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nee4speed111
02-12-2018, 10:04 PM
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1393-5

Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

Results
In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase.

Conclusions
Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

drobbah
02-12-2018, 11:42 PM
Could these Nilo-Saharans be descendants of Cushtic speakers who elite dominated certain Nilo-Saharan groups? This would make sense considering some of these Nilotic languages found in Sudan contain Cushtic loan words from perhaps groups like the Beja??



In the same period, we found evidence of a movement along the same Sahelian axis involving the internal lineages of E-M78/V32. This haplogroup probably differentiated in eastern Africa 5.99 kya, and we observed a shift in its geographic distribution towards the central Sahel, where it arrived not later than 5.17 kya. Interestingly, all the central sahelian E-V32 chromosomes belong to the internal clade E-V32/V6873, which is almost exclusively found among the Nilo-Saharans (Mann–Whitney test, p = 0.01). These findings suggest that the Nilo-Saharan spread along the Sahelian belt was probably a complex event, involving different clades and different movements from the lake Chad basin to eastern Africa and back





The sub-Saharan clades E-V264/V259 and E-V22/V3262 are restricted to central Sahel and eastern Africa (mainly the Horn of Africa), respectively, whereas E-V12/V32 is very frequent in eastern Africa but it also includes a central Sahelian clade, suggesting a Sahelian movement between 5.99 and 5.17 kya

RCO
02-12-2018, 11:50 PM
Finally assuming that movement:
Outside Africa, both A3-M13 and R-V88 harbour sub-lineages geographically restricted to the island of Sardinia and both seem to indicate ancient trans-Mediterranean contacts. The phylogeography of A3-M13 suggests that the direction of the movement was from Africa to Sardinia, while R-V88 topology indicates a Europe-to-Africa migration. Indeed, our data suggest a European origin of R-V88 about 12.3 kya, considering both the presence of two Sardinian R-V88 basal clades (R-M18 and R-V35) and that the V88 marker arose in the R-M343 background, which in turn includes Near-Eastern/European lineages[52]. It is worth noting that the arrival of R-V88 in the Sahara seems to have occurred between 8.67 and 7.85 kya (considering as an upper limit the time estimates of the last node including a European-specific lineage, while the lower limit is the coalescence age of all the African-specific lineages), refining the time frame of the trans-Saharan migration proposed in previous studies [37, 56]. The route of R-V88 toward the lake Chad basin probably passed through northeastern Africa rather than Arabia, considering the absence of R-V88 in the Horn of Africa. Interestingly, both A3-M13 and R-V88 European sub-clades coalesced in ancient times (> 7.62 kya for A3-M13/V2742 and between 12.34 and 8.67 kya for R-V88/M18 and R-V88/V35) (Additional file 2: Figures S2 and S5). So it is possible that both clades were widespread in southern Europe, where they have been replaced by the Y haplogroups brought by the following recurrent migration waves from Asia [57].

Ignis90
02-12-2018, 11:55 PM
So the Green Sahara attracted what would become 4 trans-Saharan haplogroups: E-M78 and R-V88 from the North (Northeastern Africa and Eurasia) and A-M13 and E-M2 from the South (modern central Sahel). Then the Sahara dried out completely and became a barrier, which cut out contacts from both side of the desert which means most Sub-Saharan lineages in North Africa and the Mediterranean (here Sardinia in particular) are no recent than the drying of the Green Sahara (>4.5kya) and the same is true for North African/Eurasian lineages in Subsaharan Africa.

Makes sense based on what was already known.

drobbah
02-13-2018, 12:14 AM
Could these Nilo-Saharans be descendants of Cushtic speakers who elite dominated certain Nilo-Saharan groups? This would make sense considering some of these Nilotic languages found in Sudan contain Cushtic loan words from perhaps groups like the Beja??

Nilo-Saharans like the Masalit and Fur who are predominantly V32 (71% and 68% respectively) yet have negligible amount of Afro-Asiatic maternal lineages or autosomal ancestry kinda reminds me of the R-V88 Chadics except these Cushitic men adopted the tongue of the females they mated with

ADW_1981
02-13-2018, 12:17 AM
Finally assuming that movement:

Unfortunately I have to disagree with the author's conclusions. Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge. The bigger mystery in my mind, is what group of wanderers were traveling in and around the Mediterranean during the Neolithic period in 5000 BC?

In terms of the A3-M13, how many Sardinians actually descend from this branch? Is it the same one that has popped up in Britain and the Middle East?

Megalophias
02-13-2018, 12:25 AM
Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge. The bigger mystery in my mind, is what group of wanderers were traveling in and around the Mediterranean during the Neolithic period in 5000 BC?
Cardial Ware settlers, probably obsidian traders. I doubt Sardinian I2-M26 is even Neolithic though, seems more likely Copper Age.


In terms of the A3-M13, how many Sardinians actually descend from this branch? Is it the same one that has popped up in Britain and the Middle East?
The more famous British one is A1a. A-M13 is pretty widespread but rare, it's only 0.6% in Sardinia.

blackflash16
02-13-2018, 03:22 AM
Strange. It seems like they focused on R-V88 (~17.64%) for Southern Egyptians and they didn't include any of the M78 results.(Supplementary Table 4):

21447

ffoucart
02-13-2018, 06:37 AM
So the Green Sahara attracted what would become 4 trans-Saharan haplogroups: E-M78 and R-V88 from the North (Northeastern Africa and Eurasia) and A-M13 and E-M2 from the South (modern central Sahel). Then the Sahara dried out completely and became a barrier, which cut out contacts from both side of the desert which means most Sub-Saharan lineages in North Africa and the Mediterranean (here Sardinia in particular) are no recent than the drying of the Green Sahara (>4.5kya) and the same is true for North African/Eurasian lineages in Subsaharan Africa.

Makes sense based on what was already known.

Please note that desertification was a progressive process, and during centuries Central Sahara maintained enough vegetation for pastoralism (in the mountain range). Bos were domisticated as an consequence of desertification, partially from African stock. In the end of the process, aridity became too high, and even pastoralims were not sufficient to maintain human life. Hence probably migrations to Sahel and/or Egypt, and extinction of some groups.


Unfortunately I have to disagree with the author's conclusions. Other than Sardinia harbouring some ancient neolithic lineages, I doubt it has any relationship to the African branches as no other Sardinian group such as I2-M26 has turned up in Africa to the best of my knowledge.

Mind that this is based on modern distribution, not on ancient results, with huge founder effects. This mean we can't exclude the initial presence of I2 in North Africa 7000 years ago.
But I'm agree, since R1b V88 seems more and more like a WHG specific haplogroup, the more likely scenario is the presence of R1B V88 in North Africa before the Neolithization (by a Natufian-rich population). The huge hydrographic system oriented South/North in Northern Sahara (especially in Libya and Egypt) during the Green Sahara was probably like an highway to Central Sahara for Northern Populations, and pastoralism based on goat is attested.
The probable route from Europe would be either Spain or Italy.

Squad
02-13-2018, 07:40 AM
They forgot about E-L19, E-M33 and also A1a, how foolish...

As for R-V88, I've already said that it most likely entered from Italy and not Iberia. The haplogroup is well established in the eastern portion of North Africa and Central Africa, but it is almost completely lacking in the west. Add this to the fact that Sardinia has basal sub-clades and you get the idea. Natufian-like rich, we can't know, but it is likely that their original autosomal composition (WHG) was diluted as they were moving toward lake Chad to the extent that there is almost no west eurasian autosomal signal in the populations currently heavy in R-V88. It is possible that at one point V88 predominated along the libyan coast where it would have been mixing with ''natufian-like'' North Africans.

RCO
02-13-2018, 11:12 AM
Another absence is J1, quite present in North Africa but not included in the article, so J1 arrived only in the North after the aridification of the Sahara.

beyoku
02-14-2018, 01:17 PM
What happened to the Southern Egyptians samples ? These samples are not new. What can we really learn about the Ancient Inhabitants and migrations in the Eastern Sahara without any samples from Sudan.:( The A and M78 lineages are underestimated due to the lack of Sudanese lineages IMO.

Megalophias
02-14-2018, 03:39 PM
What happened to the Southern Egyptians samples ? These samples are not new. What can we really learn about the Ancient Inhabitants and migrations in the Eastern Sahara without any samples from Sudan.:( The A and M78 lineages are underestimated due to the lack of Sudanese lineages IMO.
Southern Egyptians? You mean how the E-M78 is listed as "data not available"? Wonder what happened there. Looks like the same samples from Trombetta et al E-M35 study so should all be E-V12(xV32), probably diverse types.

Nothing from Sudan, nothing from Mali either, but it's a lot better than the usual nothing.

Omaar
02-14-2018, 05:17 PM
Nilo-Saharans like the Masalit and Fur who are predominantly V32 (71% and 68% respectively) yet have negligible amount of Afro-Asiatic maternal lineages or autosomal ancestry kinda reminds me of the R-V88 Chadics except these Cushitic men adopted the tongue of the females they mated with

"Interestingly, all the central sahelian E-V32 chromosomes belong to the internal clade E-V32/V6873, which is almost exclusively found among the Nilo-Saharans "? What is this clade?

drobbah
02-14-2018, 08:19 PM
"Interestingly, all the central sahelian E-V32 chromosomes belong to the internal clade E-V32/V6873, which is almost exclusively found among the Nilo-Saharans "? What is this clade?
I'm not sure but it is apparently 5k years old according to their estimates.

Angoliga
02-15-2018, 04:02 AM
Could these Nilo-Saharans be descendants of Cushtic speakers who elite dominated certain Nilo-Saharan groups? This would make sense considering some of these Nilotic languages found in Sudan contain Cushtic loan words from perhaps groups like the Beja??
That's a plausible scenario but hard to decipher based on linguistics. There's also quite a notable amount of Nilo-Saharan loanwords found in Beja and other adjacent Afroasiatic languages.


...In terms of the A3-M13, how many Sardinians actually descend from this branch? Is it the same one that has popped up in Britain and the Middle East?


According to Yfull's estimates, the Sardinians, some Saudis and a Scot from the same A-M13 British-line are from a branch that formed 10,300ybp:
https://i.imgur.com/tcpOi2s.png
On the Ytree, the other branch above splits from the same period, it's mostly upper-nilotic (S.Sudan/Uganda) save one Saudi. Overall it's nice to see the paper's 10.7kya formation date for A3-M13 actually matches up quite nicely with Yfull (https://www.yfull.com/tree/A-M13/)'s 10.6kya estimate :nerd:





The more famous British one is A1a. A-M13 is pretty widespread but rare, it's only 0.6% in Sardinia.

Interesting stat, where did you get that figure? I found them to be a little higher from these older papers: (1/77 = 1.3%,[Semino O, 2000] 1/22 = 4.5%[Shen P, 2000])






What can we really learn about the Ancient Inhabitants and migrations in the Eastern Sahara without any samples from Sudan.:( The A and M78 lineages are underestimated due to the lack of Sudanese lineages IMO.

Couldn't agree more! Given the significance of waterways during the aridification of the Sahara, it would've been pertinent to also obtain samples from the upper and middle Nile -- its a pretty big gap in the puzzle

drobbah
02-15-2018, 05:12 AM
That's a plausible scenario but hard to decipher based on linguistics. There's also quite a notable amount of Nilo-Saharan loanwords found in Beja and other adjacent Afroasiatic languages.


This is what I could find on the topic
21492
21493

There are still holes in my theory like the fact that these Sahelians carry a specific V32 subclade not found among us modern Cushtic speakers.For all we know they could have just absorbed this lineage because of proximity and for whatever reason this lineage became quite successful among certain ethnic groups in the Sudan/Shaad region.

Almagest
02-15-2018, 03:42 PM
"Interestingly, all the central sahelian E-V32 chromosomes belong to the internal clade E-V32/V6873, which is almost exclusively found among the Nilo-Saharans "? What is this clade?

The 3 Horn of Africa samples are 1 Ethiopian Jew 1 Amhara and 1 Eritrean Tigrai. You can see in the Figure 2, 2 of them are close to a Near East (Iran) V32, <4.6kya. So it is reasonable to assume that they belong to Y28701 (assuming the Iranian belongs to Y28701, because the other Horn of Africa sample is closer to Kenyan V32 (1 Borana 1 Luhya 1 Maasai), which is likely to be Z813). The TMRCA between the Chadians and Ethiopian/Near east is 6 +-0.7kya and given Y28701 formed 5.3kya ago, I would have to say they belong to the same branch, it's within the TMRCA calucation error. There are Chadians with DYS438=12 (2/2, 316434 and 316442) and so I would say they are Y28701*.

ADW_1981
02-15-2018, 06:11 PM
They forgot about E-L19, E-M33 and also A1a, how foolish...

As for R-V88, I've already said that it most likely entered from Italy and not Iberia. The haplogroup is well established in the eastern portion of North Africa and Central Africa, but it is almost completely lacking in the west. Add this to the fact that Sardinia has basal sub-clades and you get the idea. Natufian-like rich, we can't know, but it is likely that their original autosomal composition (WHG) was diluted as they were moving toward lake Chad to the extent that there is almost no west eurasian autosomal signal in the populations currently heavy in R-V88. It is possible that at one point V88 predominated along the libyan coast where it would have been mixing with ''natufian-like'' North Africans.

I guess you're suggesting the R-V88 guys moved from modern day "Sicily" to modern day "Tunisia" around 5000 BC?

Angoliga
02-16-2018, 03:06 AM
This is what I could find on the topic
21492
21493

There are still holes in my theory like the fact that these Sahelians carry a specific V32 subclade not found among us modern Cushtic speakers.For all we know they could have just absorbed this lineage because of proximity and for whatever reason this lineage became quite successful among certain ethnic groups in the Sudan/Shaad region.

Here's some quotes I had in mind...

This speaks more to typological features than actual loanwords being due possibly just by proximity of the two language groups
https://i.imgur.com/JZPcV2n.png


I think you'd find this pertinent to your theory...

It explains the reason of so many Nilosaharan loanwords in Beja to be the result of North-Cushitic groups gradually assimilating Nilotics pops in the southern Red Sea hills region; all within the last 5k years:
https://i.imgur.com/vHsQ0wH.jpg

Interestingly, elders in my maternal Kir-Abbain tribe (Kakwa) have mentioned coming from the Red Sea region, somewhere around the Ethiopia-Sudan border or at Kapoeta -- perhaps it's an oral history of their string of migrations. [mentioned earlier (https://anthrogenica.com/showthread.php?6465-Echoes-of-the-East-African-Slave-Trade-Distant-Diasporic-Matches-IBS-or-IBD&p=141163&viewfull=1#post141163)]

Ebizur
02-16-2018, 10:52 AM
Here's some quotes I had in mind...

"From a morphosyntactic point of view, Nilo-Saharan language groups spoken in an area ranging from northern Ethiopia and Eritrea across north-central Sudan and extending into Chad and Nigeria share typological features with Afroasiatic languages in Ethiopia. These include a basic constituent order whereby the verb occurs in final position, an extensive case marking system, verbal compounding (e.g., with 'say' or other types of light verbs, such as 'put' or 'do'), as well as the use of converbs as dependent verb forms in complex sentences, although not all properties are necessarily present in all groups. These common typological features to some extent may be due to areal diffusion as a result of long-term cultural contacts and corresponding patterns of multilingualism between speech communities in these areas."


This is an illustration of why I am no fan of theories of relationships among languages based on linguistic typology.

The list of morphosyntactic features reads like a basic outline of Japanese grammar. Of course, Japanese is spoken in a territory that is geographically greatly removed from the Nile Valley or the Sahara, but is one really much more justified in postulating "long-term cultural contacts and corresponding patterns of multilingualism between speech communities in these areas" because of their geographical proximity to one another than one would be in postulating a relationship between these speech communities and speakers of Japanese on the basis of the same linguistic evidence?

Squad
02-17-2018, 09:09 AM
I guess you're suggesting the R-V88 guys moved from modern day "Sicily" to modern day "Tunisia" around 5000 BC?

Yes, that's my stance based on the evidence we have so far, although it would be necessary to examine north african V88 to see where it fits in the phylogenetic tree.

FIREYWOTAN
02-18-2018, 06:09 PM
Thanks to all of you who helped to tell a story that needs to be told. The challenge of knowing what happens to a place in time.
Holocene Epoch: The Age of Man

By Mary Bagley, LiveScience Contributor | March 27, 2013 12:26pm ET

The Holocene Epoch is the current period of geologic time. Another term that is sometimes used is the Anthropocene Epoch because its primary characteristic is the global changes caused by human activity. This term can be misleading, though; modern humans were already well established long before the epoch began. The Holocene Epoch began 12,000 to 11,500 years ago at the close of the Paleolithic Ice Age and continues through today.

The background story sets the place for the events that followed.

As Earth entered a warming trend, the glaciers of the late Paleolithic retreated. Tundra gave way to the forest. As the climate changed, the very large mammals that had adapted to extreme colds, like mammoth and wooly rhinoceros, became extinct. Humans, once dependent on these “mega mammals” for much of their food, switched to a smaller game and increased their gathering of plant materials to supplement their diet.
Out of the heat and caught in an icebox.

Evidence indicates that about 10,800 years ago, the climate underwent a sharp cold turn lasting for several years. The glaciers did not return, but the game and plant materials would have been scarce. As temperatures began to rebound, human population began to increase and we began inventing the processes that would change the planet forever.

Talking about Africa always challenges the pictures with the realities of this massive continent.

Angoliga
11-20-2018, 10:00 PM
Yfull (https://www.yfull.com/tree/) has now added all BAM samples from this paper

Sample Reference List (Table 1 (https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-018-1393-5/MediaObjects/13059_2018_1393_MOESM1_ESM.xlsx)):


ID Former IDa Haplogroup Country Population Age Reference

S101 A00-L1086 Cameroon General population Modern present study
S102 A0-V148 Cameroon General population Modern present study
S103 A0-V148 Algeria Mozabite Berbers Modern present study
S104 S07 A1-M31 Mali General population Modern present study
S105 S08 A2-PN3 Angola !Kung Modern present study
S106 S75 A2-PN3 Cameroon General population Modern present study
S107 S73 A3-M28 Eritrea Nara Modern present study
S108 A3-M51 Angola !Kung Modern present study
S109 A3-M51 Angola !Kung Modern present study
S110 S10 A3-M13* Italy Sardinians Modern present study
S111 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S112 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S113 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S114 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S115 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S116 A3-M13/V3 Ethiopia Ethiopian Jews Modern present study
S118 A3-M13/V317 Ethiopia Amhara Modern present study
S119 A3-M13/V317 Ethiopia Oromo Modern present study
S120 A3-M13* Kenya Maasai Modern present study
S121 A3-M13* Kenya Maasai Modern present study
S122 A3-M13* Cameroon Fulbe Modern present study
S123 A3-M13/V67 Nigeria Hausa Modern present study
S124 A3-M13* Chad Shuwa arabs Modern present study
S125 A3-M13* Chad Ngambai Modern present study
S126 S77 A3-M13* Chad Massa Modern present study
S127 A3-M13* Benin General population Modern present study
S128 A3-M13* Morocco Souss Berbers Modern present study
S129 S76 A3-M13* Egypt Northern Egyptians Modern present study
S130 B-M236 Chad Gor Modern present study
S131 S14 B-M236/M146 Burkina Faso General population Modern present study
S132 B-M150/M109 Cameroon Moundang Modern present study
S133 B-M150/M109 Chad Toupouri Modern present study
S134 S74 B-M112 Cameroon General population Modern present study
S135 E-V44 Ethiopia Amhara Modern present study
S136 E-V257* (xM81) Chad Massa Modern present study
S137 E-M78/V259 Cameroon Daba Modern present study
S138 E-M78/V259 Cameroon Guidar Modern present study
S139 E-M78/V12* Cameroon Mandara Modern present study
S140 E-M78/V32 Cameroon Moundang Modern present study
S141 E-M78/V32 Chad Massa Modern present study
S142 E-M78/V32 Chad Goulaye Modern present study
S143 E-M78/V32 Chad Goulaye Modern present study
S144 E-M78/V32 Chad Madjingay Modern present study
S145 E-M78/V32 Chad Goulaye Modern present study
S146 E-M78/V12* Egypt General population Modern present study
S147 E-M78/V12* Egypt General population Modern present study
S148 E-M78/V12* Morocco Moroccan Jews Modern present study
S149 S25 E-M78/V65 Libya Libian Jews Modern present study
S150 E-M78/V65 Egypt Egyptian Berbers from Siwa Modern present study
S151 E-M78/V65 Egypt Egyptian Berbers from Siwa Modern present study
S152 E-M78/V65 Morocco Moroccan Arabs Modern present study
S153 E-M78/V65 Morocco Moroccan Arabs Modern present study
S154 E-M78/V32 Ethiopia Amhara Modern present study
S155 E-M78/V32 Eritrea/Ethiopia Tigrai Modern present study
S156 E-M78/V32 Ethiopia Ethiopian Jews Modern present study
S157 E-M78/V32 Kenya Borana Modern present study
S158 E-M78/V32 Kenya Luhya Modern present study
S159 E-M78/V32 Kenya Maasai Modern present study
S160 E-V68/V2009 Cameroon Fulbe Modern present study
S161 E-V68/V2009 Morocco Souss Berbers Modern present study
S162 E-M78/V22 Eritrea Saho Modern present study
S163 E-M2* Egypt Egyptians from Baharia Modern present study
S164 E-M2* Egypt Egyptians from Baharia Modern present study
S165 E-M2* Egypt Egyptian Berbers from Siwa Modern present study
S166 E-M2* Egypt Egyptian Berbers from Siwa Modern present study
S167 E-M2* Morocco Ouarzazate Berbers Modern present study
S168 E-M2* Morocco Ouarzazate Berbers Modern present study
S169 E-M2* Morocco Asni Berbers Modern present study
S170 E-M2* Morocco Bouhria Berbers Modern present study
S171 E-M2* Burkina Faso General population Modern present study
S173 E-M2* Senegal Mandenka Modern present study
S175 E-M2* Cameroon Ngambai Modern present study
S176 E-M2* Cameroon Fali Modern present study
S177 E-M2* Niger Songhai Modern present study
S178 S38 C-V20 Italy General population Modern present study
S179 C-M8 Japan General population Modern present study
S181 J-M172 Turkey Sephardic Turkish Modern present study
S182 J-M267/P58 Chad Gor Modern present study
S183 R-V88* Benin General population Modern present study
S184 R-V88* Benin General population Modern present study
S185 R-V88* Cameroon Ouldeme Modern present study
S186 R-V88/V69 Cameroon Moundang Modern present study
S187 R-V88/V69 Cameroon Fulbe Modern present study
S188 R-V88/V69 Cameroon Toupouri Modern present study
S189 R-V88/V69 Chad Toupouri Modern present study
S190 R-V88* Chad Madjingay Modern present study
S191 R-V88/V69 Chad Toupouri Modern present study
S192 R-V88* Chad Toupouri Modern present study
S193 R-V88* Chad Moundang Modern present study
S194 R-V88* Chad Massa Modern present study
S195 R-V88/V8 Chad Gor Modern present study
S196 R-V88* Cameroon Ewondo Modern present study
S197 R-V88* Bulgaria Sephardic Bulgarians Modern present study
S198 R-V88* Algeria Mozabite Berbers Modern present study
S200 R-V88* Morocco Ouarzazate Berbers Modern present study
S201 R-V88* Egypt General population Modern present study
S202 R-V88* Egypt General population Modern present study
S203 TV18 R-V88* Egypt General population Modern present study
S204 R-V88* Egypt Northern Egyptians Modern present study
S206 J-M267/P58 Ethiopia Amhara Modern present study
S207 J-M267* (xP58) Ethiopia Oromo Modern present study
S208 J-M267/P58 Algeria Mozabite Berbers Modern present study
S209 J-M267* (xP58) Yemen Yemenites Modern present study
S210 J-M267* (xP58) Ethiopia Amhara Modern present study
GS16204 A-M13/V243b Ethiopia Ethiopian Jews Modern 1
GS35245 E-M2/U174b Congo Congo-pygmies Modern 1
GS16179 E-V32b Iran Iranians Modern 1
GS16217 E-M4145b Israel Arab-Christian Modern 1
GS16206 E-M34b Israel Arab-Christian Modern 1
GS13741 J1c-PF7256b Azerbaijan Azeri Modern 1
GS14421 J1a1-B232b Russia Tabas-saran Modern 1
GS13724 J1a2-B234b Russia Lezgin Modern 1
GS35126 J1b6-PR6622b Armenia Armenian Modern 1
GS35125 J1b5-CTS11284b Armenia Armenian Modern 1
GS14474 J1b4-B235b Jordan Jordanian Modern 1
GS16136 J1b2-L829b Israel Druze Modern 1
GS16180 J1b1-B243b Saudi Arabia Arabian Modern 1
GS35124 J1b3-B382b Armenia Armenian Modern 1
NA18940 D2-M55b Japan JPT Modern 2
NA19239 E1a-P110b Nigeria YRI Modern 2
NA18504 E1b1a-U174b Nigeria YRI Modern 2
NA19026 E1b1a-U174b Kenya LWK Modern 2
NA19834 E1b1a-U174b USA ASW Modern 2
NA19703 E1b1a-U181b USA ASW Modern 2
NA18501 E1b1a-U209* (xU290)b Nigeria YRI Modern 2
NA19020 E1b1a-U209* (xU290)b Kenya LWK Modern 2
NA19025 E1b1a-U209* (xU290)b Kenya LWK Modern 2
NA19700 E1b1a-U290* (xU181)b USA ASW Modern 2
NA20510 E1b1b-V13b Italy TSI Modern 2
NA21732 E1b1b-V22b Kenya MKK Modern 2
NA21737 E1b1b-V22b Kenya MKK Modern 2
NA19670 G-U8b USA MXL Modern 2
NA06994 I1-M253b USA CEU Modern 2
NA12891 I1-M253b USA CEPH/Utah Pedigree 1463 Modern 2
NA20511 I1-M253b Italy TSI Modern 2
NA18558 N-M231b China CHB Modern 2
NA19735 Q1a-M3b USA MXL Modern 2
NA20846 R1a-M17b USA GIH Modern 2
NA20850 R1a-M17b USA GIH Modern 2
NA10851 R1b1-M529* (xM222)b USA CEU Modern 2
NA12889 R1b1-P312* (xDF27,U152,M529,L238)b USA CEPH/Utah Pedigree 1463 Modern 2
HG00731 R1b1-U152b USA PUR Modern 2
NA07357 R1b1-U152b USA CEU Modern 2
NA19649 R1b1-U152b USA MXL Modern 2
NA20509 R1b1-U152b Italy TSI Modern 2
NA20845 R2-M124b USA GIH Modern 2
Ust'-Ishim NOc Siberia - 45 kya 3
Bichon I2ab Switzerland - 13.7 kya 4
Kotias J2b Georgia - 9.7 kya 4
Loschbour I2c Luxembourg - 8 kya 5


I requested a few A-M13s a week ago and was delightfully surprised to see all samples added just a few days later -- the folks at Yfull are amazing!
Given this paper came out early 2018, it's pretty funny no one had thought to request these earlier

Megalophias
11-21-2018, 01:47 AM
Great to see some Africans in the African branches previously represented entirely by Arabs. :biggrin1:

Lank
11-21-2018, 12:19 PM
Yfull (https://www.yfull.com/tree/) has now added all BAM samples from this paper

I requested a few A-M13s a week ago and was delightfully surprised to see all samples added just a few days later -- the folks at Yfull are amazing!
Given this paper came out early 2018, it's pretty funny no one had thought to request these earlier
Thanks for sharing and for bringing it to their attention! Nice to see some more Africans in the YFull phylogeny. Some interesting results here, looks like the most common Saudi A-M13 lineage shares a recent (<3 ky old) TMRCA with Ethiopian A-M13. Would have been nice if we could also have some more Z830/V1515 samples, but I'll try to be patient for a while longer. :P

BTW, for any Africans interested in getting sequenced, Dante Labs (https://www.dantelabs.com/products/whole-genome-sequencing) have a promotion until Nov 26th offering WGS 30x sequencing for just $199/€169 (free worldwide shipping). They've had some issues with delays in the past, but this is still a great deal.

NetNomad
11-21-2018, 03:52 PM
BTW, for any Africans interested in getting sequenced, Dante Labs (https://www.dantelabs.com/products/whole-genome-sequencing) have a promotion until Nov 26th offering WGS 30x sequencing for just $199/€169 (free worldwide shipping). They've had some issues with delays in the past, but this is still a great deal.

It's not so good with the Y-Chrom though. It misses a lot of info the Big Y covers IIRC.

NetNomad
11-21-2018, 04:16 PM
Great to see some Africans in the African branches previously represented entirely by Arabs. :biggrin1:

:biggrin1: However, most of the E-M35 subclades among Peninsular Arabs do not seem post-Islamic.

The Arabian Peninsula should be viewed as ''North Africa'' when it comes to human genetics. 23andMe were on to something when they lumped them with Berbers.

Lank
11-21-2018, 05:28 PM
So far the 6 Cameroonian/Chadian V32 samples are all Y28701*, potentially representing an early split from the Cushitic types, not sure if it's still updating though? The 3 Habesha/Jewish V32 samples are in different branches, as you might expect there is some diversity in the Ethiopian highlands. 2 Kenyan Borana/Maasai are Y15945*, and the last new Kenyan sample, a Luhya, belongs to a subclade shared with 2 other Luhya samples.

As for J1, 2/3 samples (an Amhara and an Oromo) belong to J1-P56. A tiny sample size, but it does fit with Agamemnon's suggestion that most Ethiopian J1 may be P56. P56 is a fairly old clade that's surprisingly rare (https://www.yfull.com/tree/J-P56/) across the sea in Arabia. I wouldn't be surprised at this point if modern Arabian J1-P56 represents African back-migration. The last Ethiopian J1 sample, an Amhara, belongs to a small P58 clade (https://www.yfull.com/tree/J-Y6370/) that also includes the only Eritrean J1 sample in YFull's tree.


It's not so good with the Y-Chrom though. It misses a lot of info the Big Y covers IIRC.
I haven't had either test, but I don't think they are directly comparable as the Big Y doesn't sequence the entire Y chromosome. So normal WGS tests actually reveal more novel variants compared to the Big Y. The latter does offer higher coverage, but the Y-DNA coverage offered by 30x WGS tests including Dante Labs doesn't look too shabby either. A poster who did both tests ran some stats (https://anthrogenica.com/showthread.php?12075-Dante-Labs-(WGS)&p=299912&viewfull=1#post299912) comparing the two (https://anthrogenica.com/showthread.php?12075-Dante-Labs-(WGS)&p=299655&viewfull=1#post299655). Here are some other statistics (http://www.haplogroup-r.org/stats.html).

And of course, the WGS test is a lot cheaper with this offer, and you also get to sequence the rest of your genome at a decent coverage. :)

Ruderico
11-21-2018, 05:42 PM
:biggrin1: However, most of the E-M35 subclades among Peninsular Arabs do not seem post-Islamic.

Of course not, E-M35 is some 24000 years old. Even E-M123 is 11k yo, it's old as balls, possibly even older than Proto-Afroasiatic languages

Megalophias
11-21-2018, 08:02 PM
The Arabian Peninsula should be viewed as ''North Africa'' when it comes to human genetics.
This is biogeographically accurate. South Arabia is part of the Afrotropics, and the Saharo-Arabian desert belt can be considered as one macro-region also. So yeah, Arabia is the part of North Africa which borders on Iran and India. ;)

Awale
11-21-2018, 08:28 PM
The Arabian Peninsula should be viewed as ''North Africa'' when it comes to human genetics. 23andMe were on to something when they lumped them with Berbers.

Honestly, they're pretty similar to Egyptians, namely Copts. The main basal difference, from what I remember, being that Copts have more of an Anatolian-Farmer/Dzudzuana shift while Arabians have more of a CHG/Iran-N shift which makes sense geographically, I suppose. Discounting some outlier groups (more significant than you'd think in the peninsula) who have more recent outside admixtures, I'd personally say you could cluster Arabians, Egyptians and Southern Levantines together as a sort of biogeographic group.

notasuckah
11-24-2018, 07:15 AM
I'd wager that Copts have the same amount of Iran_N-related ancestry as Arabians, more or less. The basic difference would be that they would have less Natufian-related and much more Anatolian-related ancestry. I don't know how that would be reflected in terms of Dzudzuana ancestry though. But yes, Copts and Arabians are very similar nonetheless. They could constitute a biogeographical group as you guys proposed.

Looking at Yemenite Jews, they have less Natufian, more Iran_N and Anatolia_N in comparison to Saudis. I'm thinking Copts are something like this just with lower Iran_N relative to Yemenite Jews (same as Saudis more or less), and more Anatolia_N.

But yes this would depend on what Arabian group you're looking at as it has been pointed out that the Arabian Peninsula is very diverse genetically (lots of Arabians are heavily admixed with foreign groups).

Censored
11-24-2018, 07:18 AM
I apologize that I'm sort of late to the party, but can someone explain who the west eurasian ancestors of Berbers and horner Africans are? I read somewhere that they weren't part of the neolithic expansion and came before it or something along those lines...

NetNomad
11-24-2018, 07:16 PM
I apologize that I'm sort of late to the party, but can someone explain who the west eurasian ancestors of Berbers and horner Africans are? I read somewhere that they weren't part of the neolithic expansion and came before it or something along those lines...

From what I gather:

For Berbers, it is a combination of Late Paleolithic/Neolithic South Levantine (still a debate/uncertainty whether it is that or just Ancestral North African) and Anatolian Neolithic farmers who went to Southern Europe and then entered the Maghreb via the Strait of Gibraltar (pre-Indo-European).

For Horners, it is the first group without the latter.

NetNomad
02-15-2019, 09:19 PM
BTW, for any Africans interested in getting sequenced, Dante Labs (https://www.dantelabs.com/products/whole-genome-sequencing) have a promotion until Nov 26th offering WGS 30x sequencing for just $199/€169 (free worldwide shipping). They've had some issues with delays in the past, but this is still a great deal.

Hi Lank,

Did you order this? If so, how long until the results. I hear it takes months with Dante.

Lank
02-16-2019, 08:47 AM
Hi Lank,

Did you order this? If so, how long until the results. I hear it takes months with Dante.
I don't know when they will be ready. Honestly don't think anyone should go for Dante if you want results on time, but I was never in a rush to get sequenced anyway so I don't mind the wait.

diini95
03-10-2020, 07:00 PM
From what I gather:

For Berbers, it is a combination of Late Paleolithic/Neolithic South Levantine (still a debate/uncertainty whether it is that or just Ancestral North African) and Anatolian Neolithic farmers who went to Southern Europe and then entered the Maghreb via the Strait of Gibraltar (pre-Indo-European).

For Horners, it is the first group without the latter.

what about the African ancestry in Horn Africa Like Dinka?