Iberomaurusian,19.6
MWI_Fingira_2500BP,6.4
MAR_EN,4
Anatolia_N_Kumtepe_low_res,0.2
BLZ_SakiTzul_7400BP,0.1
PER_Laramate_900BP,0.1


These levels agree with other independent methods for identifying archaic ancestry from (Durvasula, 2019); more posted here (https://anthrogenica.com/showthread.php?17561-G25-nMonte-Inferring-ANA-Eurasian-layers-in-SSA-pops&p=579168&viewfull=1#post579168)



Here's a demonstration with Mende and Yoruba as a W-African proxy:

https://i.imgur.com/SK6xyX1.png
The KEN_LSA forager affinities in KEN_IA_Deloraine are nearly halved due to inflated archaic West-African in Mende. Since the same can be observed with moderns, it's worth cautioning which W-African sources are used since they can drastically effect your results.

From the samples we have available, I'm generally comfortable with Yoruba/Igbo since they're not *too far from contested proto-Bantu migrations, anything further west can get complicated with archaic affinities and further NW has too much blatant Dinka/NAfrican.

Megalophias
12-11-2019, 11:42 PM
East African hunter-gatherers shouldn't be representing West African archaic, but the other way around: they are much more closely related to the non-archaic part of West Africans, so Yoruba should be modelled as Mende + East African, not vice versa. (Unless you figure Kenya LSA actually has the archaic ghost ancestry?) To me it looks like the extra pops are cancelling out specific drift, rather than representing something real.

Chad Rohlfsen
12-12-2019, 12:01 AM
I have serious doubts about ancient West African. There are a few reasons. One: branching Mota and West Africans will necessitate something deeper to West Africa, as they are less Eurasian. Mota is not pure anything. Mota having more affinity to South Africa than West Africa is going to skew this too. Two: the Sahara was much bigger. This means SSA was likely restricted to the southern half of Africa for probably over 100K years BP. To say there was some slow split as humans spread is likely bogus. There was probably a ton of genetic sharing going on. This would all help to explain the archaic sharing in Africa, without Eurasians and also Iberomaurusian-related people.

Chad Rohlfsen
12-12-2019, 12:10 AM
Also, think back to the Altai paper. The AMH is deeper than the San. San have some Eurasian, so no biggy. But, if the San split 200K or more ago, why isn't this AMH closer to Mbuti, Yoruba, or Somali? Shouldn't there be another 100K of shared drift with Africans further north? I think African population history is stuck in something more complicated than need be. This pure branch thing needs to be drpped. Same with Eurasians.

Angoliga
12-12-2019, 02:59 AM
If these East-African_HGs are incorrect as proxies for archaic, why would the %s corroborate with analysis from independent studies?


While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations.

Admixture fractions from this paper are within range of arachaic affinities seen in G25 for W-Africans pops (Fig2. b):
https://i.imgur.com/WPVlYPV.png
Given the time-frame of introgression, it might be wrong to fixate on East/South-Africa as a secluded region for these pops of similar HG-affinities.

To reiterate, the affinities rendered from these proxies shouldn't be taken as literal i.e. minor Ju_hoan_North affinities in Mende wouldn't have to translate modern SA pops strolling deep into West-Africa neither would it for Mbuti or Hadza-like affinities. The HG splits we're seeing in West-African archaic are analogous to the MWI_HGs runs in the Skoglund paper; the trio would be an ancestral composite similar to the "HG package" seen in MWI_HGs.

Another consideration for validating these proxies, is the general lack of these HG affinities in Ancestral-East-African pops (Dinka) compared to W-Africans -- what would be a viable explanation from the data?



Unscaled deep-later runs without SSA moderns
*only 3 SSAproxies used

Dinka

MWI_Fingira_6100BP,72.5
MAR_Iberomaurusian,20.7
MAR_EN,4.5
MWI_Fingira_2500BP,2
Eskimo_Sireniki,0.1
BRA_Laranjal_6700BP,0.1
PER_Lauricocha_3500BP,0.1



[INDENT]1] "distance%=31.1751"

Esan_Nigeria

MWI_Fingira_6100BP,67.1
MAR_Iberomaurusian,15.5
MWI_Fingira_2500BP,12.4
MAR_EN,4.1
RUS_Ust_Ishim,0.4
Anatolia_N_Kumtepe_low_res,0.4



[1] "distance%=29.943"

Igbo

MWI_Fingira_6100BP,69.5
MAR_Iberomaurusian,16
MWI_Fingira_2500BP,10.9
MAR_EN,3.3
Anatolia_N_Kumtepe_low_res,0.3



[1] "distance%=28.0652"

Mende_Sierra_Leone

MWI_Fingira_6100BP,63.7
MWI_Fingira_2500BP,16.3
MAR_Iberomaurusian,15.2
MAR_EN,3.8
Anatolia_N_Kumtepe_low_res,0.4
RUS_Ust_Ishim,0.3
CHN_Tianyuan,0.1
Jarawa,0.1
VNM_BA_all,0.1



[1] "distance%=31.2193"

Yoruba

MWI_Fingira_6100BP,70.6
MAR_Iberomaurusian,15.8
MWI_Fingira_2500BP,8.5
MAR_EN,4.7
BLZ_SakiTzul_7400BP,0.2
CHL_LosRieles_5100BP,0.1
Anatolia_N_Kumtepe_low_res,0.1



[1] "distance%=28.1667"

Gambian

MWI_Fingira_6100BP,68.7
MAR_Iberomaurusian,19
MWI_Fingira_2500BP,7.3
MAR_EN,4.6
Anatolia_N_Kumtepe_low_res,0.3


-- Since the paper is provisional, I'm completely open to alternative reasoning with counter-arguments.

Angoliga
12-12-2019, 03:49 AM
"KEN_KABETE_KIKUYU" sample added:



https://i.imgur.com/3V3r4vx.png

Updated PCA (All Africans + Kikuyu Individuals below [as requested]):

https://i.imgur.com/6wUzbZa.png




KEN_KABETE_KIKUYU + Kikuyu_Ayodo individual samples

https://i.imgur.com/BEREcTS.png



◇= Ancients
X= Active users
ē = Samples/Modern Avgs


3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

2D PCA: https://plot.ly/~Angoliga/4/


+ Deep-layer run:
https://i.imgur.com/EcKXQmf.png


Source Samples:

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

Angoliga
12-12-2019, 08:38 PM
The Kabete_Kikuyu's West-African affinity (Yoruba) along with these other Kikuyu samples seems a lot lower than expected. Most of these sample's nilotic affinity (Dinka) appears to be highly elevated +20% compared to ADMIXTURE seen in past papers :

(Tishkoff, 2009), (Hollfelder, 2017)




* (orange representing W-African ancestry)
https://i.imgur.com/9loVGa7.png

https://i.imgur.com/f4UO8dP.jpg


The 4 Kikuyu samples were collected from this paper : "....We collected samples from the Masai and Kikuyu from secondary schools in Narok and Nyeri, Kenya, respectively ,(Ayodo, 2007 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950820/))"

One explanation might be, our current limited-dataset (n=5) isn't capturing the full variation of the Kikuyu population (largest ethnic group in Kenya).

*The Kit's provider made some noteworthy observations, relating findings from the paper with these G25/ADMIXTURE discrepancies.

... hoping they'll shortly post their observations to add value to the discussion

Wangari
12-13-2019, 12:12 AM
*The Kit's provider made some noteworthy observations, relating findings from the paper with these G25/ADMIXTURE discrepancies.

... hoping they'll shortly post their observations to add value to the discussion

Thanks Ben for doing this. I'll add the following observations (which we've already discussed in PM).

The KEN_KABETE_KIKUYU tester is from a region that borders Maasai territory to the west and south which may suggest a common genetic ancestry; however, the G25 results below may suggest that the Nilotic and SW Asian ancestry in Kikuyu and similar Bantu groups such as the Kamba and Meru, may have occurred prior to their arrival in their current location due to the higher Levant_PPNC, and near absence of KEN_pastoral_N which is quite prevalent in certain Maasai and horner groups.

https://i.imgur.com/66W3t3o.png

When I did my own runs and kept getting elevated "Dinka", I was rather confounded by the nilotic affinities which seem so high! I assumed I was doing it all wrong, but after reading the Ayodo article (see excerpt below) , it's evident that more research is necessary. There is obviously some aspect of Kikuyu ancestry that has been long forgotten or lost.



....We found that the Luo and Masai do not cluster genetically, despite the fact that they both speak Nilotic languages, whereas the Masai and Kikuyu are closely related (despite the fact that the Kikuyu speak a Bantu language) (fig. 1). These results show that the linguistic patterns in Kenya do not correlate with the genetic patterns, which is at odds with what has been suggested elsewhere (Tishkoff, 2009). Sampling of more populations should elucidate the relationships between genetic and linguistic groups in East Africa. Ayodo, 2007 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950820/)



http://www2.ministries-online.org/wagare/_20191210_014137.JPGAyodo, 2007 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950820/)


Some questions:

Is it possible that proto-Kikuyu went through a language-shift (similar to the Tutsi) perhaps from initially being Southern-Nilotic and then Bantu?

Does the data from Tishkoff, Hollfelder and now Ayodo suggest that the Kikuyu language was at some point used as a Lingua Franca of sorts in the region by genetically different groups (Bantu and Nilotic) similar to how Kinyarwanda is used by the farmer Hutu and Pastoralist Tutsi? If so, these proto-Kikuyu groups must have eventually lost their cultural distinctions quite a while back.

Espoir
12-13-2019, 05:41 AM
Thanks Ben for doing this. I'll add the following observations (which we've already discussed in PM).

The KEN_KABETE_KIKUYU tester is from a region that borders Maasai territory to the west and south which may suggest a common genetic ancestry; however, the G25 results below may suggest that the Nilotic and SW Asian ancestry in Kikuyu and similar Bantu groups such as the Kamba and Meru, may have occurred prior to their arrival in their current location due to the higher Levant_PPNC, and near absence of KEN_pastoral_N which is quite prevalent in certain Maasai and horner groups.

https://i.imgur.com/66W3t3o.png

When I did my own runs and kept getting elevated "Dinka", I was rather confounded by the nilotic affinities which seem so high! I assumed I was doing it all wrong, but after reading the Ayodo article (see excerpt below) , it's evident that more research is necessary. There is obviously some aspect of Kikuyu ancestry that has been long forgotten or lost.






http://www2.ministries-online.org/wagare/_20191210_014137.JPGAyodo, 2007 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950820/)


Some questions:

Is it possible that proto-Kikuyu went through a language-shift (similar to the Tutsi) perhaps from initially being Southern-Nilotic and then Bantu?

Does the data from Tishkoff, Hollfelder and now Ayodo suggest that the Kikuyu language was at some point used as a Lingua Franca of sorts in the region by genetically different groups (Bantu and Nilotic) similar to how Kinyarwanda is used by the farmer Hutu and Pastoralist Tutsi? If so, these proto-Kikuyu groups must have eventually lost their cultural distinctions quite a while back.
That chart is hard to understand. But it looks like there is a huge overlap between Masai and Kikuyu which is quite a surprise to me. I know Masai are a heterogeneous group. I don’t know if it’s those Masai that Bantu admixed or the Kikuyu that are Masai admixed or bilateral.
Do u think that on average Kikuyus can genetically cluster with these five we have here?


According to a Y-Chromosome DNA study by Wood et al. (2005), around 73% of Gĩkũyũs belong to the common paternal haplogroup E1b1a. The remainder carry other clades: 19% E1b1b with E-M293 contributing 11%, 2% A, and 2% B.

In terms of maternal lineages, Gĩkũyũs closely cluster with other Eastern Bantu groups like the Sukuma. Most belong to various Africa-centered mtDNA macro-haplogroup L lineages such as L0f, L3x, L4g and L5 per Castrž et al. (2009). According to Salas et al. (2002), other Gĩkũyũs largely carry the L1a clade, which is one of the African mtDNA Haplogroups.
From a genetic stand point, it looks like Kikuyu absorbed absorbed cushitic/Nilotic speaking groups. It can also be the other way round but very unlikely.

drobbah
12-13-2019, 08:53 PM
19% Cushitic Y-Haplogroups is a lot for a population with only minor admixture from ancient Cushitic pastoralists.How much E1b1b/T-M70 do the Tutsis have in comparison?

pgbk87
12-13-2019, 09:40 PM
19% Cushitic Y-Haplogroups is a lot for a population with only minor admixture from ancient Cushitic pastoralists.How much E1b1b/T-M70 do the Tutsis have in comparison?

This is strictly observational, but Kikuyu and Kamba seem to be at least 50% Cushitic and Nilotic (combined) just based on my visit to Kenya. Kenya is highly Cushitic and Nilotic admixed. If 33% of Kenyans speak non-Bantu languages, I'd guess at least 50% of the genepool is non-Bantu.

Espoir
12-13-2019, 11:48 PM
19% Cushitic Y-Haplogroups is a lot for a population with only minor admixture from ancient Cushitic pastoralists.How much E1b1b/T-M70 do the Tutsis have in comparison?

Here you go. No T-M70 btw

35299

No:60
Male: 48

drobbah
12-14-2019, 01:35 AM
This is strictly observational, but Kikuyu and Kamba seem to be at least 50% Cushitic and Nilotic (combined) just based on my visit to Kenya. Kenya is highly Cushitic and Nilotic admixed. If 33% of Kenyans speak non-Bantu languages, I'd guess at least 50% of the genepool is non-Bantu.
The Kikuyu are essentially half Maasai? The Maasai from what I recall are about 50% Cushitic

pgbk87
12-14-2019, 02:20 AM
The Kikuyu are essentially half Maasai? The Maasai from what I recall are about 50% Cushitic
I don't think that that is quite the case. I think a lot of formerly Cushitic and Nilotic groups were assimilated and/or shifted languages over that past 2,000 years throughout Kenya. Most groups in Kenya are really a mix of Bantu, Cushitic and Nilotic (of course to varying degrees) regardless of linguistic affiliation.

Wangari
12-14-2019, 03:34 AM
That chart is hard to understand. But it looks like there is a huge overlap between Masai and Kikuyu which is quite a surprise to me. I know Masai are a heterogeneous group. I don’t know if it’s those Masai that Bantu admixed or the Kikuyu that are Masai admixed or bilateral.
Do u think that on average Kikuyus can genetically cluster with these five we have here?


I wondered the same. It would be interesting to see the G25 results of the Maasai samples used by Ayodo.


The Kikuyu are essentially half Maasai? The Maasai from what I recall are about 50% Cushitic

I initially thought that but the few Kikuyu samples we have seen so far show very little to no KEN_pastoral_N which is quite prevalent in Maasai. Some of the G25 runs I did showed a strong Sengwer affinity. I wonder why?

35312

35313

What I'd like to see is an in-depth genetic analysis of Kikuyu from various regions in order to determine why Ayodo et al doesn't agree with Tishkoff et al. Does the discrepancy point to the possibility that some Kikuyu descended from a predominantly nilo-hamitic group that eventually adopted and absorbed their Bantu neighbor's culture, language and genetics?




+ Deep-layer run:
https://i.imgur.com/EcKXQmf.png





19% Cushitic Y-Haplogroups is a lot for a population with only minor admixture from ancient Cushitic pastoralists.How much E1b1b/T-M70 do the Tutsis have in comparison?

It would be interesting to find out the haplogroups of the 37 Kikuyu sampled in the Ayodo study seeing that they essentially overlap the Maasai samples.

Angoliga
12-14-2019, 04:50 AM
Some questions:

Is it possible that proto-Kikuyu went through a language-shift (similar to the Tutsi) perhaps from initially being Southern-Nilotic and then Bantu?

Does the data from Tishkoff, Hollfelder and now Ayodo suggest that the Kikuyu language was at some point used as a Lingua Franca of sorts in the region by genetically different groups (Bantu and Nilotic) similar to how Kinyarwanda is used by the farmer Hutu and Pastoralist Tutsi? If so, these proto-Kikuyu groups must have eventually lost their cultural distinctions quite a while back.

Based on the data we're seeing so far, that would definitely seem plausible alongside these descriptions of ancient interaction in the Rift-Valley:


"....Recent commentaries have highlighted the importance of subsistence mosaics during the agricultural transition, broadly defined as landscapes of interaction between co-existing peoples with diverse (and often overlapping) ethnic, linguistic, political, economic and social backgrounds (Moore, 1985, Kusimba, 2003, Stahl, 2004, Kusimba and Kusimba, 2005, Kusimba et al., 2005, Shipton et al., 2013). Thus, rather than chronologically bounded cultural groups replacing one another in progression, as implicit in the traditional Bantu migration model, evidence suggests that there existed an ethnically and economically diverse frontier in which groups interacted at different spatial and temporal scales in relationships involving competition, conflict, exchange, symbiosis and/or assimilation. Certainly, eastern Africa's wide environmental diversity would have promoted the co-existence of different subsistence groups (Lane, 2004, Shipton et al., 2013). (Crowther, 2017 (https://www.sciencedirect.com/science/article/pii/S1040618216302890#fig1))"

East-African anthropology appears very complicated but we're desperately trying to force rigid models in an attempt to systematically correlate linguistic groups (Bantu/Nilotic/Cushitic) with ancestry (Y-DNA,mtDNA,ADMIXTURE..) -- it's this overlap and co-existence of different groups that's mainly causing confusion.


Here's a comparison with G25/PCA/ADMIXTURE:

(Masai,Kikuyu,Luo)


PCA:

https://i.imgur.com/BOBIwwK.png



G25 run
https://i.imgur.com/A5suu7u.png

Target, Source Samples (Scaled):

Target:
Masai:NA21400,-0.437081,0.076165,-0.014708,-0.040052,-0.002154,-0.024263,-0.00658,0.004384,0.101035,-0.090936,-0.018675,0.000599,-0.022002,-0.006606,0.013436,-0.012861,0.033248,-0.003167,0.015335,-0.017258,-0.007986,0.003091,-0.003944,-0.00012,0.003952
Masai:NA21425,-0.425698,0.07718,-0.012445,-0.04199,0.001231,-0.019522,-0.005405,0.008769,0.121692,-0.113898,-0.020136,0.001948,-0.03107,0.005367,0.024158,-0.036064,0.029206,-0.004307,0.036327,-0.03214,-0.004118,-0.000989,-0.008381,-0.001687,0.006466
Masai:NA21487,-0.451878,0.078196,-0.012068,-0.033269,-0.004616,-0.019522,-0.00235,0.002308,0.091422,-0.087473,-0.012342,0.008992,-0.029137,-0.003853,0.002579,-0.015911,0.020601,-0.007095,0.007165,-0.012256,-0.001622,0.003339,0.000986,-0.000602,0.002754
Masai:NA21514,-0.402934,0.07718,-0.013576,-0.027455,-0.005232,-0.020917,-0.00517,0.003923,0.100012,-0.0913,-0.018512,0.008992,-0.023934,0.001514,0.013436,-0.026253,0.022426,-0.00114,0.025768,-0.027763,-0.002496,-0.001607,-0.005546,-0.000843,0.003353
Masai:NA21581,-0.440495,0.073118,-0.009051,-0.038114,-0.00954,-0.024821,-0.00329,0.002077,0.106352,-0.089842,-0.016888,0.012439,-0.037611,-0.006744,0.010315,-0.016441,0.028163,-0.009122,0.022374,-0.020635,-0.00025,-0.002349,0.000863,-0.003735,0.005628
Masai:NA21648,-0.438219,0.073118,-0.010936,-0.04522,-0.005847,-0.019243,-0.015511,0.005538,0.099603,-0.09294,-0.014615,0.001049,-0.029286,-0.001927,0.018051,-0.016441,0.02725,-0.001774,0.015587,-0.024387,0.001123,-0.004699,-0.011585,-0.011447,0.002874
Masai:Ayodo_101M,-0.457569,0.075149,-0.013576,-0.028424,-0.005232,-0.010598,-0.00893,0.000462,0.086923,-0.080366,-0.020299,0.006744,-0.019029,0.001514,0.008007,-0.012463,0.009518,-0.005574,0.017598,-0.010005,0.004742,-0.001855,-0.005423,-0.003856,0.005389
Masai:Ayodo_103M,-0.458707,0.079211,-0.004525,-0.031977,-0.007078,-0.010319,-0.005405,0.006,0.076492,-0.073077,-0.013316,0.005845,-0.012933,0.001239,0.005022,-0.008884,0.012908,-0.012922,0.007416,-0.014882,0.001248,0.004081,-0.00986,-0.004458,0.00946
Kikuyu:Ayodo_47K,-0.506513,0.07718,-0.002263,-0.019057,-0.000615,-0.010877,-0.014101,0.013615,0.044995,-0.045923,-0.004222,-0.002548,-0.02661,-0.000275,-0.000814,0.00358,0.008475,0.011655,0.008799,-0.003627,0.006863,0.001855,0.007148,0.003735,0.001 197
Kikuyu:Ayodo_61K,-0.487163,0.071087,0.001886,-0.0323,-0.008309,-0.01255,-0.01034,0.011076,0.05604,-0.048839,-0.004872,0.004346,-0.015163,-0.001514,0.000136,-0.006497,0.008605,0.006081,0.003897,-0.008254,0.006863,0.003215,0.002342,-0.001325,0.001197
Kikuyu:Ayodo_67K,-0.512204,0.076165,0.000754,-0.020026,0.001539,-0.003904,-0.017861,0.015461,0.052563,-0.04647,-0.011205,0.001649,-0.012339,-0.003028,-0.003122,-0.00305,-0.000522,0.005448,-0.001634,0.002126,0.006738,-0.000866,0.007272,-0.002169,-0.005508
Kikuyu:Ayodo_83K,-0.483748,0.078196,-0.005657,-0.025194,-0.002462,-0.016455,-0.004465,0.011999,0.044791,-0.037905,-0.002436,0.002248,-0.015015,0.001927,0.001493,0,0.003129,-0.002787,-0.001257,-0.003752,-0.006364,0.004946,-0.001109,-0.006025,-0.003592
Luo:Ayodo_412C,-0.604401,0.060932,0.013576,0.010982,-0.006155,0.00251,-0.00987,0.012692,0.002659,-0.020046,-0.007632,0.015436,-0.032111,-0.002064,-0.028094,0.016309,-0.019427,-0.000507,-0.006159,0,-0.000998,0.004822,0.005423,-0.001928,-0.002275
Luo:Ayodo_423C,-0.597571,0.062963,0.022627,0.010982,-0.005539,0.008088,-0.00987,0.014538,-0.001636,-0.034625,-0.00682,0.01094,-0.023934,0.00812,-0.021037,0.010872,-0.019036,-0.005448,-0.007165,0.001126,0.002371,0.002597,-0.001356,-0.009881,-0.003712
Luo:Ayodo_430C,-0.602124,0.057885,0.014708,-0.001938,0.001231,0.008367,-0.00658,0.021461,0.016771,-0.037905,-0.005034,0.009142,-0.02884,-0.003441,-0.019408,0.018032,-0.009257,-0.002407,-0.012067,-0.003126,0.005865,-0.006677,0.008011,0.009399,-0.001557
Luo:Ayodo_438C,-0.593018,0.069056,0.013953,0.007106,-0.001539,0.01004,-0.011281,0.016153,0.013908,-0.032985,-0.01429,0.019183,-0.029286,-0.00289,-0.022937,0.007955,-0.012778,-0.003801,-0.004651,0.001876,-0.000374,0.002844,-0.001972,0.005302,-0.007544
Luo:Ayodo_458C,-0.610092,0.063978,0.018479,0.004522,-0.005232,0.009482,-0.014101,0.009692,0.007976,-0.019681,-0.01023,0.008093,-0.031367,-0.002064,-0.024837,0.019888,-0.019166,-0.00152,-0.007919,0.000625,-0.000749,0.001731,0.002958,0.008435,-0.000359
Luo:Ayodo_460C,-0.59871,0.067025,0.017725,0.010659,-0.001539,0.012271,-0.013631,0.011769,0.005931,-0.019864,-0.007795,0.013938,-0.033746,-0.004129,-0.023344,0.016574,-0.021383,-0.010388,-0.008045,0.005253,0.006114,-0.001237,0.001972,0.007832,-0.002634
Luo:Ayodo_502C,-0.607815,0.060932,0.010936,0.001615,-0.004308,0.006972,-0.015041,0.016384,0.011862,-0.029522,-0.006658,0.017235,-0.033003,0.002752,-0.021172,0.012861,-0.01343,0.002914,-0.000251,-0.005378,0.002745,0.000989,0.000123,-0.005422,-0.001557
Luo:Ayodo_604C,-0.597571,0.066009,0.021873,0.007429,0.000308,0,-0.014336,0.020307,0.008385,-0.020593,-0.003573,0.003747,-0.031813,0.010459,-0.024837,0.012198,-0.017211,-0.00038,-0.006662,0.008129,-0.00262,-0.000371,0.006286,-0.000241,0.00455

Source Samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534




K14 ADMIXTURE:

- KEN_LSA affinities are only detected in K14/K9 runs

https://i.imgur.com/fziPTiy.jpg

Observations:


Masai appear mostly a split of Cushitic and Nilotic pops (KEN_Pastoral_N, Dinka respectively).
Interestingly, only the samples from the Ayodo paper have Bantu affinities (Yoruba), these samples were taken from Narok, a town west of Nairobi. The rest were taken from further south of the Rift-Valley in Kinyawa, bordering Tanzania.
Kikuyu appear mostly Nilotic and Bantu, with a more steady affinity for Levant_PPNC and Levant_Natufian.
The Eurasian in Masai is mostly derived from a Cushtic source (KEN_PN) whereas in Kikuyu, it's mostly gravitating towards (Levant_PPNC/Natufian).
ADMIXTURE for E-African forager ancestry (KEN_LSA ) is being captured but only at K14/K9; several runs show it as simply West-African.


Conclusions:


Similar to what we're seeing with Tutsi-related samples, the rejection of Cushitic KEN_PN for Levant_PPNC/Natufian in Kikuyu is likely a proxy for North-Sudanese ancestry which would date from *at least the Iron-Age and prior periods; this would reflect the influx of Pastoral-Iron Age "Sudanese" ancestry cited in the Prendergast paper.
Eurasian affinities in the Masai and Kikuyu cause them to overlap on the PCA but it's for different reasons; Masai appear to be a clearer inter-mixture of Erythraeic-related groups (HOAs) + Nilotic (Dinka-like), whereas the Kikuyu appear mostly derived from the PIA-Sudanese groups (Southern-Nilotic speakers [demonstrated here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613126&viewfull=1#post613126)] ) who've mostly intermixed with Bantu pops.
Results from ADMIXTURE can drastically vary depending on the preferred run, some degree of discretion should always be used.


Here's a few points that might be causing us confusion:


Limited awareness for the existence/population history of Southern-Nilotic speakers
Over-focus on Luo and Masai-related migrations which did not have as far reaching an impact on E-African pop history
Lack of G25 samples from Northern-Sudan to validate S-N speakers with Levant_PPNC/Levant_Natufian affinities
Lack of understanding for the fluid overlap and coexistence of E-African pops as a mosaic throughout the Pastoral-Neolithic (i.e. forcing rigid correlation models with genetic data[Y-DNA, mtDNA, ADMIXTURE...])
Assuming all non-negligible Eurasian affinities in East-African pops are derived from Erythraeic-speakers


*Playing devil's advocate here, this is a valid call-out for skepticism on the whole "S-Nilotic hypothesis": If there's a connection between S-Nilotic speakers and North-Sudan, why aren't we seeing a trace of Levant_PPNC/Natufian in S.Sudanese pops?








Side by side: Here's another deep-layer run of Tutsi-Related & Horner (Erythraeic Speakers) samples

What are your observations?



https://i.imgur.com/Z34gkJ6.png


Source Samples:

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

drobbah
12-14-2019, 04:58 AM
I don't think that that is quite the case. I think a lot of formerly Cushitic and Nilotic groups were assimilated and/or shifted languages over that past 2,000 years throughout Kenya. Most groups in Kenya are really a mix of Bantu, Cushitic and Nilotic (of course to varying degrees) regardless of linguistic affiliation.

I think the cushitic/Eurasian ancestry found in countries south of the Horn are probably from nilotic-speaking populations who had significantly intermingled with
South Cushitic speakers.I don't think there was a cushitic speaking population that was absorbed by the Kikuyu or other Bantu groups.

Espoir
12-14-2019, 05:42 AM
Based on the data we're seeing so far, that would definitely seem plausible alongside these descriptions of ancient interaction in the Rift-Valley:



East-African anthropology appears very complicated but we're desperately trying to force rigid models in an attempt to systematically correlate linguistic groups (Bantu/Nilotic/Cushitic) with ancestry (Y-DNA,mtDNA,ADMIXTURE..) -- it's this overlap and co-existence of different groups that's mainly causing confusion.


Here's a comparison with G25/PCA/ADMIXTURE:

(Masai,Kikuyu,Luo)


PCA:

https://i.imgur.com/BOBIwwK.png



G25 run
https://i.imgur.com/A5suu7u.png

Target, Source Samples (Scaled):

Target:
Masai:NA21400,-0.437081,0.076165,-0.014708,-0.040052,-0.002154,-0.024263,-0.00658,0.004384,0.101035,-0.090936,-0.018675,0.000599,-0.022002,-0.006606,0.013436,-0.012861,0.033248,-0.003167,0.015335,-0.017258,-0.007986,0.003091,-0.003944,-0.00012,0.003952
Masai:NA21425,-0.425698,0.07718,-0.012445,-0.04199,0.001231,-0.019522,-0.005405,0.008769,0.121692,-0.113898,-0.020136,0.001948,-0.03107,0.005367,0.024158,-0.036064,0.029206,-0.004307,0.036327,-0.03214,-0.004118,-0.000989,-0.008381,-0.001687,0.006466
Masai:NA21487,-0.451878,0.078196,-0.012068,-0.033269,-0.004616,-0.019522,-0.00235,0.002308,0.091422,-0.087473,-0.012342,0.008992,-0.029137,-0.003853,0.002579,-0.015911,0.020601,-0.007095,0.007165,-0.012256,-0.001622,0.003339,0.000986,-0.000602,0.002754
Masai:NA21514,-0.402934,0.07718,-0.013576,-0.027455,-0.005232,-0.020917,-0.00517,0.003923,0.100012,-0.0913,-0.018512,0.008992,-0.023934,0.001514,0.013436,-0.026253,0.022426,-0.00114,0.025768,-0.027763,-0.002496,-0.001607,-0.005546,-0.000843,0.003353
Masai:NA21581,-0.440495,0.073118,-0.009051,-0.038114,-0.00954,-0.024821,-0.00329,0.002077,0.106352,-0.089842,-0.016888,0.012439,-0.037611,-0.006744,0.010315,-0.016441,0.028163,-0.009122,0.022374,-0.020635,-0.00025,-0.002349,0.000863,-0.003735,0.005628
Masai:NA21648,-0.438219,0.073118,-0.010936,-0.04522,-0.005847,-0.019243,-0.015511,0.005538,0.099603,-0.09294,-0.014615,0.001049,-0.029286,-0.001927,0.018051,-0.016441,0.02725,-0.001774,0.015587,-0.024387,0.001123,-0.004699,-0.011585,-0.011447,0.002874
Masai:Ayodo_101M,-0.457569,0.075149,-0.013576,-0.028424,-0.005232,-0.010598,-0.00893,0.000462,0.086923,-0.080366,-0.020299,0.006744,-0.019029,0.001514,0.008007,-0.012463,0.009518,-0.005574,0.017598,-0.010005,0.004742,-0.001855,-0.005423,-0.003856,0.005389
Masai:Ayodo_103M,-0.458707,0.079211,-0.004525,-0.031977,-0.007078,-0.010319,-0.005405,0.006,0.076492,-0.073077,-0.013316,0.005845,-0.012933,0.001239,0.005022,-0.008884,0.012908,-0.012922,0.007416,-0.014882,0.001248,0.004081,-0.00986,-0.004458,0.00946
Kikuyu:Ayodo_47K,-0.506513,0.07718,-0.002263,-0.019057,-0.000615,-0.010877,-0.014101,0.013615,0.044995,-0.045923,-0.004222,-0.002548,-0.02661,-0.000275,-0.000814,0.00358,0.008475,0.011655,0.008799,-0.003627,0.006863,0.001855,0.007148,0.003735,0.001 197
Kikuyu:Ayodo_61K,-0.487163,0.071087,0.001886,-0.0323,-0.008309,-0.01255,-0.01034,0.011076,0.05604,-0.048839,-0.004872,0.004346,-0.015163,-0.001514,0.000136,-0.006497,0.008605,0.006081,0.003897,-0.008254,0.006863,0.003215,0.002342,-0.001325,0.001197
Kikuyu:Ayodo_67K,-0.512204,0.076165,0.000754,-0.020026,0.001539,-0.003904,-0.017861,0.015461,0.052563,-0.04647,-0.011205,0.001649,-0.012339,-0.003028,-0.003122,-0.00305,-0.000522,0.005448,-0.001634,0.002126,0.006738,-0.000866,0.007272,-0.002169,-0.005508
Kikuyu:Ayodo_83K,-0.483748,0.078196,-0.005657,-0.025194,-0.002462,-0.016455,-0.004465,0.011999,0.044791,-0.037905,-0.002436,0.002248,-0.015015,0.001927,0.001493,0,0.003129,-0.002787,-0.001257,-0.003752,-0.006364,0.004946,-0.001109,-0.006025,-0.003592
Luo:Ayodo_412C,-0.604401,0.060932,0.013576,0.010982,-0.006155,0.00251,-0.00987,0.012692,0.002659,-0.020046,-0.007632,0.015436,-0.032111,-0.002064,-0.028094,0.016309,-0.019427,-0.000507,-0.006159,0,-0.000998,0.004822,0.005423,-0.001928,-0.002275
Luo:Ayodo_423C,-0.597571,0.062963,0.022627,0.010982,-0.005539,0.008088,-0.00987,0.014538,-0.001636,-0.034625,-0.00682,0.01094,-0.023934,0.00812,-0.021037,0.010872,-0.019036,-0.005448,-0.007165,0.001126,0.002371,0.002597,-0.001356,-0.009881,-0.003712
Luo:Ayodo_430C,-0.602124,0.057885,0.014708,-0.001938,0.001231,0.008367,-0.00658,0.021461,0.016771,-0.037905,-0.005034,0.009142,-0.02884,-0.003441,-0.019408,0.018032,-0.009257,-0.002407,-0.012067,-0.003126,0.005865,-0.006677,0.008011,0.009399,-0.001557
Luo:Ayodo_438C,-0.593018,0.069056,0.013953,0.007106,-0.001539,0.01004,-0.011281,0.016153,0.013908,-0.032985,-0.01429,0.019183,-0.029286,-0.00289,-0.022937,0.007955,-0.012778,-0.003801,-0.004651,0.001876,-0.000374,0.002844,-0.001972,0.005302,-0.007544
Luo:Ayodo_458C,-0.610092,0.063978,0.018479,0.004522,-0.005232,0.009482,-0.014101,0.009692,0.007976,-0.019681,-0.01023,0.008093,-0.031367,-0.002064,-0.024837,0.019888,-0.019166,-0.00152,-0.007919,0.000625,-0.000749,0.001731,0.002958,0.008435,-0.000359
Luo:Ayodo_460C,-0.59871,0.067025,0.017725,0.010659,-0.001539,0.012271,-0.013631,0.011769,0.005931,-0.019864,-0.007795,0.013938,-0.033746,-0.004129,-0.023344,0.016574,-0.021383,-0.010388,-0.008045,0.005253,0.006114,-0.001237,0.001972,0.007832,-0.002634
Luo:Ayodo_502C,-0.607815,0.060932,0.010936,0.001615,-0.004308,0.006972,-0.015041,0.016384,0.011862,-0.029522,-0.006658,0.017235,-0.033003,0.002752,-0.021172,0.012861,-0.01343,0.002914,-0.000251,-0.005378,0.002745,0.000989,0.000123,-0.005422,-0.001557
Luo:Ayodo_604C,-0.597571,0.066009,0.021873,0.007429,0.000308,0,-0.014336,0.020307,0.008385,-0.020593,-0.003573,0.003747,-0.031813,0.010459,-0.024837,0.012198,-0.017211,-0.00038,-0.006662,0.008129,-0.00262,-0.000371,0.006286,-0.000241,0.00455

Source Samples:
KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534




K14 ADMIXTURE:

- KEN_LSA affinities are only detected in K14/K9 runs

https://i.imgur.com/fziPTiy.jpg

Observations:


Masai appear mostly a split of Cushitic and Nilotic pops (KEN_Pastoral_N, Dinka respectively).
Interestingly, only the samples from the Ayodo paper have Bantu affinities (Yoruba), these samples were taken from Narok, a town west of Nairobi. The rest were taken from further south of the Rift-Valley in Kinyawa, bordering Tanzania.
Kikuyu appear mostly Nilotic and Bantu, with a more steady affinity for Levant_PPNC and Levant_Natufian.
The Eurasian in Masai is mostly derived from a Cushtic source (KEN_PN) whereas in Kikuyu, it's mostly gravitating towards (Levant_PPNC/Natufian).
ADMIXTURE for E-African forager ancestry (KEN_LSA ) is being captured but only at K14/K9; several runs show it as simply West-African.


Conclusions:


Similar to what we're seeing with Tutsi-related samples, the rejection of Cushitic KEN_PN for Levant_PPNC/Natufian in Kikuyu is likely a proxy for North-Sudanese ancestry which would date from *at least the Iron-Age and prior periods; this would reflect the influx of Pastoral-Iron Age "Sudanese" ancestry cited in the Prendergast paper.
Eurasian affinities in the Masai and Kikuyu cause them to overlap on the PCA but it's for different reasons; Masai appear to be a clearer inter-mixture of Erythraeic-related groups (HOAs) + Nilotic (Dinka-like), whereas the Kikuyu appear mostly derived from the PIA-Sudanese groups (Southern-Nilotic speakers [demonstrated here (https://anthrogenica.com/showthread.php?18428-PCA-G25_scaled-Africans-only-(Users-amp-Ancients-Modern-Avgs)&p=613126&viewfull=1#post613126)] ) who've mostly intermixed with Bantu pops.
Results from ADMIXTURE can drastically vary depending on the preferred run, some degree of discretion should always be used.


Here's a few points that might be causing us confusion:


Limited awareness for the existence/population history of Southern-Nilotic speakers
Over-focus on Luo and Masai-related migrations which did not have as far reaching an impact on E-African pop history
Lack of G25 samples from Northern-Sudan to validate S-N speakers with Levant_PPNC/Levant_Natufian affinities
Lack of understanding for the fluid overlap and coexistence of E-African pops as a mosaic throughout the Pastoral-Neolithic (i.e. forcing rigid correlation models with genetic data[Y-DNA, mtDNA, ADMIXTURE...])
Assuming all non-negligible Eurasian affinities in East-African pops are derived from Erythraeic-speakers


*Playing devil's advocate here, this is a valid call-out for skepticism on the whole "S-Nilotic hypothesis": If there's a connection between S-Nilotic speakers and North-Sudan, why aren't we seeing a trace of Levant_PPNC/Natufian in S.Sudanese pops?








Side by side: Here's another deep-layer run of Tutsi-Related & Horner (Erythraeic Speakers) samples

What are your observations?



https://i.imgur.com/Z34gkJ6.png


Source Samples:

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534


Iím getting more and more convinced by your theory bro. The only thing Iím skeptical about is the tools we are using.

Anyway, going ahead and take this as we see it, there is a clear pattern observable here, levant PPNC is detected in populations that are along the the route followed by S. Nilotic migration.
Thatís why itís very reasonable to attribute it to them.

Another thing you mentioned before, 23andMe is giving Tutsis high Sudanese that is above or less than 50%. Individuals reaching 65%, lowest Iíve seen being 30% and a little elevated than average Ethiopia/Eritrea(33%). The rest score little Ethio. Rejection of Ethiopia/Eritrea and Somali for Sudan; rejection of KEN_PN for Levant PPNC; tells us something.
this alongside Vahaduo and nMonte results can back this theory that populations showing significant PPNC have affinities to North Sudan.

Espoir
12-14-2019, 07:11 AM
These Kikuyu seem over half Masai, which is a surprise to me.

"sample": "Custom:KikuyuAyodo_47K",
"fit": 3.3999,
"Masai": 53.33,
"Bantu_Kenya": 46.67,

"sample": "Custom:KikuyuAyodo_61K",
"fit": 3.1357,
"Masai": 73.33,
"Bantu_Kenya": 26,6

"sample": "Custom:KikuyuAyodo_67K",
"fit": 3.2521,
"Masai": 60,
"Bantu_Kenya": 40,

"sample": "Custom:KikuyuAyodo_83K",
"fit": 3.9016,
"Masai": 72.5,
"Bantu_Kenya": 27.5,

Makes sense why the cluster closer to Masai.
As small as the sample is, we still see heterogeneity among Kikuyu.

Wangari
12-14-2019, 07:19 AM
Results from ADMIXTURE can drastically vary depending on the preferred run, some degree of discretion should always be used.
(NOT) all non-negligible Eurasian affinities in East-African pops are derived from Erythraeic-speakers
If there's a connection between S-Nilotic speakers and North-Sudan, why aren't we seeing a trace of Levant_PPNC/Natufian in S.Sudanese pops?



These points/observations are noteworthy.

Chad Rohlfsen
12-14-2019, 08:38 AM
35321

Chad Rohlfsen
12-14-2019, 08:40 AM
You won't see the relationship with the Dinka in heavily Natufian pops. It is more the Levant ChL and Iran ChL where you get significant stats, along with the Iberomaurusians.

Generalissimo
12-14-2019, 08:44 AM
35321

That's a very complex tree, with a lot of admix edges, and the Z score is still >3.

Chad Rohlfsen
12-14-2019, 01:39 PM
That's a very complex tree, with a lot of admix edges, and the Z score is still >3.

It's a lot less edges than if I used Chalcolithic West Asians. The Z being a little over 3 is not a big deal at all. The model works.

Generalissimo
12-14-2019, 01:41 PM
It's a lot less edges than if I used Chalcolithic West Asians. The Z being a little over 3 is not a big deal at all. The model works.

How many Z scores over/below 2?

Chad Rohlfsen
12-14-2019, 02:40 PM
The terminal makes it hard to count them without scrolling past, but I'd say there's around 30 sitting by 2. I've had my threshold at 2 for a couple years or more. I could remove Sunghir and drop some of the complexity and Z-score. I could add Iran ChL and Levant ChL and have an extra edge or two to Mota and Mende, but I'm just going for simple here. Having the archaics makes up about half of the admixture edges. It simplifies after that.

Generalissimo
12-14-2019, 02:45 PM
The terminal makes it hard to count them without scrolling past, but I'd say there's around 30 sitting by 2.

Well that's not really a model that works.

Chad Rohlfsen
12-14-2019, 02:50 PM
It actually is. If I had a final Z around 5 or 6, that's a different story.

Generalissimo
12-14-2019, 02:53 PM
It actually is. If I had a final Z around 5 or 6, that's a different story.

Models that work don't have more than a few Zs over/below 2. Any more than a handful and clearly the model doesn't reflect reality in some fundamental ways.

Chad Rohlfsen
12-14-2019, 03:14 PM
Mix archaics, African, and Eurasians will give some extra Z's than not using them. Pretty much every Z involved an archaic in the mix. The model is fine. Trust me.

Generalissimo
12-14-2019, 03:23 PM
Mix archaics, African, and Eurasians will give some extra Z's than not using them. Pretty much every Z involved an archaic in the mix. The model is fine. Trust me.

The model's too complex to prove anything IMHO.

And with over 20 Z scores below/over 2? Come on.

Chad Rohlfsen
12-14-2019, 04:56 PM
Already talked to Nick about it. Since they almost all include archaics, it's likely them not being a perfect representative of that group that admixed into them. It's. Fine.

Chad Rohlfsen
12-14-2019, 08:30 PM
Based on the Dstats and several graphs I have looked at, it appears the North African part of Iberomaurusians makes up a sizeable chunk of the ancestry of modern Africans. I think the Anatolian or Dzudzuana stuff entered Iberomaurusians after this event. There may be minor actual Iberomaurusian admixture in West Africans, but I am trying to flesh that out. I think that part of the reason the paper on Eurasian admixture in Ethiopians had the source like MInoans rather than Levant ChL is not accounting for the deep stuff in Iberomaurusians that does not contain Sub-Saharan admixture being taken as an actual African component rather than an early split before OoA. If you add a little North African into that supposed Minoan-like cluster, you then get to Levant_ChL.

Espoir
12-14-2019, 09:55 PM
Based on the Dstats and several graphs I have looked at, it appears the North African part of Iberomaurusians makes up a sizeable chunk of the ancestry of modern Africans. I think the Anatolian or Dzudzuana stuff entered Iberomaurusians after this event. There may be minor actual Iberomaurusian admixture in West Africans, but I am trying to flesh that out. I think that part of the reason the paper on Eurasian admixture in Ethiopians had the source like MInoans rather than Levant ChL is not accounting for the deep stuff in Iberomaurusians that does not contain Sub-Saharan admixture being taken as an actual African component rather than an early split before OoA. If you add a little North African into that supposed Minoan-like cluster, you then get to Levant_ChL.
At what percentage did that North African ancestry contribute into various African populations?
And are we talking about all or some African populations?

Espoir
12-14-2019, 10:54 PM
Repost

Generalissimo
12-15-2019, 12:12 AM
Already talked to Nick about it. Since they almost all include archaics, it's likely them not being a perfect representative of that group that admixed into them. It's. Fine.

Well it depends what Nick means by "fine".

If he means that it's fine for a exploratory, highly speculative effort as we wait for more relevant samples, then yeah, it's fine.

But please don't make out like this shows some kind of truth. It's nowhere near that.

Chad Rohlfsen
12-15-2019, 12:42 AM
Nowhere near that? I have a lot of graphs that I've done and have more coming showing this North African ancestry is spread around. It agrees completely with Dstats. The archaic in South Africans that is said to be less in others Africa is represented successfully in that graph. I was showing that a single pop could be responsible for spreading this around. Everything that is done is speculative without the samples. Where did I say this is a fact and can't change? So, you please don't make this out to be something it's not.

sum1
12-15-2019, 12:49 AM
Do you have any graphs relating to Nilotic populations like Dinka or Mursi?

Do they also carry this North African Ancestry ?

Chad Rohlfsen
12-15-2019, 12:57 AM
Yes. I am going to include the Dinka, Mende, and Mbuti. All three are also showing Chalcolithic West Asian ancestry.

Angoliga
12-15-2019, 03:49 PM
I think the cushitic/Eurasian ancestry found in countries south of the Horn are probably from nilotic-speaking populations who had significantly intermingled with
South Cushitic speakers.

Wow, literally checked all regional modern pops against afmd source samples, couldn't find an instance of cushitic influence (KEN_PN) without sizable nilotic-affinities (Dinka).



I don't think there was a cushitic speaking population that was absorbed by the Kikuyu or other Bantu groups.

That seems the case atm based on limited SE-Cushitic speaking samples.

These Iraqw have negligible West-African affinities (Yoruba), so they couldn't have been absorbed by modern Kikuyo or other Bantu populations. Their elevated Dinka against KEN_PN and noticeable Levant_PPNC would translate sizable contribution from Southern-Nilotic pops:

https://i.imgur.com/T5au4nf.png

Target/Source Samples:

Iraqw:T_Iraqw-1.DG,-0.351713,0.088351,-0.025267,-0.053295,0.000923,-0.026495,-0.00188,-0.011076,0.109216,-0.082735,-0.01023,-0.005845,-0.009068,0.001789,0.018051,-0.023601,0.017602,0.011022,0.004022,-0.010005,-0.001747,0.006554,0.002958,-0.005302,0.002634
Iraqw:T_Iraqw-2.DG,-0.357405,0.083273,-0.017348,-0.059432,-0.000615,-0.032072,0.000235,-0.012923,0.103489,-0.07089,-0.004222,-0.006744,-0.008176,-0.002064,0.020629,-0.016309,0.017341,0.010642,0.004525,-0.004502,-0.000374,0.004822,-0.00037,-0.002048,0.002754

KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534

This is strictly observational, but Kikuyu and Kamba seem to be at least 50% Cushitic and Nilotic (combined) just based on my visit to Kenya. Kenya is highly Cushitic and Nilotic admixed. If 33% of Kenyans speak non-Bantu languages, I'd guess at least 50% of the genepool is non-Bantu.

How was your trip to Kenya? Super cool that you went - hope you had a great time! Without delving too deep in a tangent, I'm genuinely interested to know your experience and how the cultural vibe compared to Central-America (*assuming you've been to native-Belize).

I went to Kenya a year ago for the first time, mostly on the coast (Malindi/Watamu, Mombasa).From visits to Uganda, I'd subjectively say the same, more or less, regarding the wide-array of phenotypes observed in native Kenyans.

Michalis Moriopoulos
12-16-2019, 02:20 AM
Did you guys see the St. Helena slave paper (https://www.biorxiv.org/content/10.1101/787515v1.full.pdf) (and supplement (https://www.biorxiv.org/content/10.1101/787515v1.supplementary-material))? There are some interesting admixture runs and PCAs in it relevant to SSA variation.

I threw this together to illustrate the trends (at K=7):
https://i.imgur.com/IEBPYSV.png

Obviously Nilotes, Horners, and Khoisan get their own components here, but for the first time (that I've ever seen anyway) basic structure in West African populations and their Bantu descendants is also made evident.

You can see a grey "Senegambian" component maximized in the Jola, a blue-grey "Guinean" component maximized in Fon and Yoruba, a light blue "Central African Bantu" component maximized in Gabon Bantus, and an orange "Rift Valley Bantu" component maximized in Kenyan Bantus. Notice that the Angolan and Namibian Bantus are like Central African Bantus. The South African Bantus look like Rift Valley Bantus with some Khoisan ancestry. These trends support the notion of two separate major Bantu expansion paths (https://sites.google.com/site/wwwbantumigration/_/rsrc/1364865634923/home/bantumigration.jpg) into Southern Africa. The difference between the Nigerian and Cameroon populations is awesome to see.

blackflash16
12-16-2019, 08:41 PM
Did you guys see the St. Helena slave paper (https://www.biorxiv.org/content/10.1101/787515v1.full.pdf) (and supplement (https://www.biorxiv.org/content/10.1101/787515v1.supplementary-material))? There are some interesting admixture runs and PCAs in it relevant to SSA variation.

I threw this together to illustrate the trends (at K=7):
https://i.imgur.com/IEBPYSV.png

Obviously Nilotes, Horners, and Khoisan get their own components here, but for the first time (that I've ever seen anyway) basic structure in West African populations and their Bantu descendants is also made evident.

You can see a grey "Senegambian" component maximized in the Jola, a blue-grey "Guinean" component maximized in Fon and Yoruba, a light blue "Central African Bantu" component maximized in Gabon Bantus, and an orange "Rift Valley Bantu" component maximized in Kenyan Bantus. Notice that the Angolan and Namibian Bantus are like Central African Bantus. The South African Bantus look like Rift Valley Bantus with some Khoisan ancestry. These trends support the notion of two separate major Bantu expansion paths (https://sites.google.com/site/wwwbantumigration/_/rsrc/1364865634923/home/bantumigration.jpg) into Southern Africa. The difference between the Nigerian and Cameroon populations is awesome to see.

The website for the PANAF2018 conference doesn't seem to be up anymore, but I posted this from the book of abstracts earlier this year:



Towards an ancient DNA record of Africa's past

Pontus Skoglund

Genomic sequencing of archaeological material has revolutionized our understanding of the human past in Eurasia, but ancient DNA sequencing has yet to be comprehensively brought to benefit the study of Africa's past. I will review our current state of understanding of the genomic record of past African populations, how this record can be interpreted together with the archaeological record, and how scholars from diverse disciplines can engage with this source of information in their own research. Example insights from this recent research has included a new understanding of long-distance interconnectivity between early Holocene southern African and eastern African populations, support for an expansion of Cushitic-speakers from eastern to southern Africa, and new models of deep human population structure in Africa around the time of emergence of anatomically modern humans. I will present new results suggesting that multiple waves of agricultural expansion underpin the ancestry of Bantu-speaking populations today, and that these expansions occurred in concert with adaptive genomic variants contributing to infectious disease resistance. These initial results highlight the potential for future research in the interphase of archaeology and ancient genomics, and I will present the preliminary design of a new ancient DNA enrichment SNP array specifically geared to capture African genetic diversity.


The new SNP array sounds exciting and is probably related to the update to "1240k" snp capture mentioned in this tweet from last year (https://twitter.com/amwkim/status/1043079659712405504).

Two images from that twitter thread that might be relevant to Chad's models:


https://imgur.com/olw8HTd.jpg

https://imgur.com/3ZaFZHI.jpg


If I'm understanding it correctly. Chad's model has a 'pan-African structure' for SSA with additional south-African admixture into Mota and additional admixture with an unknown North-African population at 52%, 39%, 19% and 15% into Mota, the Iberomaurusians, the Yoruba and 2000BP South Africans respectively.

While the model that has been produced by Reich and Jakobssen labs introduces a new basal African population to explain the asymmetric relationship between 2000BP South-Africans and other sub-Saharan populations.

Angoliga
12-17-2019, 02:00 AM
Did you guys see the St. Helena slave paper (https://www.biorxiv.org/content/10.1101/787515v1.full.pdf) (and supplement (https://www.biorxiv.org/content/10.1101/787515v1.supplementary-material))? There are some interesting admixture runs and PCAs in it relevant to SSA variation.

I threw this together to illustrate the trends (at K=7):
https://i.imgur.com/IEBPYSV.png

Obviously Nilotes, Horners, and Khoisan get their own components here, but for the first time (that I've ever seen anyway) basic structure in West African populations and their Bantu descendants is also made evident.

You can see a grey "Senegambian" component maximized in the Jola, a blue-grey "Guinean" component maximized in Fon and Yoruba, a light blue "Central African Bantu" component maximized in Gabon Bantus, and an orange "Rift Valley Bantu" component maximized in Kenyan Bantus. Notice that the Angolan and Namibian Bantus are like Central African Bantus. The South African Bantus look like Rift Valley Bantus with some Khoisan ancestry. These trends support the notion of two separate major Bantu expansion paths (https://sites.google.com/site/wwwbantumigration/_/rsrc/1364865634923/home/bantumigration.jpg) into Southern Africa. The difference between the Nigerian and Cameroon populations is awesome to see.

Thanks for sharing Michalis, it's interesting seeing how the paper's PCA compares with others.

It seems the grey "Senegambian" component has more Atlantic West-Africans drifting the opposite direction of the S-African cline, here's a comparison with the thread's PCA:
https://i.imgur.com/4eliJrk.jpg



PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs):

https://i.imgur.com/TRCwJS4.png
Have you noticed the same contrast with Africans on your PCA?

Angoliga
12-17-2019, 03:39 AM
Duplicate

Brwn_trd
12-17-2019, 01:50 PM
Does anyone know any papers on the Haratin? It would shed more light on population movements in the Sahara if we had genetic data on the Haratin. I find the consensus of this population as enslaved Africans from further south rather dubious and for various reasons I am inclined to view them as a subjugated indigenous population.

Michalis Moriopoulos
12-17-2019, 02:29 PM
Have you noticed the same contrast with Africans on your PCA?

I can't get my SSA PCA to look quite the same; all the West Africans basically cluster in the same corner, including the Gambians. There are a lot more Tropical African samples in that paper than in the G25 so that might have something to do with it. Though the Nilotes do pull toward the Eurasian-admixed side of the PCA in both my G25 version and the St. Helena paper's PCA, interestingly.

It does look like the Jola-maximized component can be correlated with Atlantic speech. The Mande speakers look intermediate between the Atlantic speakers and Guinea Coast West Africans.

pgbk87
12-18-2019, 05:21 PM
How was your trip to Kenya? Super cool that you went - hope you had a great time!
E.P.I.C... Views that will never leave my mind. Only South Africa and Tanzania can really compare to the raw African beauty of Kenya. Definitely a top 5 most epic places to see before you die. The drone video footage I have is amazing.


Without delving too deep in a tangent, I'm genuinely interested to know your experience and how the cultural vibe compared to Central-America (*assuming you've been to native-Belize).

The Bongo (Tanzanian music) that young Kenyans love is similar to Punta music from Belize. Watamu reminds me of an even more epic version of Ambergris Caye. They were not familiar with Belize. Some people thought we were "Jamaican" though. I can pass as a coastal Kenyan or Cushitic admixed Bantu. My wife doesn't pass as Kenyan though.


I went to Kenya a year ago for the first time, mostly on the coast (Malindi/Watamu, Mombasa).
Same for me. Just add Marafa, Gede Ruins, Che Shale, Amboseli National Park and Nairobi for me.


From visits to Uganda, I'd subjectively say the same, more or less, regarding the wide-array of phenotypes observed in native Kenyans.

It seems like sedentary agriculture overwhelmed pastoralists and hunter-gatherers in similar fashion. Once you go sedentary agriculturalist, you don't go back lol.

Espoir
12-20-2019, 11:28 PM
It seems like sedentary agriculture overwhelmed pastoralists and hunter-gatherers in similar fashion. Once you go sedentary agriculturalist, you don't go back lol.
I guess they were overwhelmed bcz sedentary agriculturists tend to have high fertility and lower mortality late compared to pastoral nomads and Hunter-gatherers.

Ajeje Brazorf
12-25-2019, 01:05 PM
There is a particular sample called "BantuKenya-2.DG" that differs from all the others in Global25, what are its origins and what causes his isolation?

Distance to: Bantu_Kenya_S_BantuKenya-2.DG
0.08409637 Luhya_Kenya_NA19023
0.08567514 Luhya_Kenya_NA19026
0.08645694 Bantu_Kenya_S_BantuKenya-1.DG
0.09053025 Luhya_Kenya_NA19019
0.09144906 Bantu_Kenya_HGDP01417
0.09758890 Luhya_Kenya_NA19024
0.09782620 Luhya_Kenya_NA19017
0.09819727 Luo_Ayodo_412C
0.09998573 Luhya_Kenya_NA19020

pgbk87
12-25-2019, 03:21 PM
Did you guys see the St. Helena slave paper (https://www.biorxiv.org/content/10.1101/787515v1.full.pdf) (and supplement (https://www.biorxiv.org/content/10.1101/787515v1.supplementary-material))?


Curious what is accounting for the hunter-gatherer affinities in groups like the Mende, Yacouba, Ahizi even in Akans, but negligible to non-existent in the Yoruba and Esan. Some ancient far west African hunter-gatherer population?

The West African affinities of South Sudanese and Anuak best matches the Bariba and Yoruba. I am curious what the Hausa would look like in this run

There is a small but consistent Horn-African affinity along coastal East Africa. It is probably a mix of Omani Arab and Cushitic influence imo

The yellow Horn African component is maximized in the Afars and not Somalis. Are these genuine Afars this time (unlike an old Pagani et. al study)?

There is a minor and probably basal East-Central African ("Nilotic-like") component spread throughout the groups in all but southernmost Africa

Espoir
12-27-2019, 11:13 PM
35642
Screenshot from supplements of the Saint-Helena paper showing haplogroups of the 20 individuals.
Circled in blue is subclade of G. How on earth do we get it in West Central Africa? I wouldnít be surprised if it was R, but G is shockingly surprising to me.