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Piquerobi
02-16-2015, 12:01 AM
I ordered the table provided on the page 26 of the recent study on them (Haak et al, 2015) so that it would be easier to read it. It includes the old samples too, and a comparison to EHG and WHG.


Armenian 0.030
Baalberge_MN 0.054
Basque 0.034
BedouinB 0.060
Belarusian 0.020
Bell_Beaker_LN 0.016
BenzigerodeHeimburg_LN 0.013
Bergamo 0.028
Bulgarian 0.023
Corded_Ware_LN 0.011
Croatian 0.022
Czech 0.020
EHG 0.028
English 0.021
Estonian 0.020
French 0.022
Greek 0.026
Han 0.118
Hungarian 0.020
HungaryGamba_BA 0.023
HungaryGamba_EN 0.050
Icelandic 0.020
Iraqi_Jew 0.037
Karitiana 0.204
LBK_ 0.052
Lezgin 0.019
Lithuanian 0.022
Mala 0.056
Mordovian 0.018
Motala_HG 0.063
Norwegian 0.021
Onge 0.178
Orcadian 0.022
Papuan 0.197
Russian 0.019
Sardinian 0.044
Sicilian 0.030
Sindhi 0.028
Spain_EN 0.060
Spain_MN 0.053
Spanish 0.027
SwedenSkoglund_NHG 0.062
Turkish 0.026
Unetice_EBA 0.012
WHG 0.076


The 10 closest modern groups to Yamnaya:


1-Mordovian 0.018
2-Lezgian/Russian 0.019
3- Czech/Belarusian/Estonian/Hungarian/Icelandic 0.020
4-Norwegian/English 0.021
5-Croatian/French/Lithuanian/Orcadian 0.022
6- Bulgarian 0.023
7- Greek/Turkish 0.026
8-Spanish 0.027
9- Sindhi/Bergamo 0.028
10- Armenian/Sicilian 0.030

Including the ancient samples:


1-Corded_Ware_LN 0.011
2-Unetice_EBA 0.012
3-BenzigerodeHeimburg 0.013
4-Bell_Beaker_LN 0.016
5-Mordovian 0.018
6-Lezgian/Russian 0.019
7-Czech/Belarusian/Estonian/Hungarian/Icelandic 0.020
8-Norwegian/English 0.021
9-Croatian/French/Lithuanian/Orcadian 0.022
10-Bulgarian 0.023

Silesian
02-16-2015, 12:32 AM
I ordered the table provided on the page 26 of the recent study on them (Haak et al, 2015) so that it would be easier to read it. It includes the old samples too, and a comparison to EHG and WHG. ...............


1-Mordovian 0.018
2-Lezgian/Russian 0.019
3- Czech/Belarusian/Estonian/Hungarian/Icelandic 0.020
4-Norwegian/English 0.021
5-Croatian/French/Lithuanian/Orcadian 0.022
6- Bulgarian 0.023
7- Greek/Turkish 0.026
8-Spanish 0.027
9- Sindhi/Bergamo 0.028
10- Armenian/Sicilian 0.030

Just out of curiosity and off the top of my head all the areas highlighted in red you can find [Yamnaya]R1b-Z2103 for whatever reason.

newtoboard
02-16-2015, 12:59 AM
Out of curiosity why do the Sindhi show up? Among south asian and central asian groups Tajiks, Pamiris, Pashtuns, Burusho, dardic speakers (including the Kalash), Nuristanis, Kashmiris, Punjabis should al be higher up.

Piquerobi
02-16-2015, 01:00 AM
Out of curiosity why do the Sindhi show up? Among south asian and central asian groups Tajiks, Pamiris, Pashtuns, Burusho, dardic speakers (including the Kalash), Nuristanis, Kashmiris, Punjabis should al be higher up.

The results are out of the samples they have. It would have been interesting if they had collected samples from Kashmir, Punjab, and other places. But they have not.

Piquerobi
02-16-2015, 12:02 PM
Including the ancient samples:
1-Corded_Ware_LN 0.011
2-Unetice_EBA 0.012
3-BenzigerodeHeimburg 0.013
4-Bell_Beaker_LN 0.016
5-Mordovian 0.018
6-Lezgian/Russian 0.019
7-Czech/Belarusian/Estonian/Hungarian/Icelandic 0.020
8-Norwegian/English 0.021
9-Croatian/French/Lithuanian/Orcadian 0.022
10-Bulgarian 0.023


They list Benzingerode-Heimburg culture as Bell Beaker:

I0059 Bell Beaker? LN Benzingerode-Heimburg, Germany; BZH6, grave 2, feature/find 1287/1036 2286-2153 cal BCE (MAMS 21486) Germany F H1 /H1b'ad 241081
I0058 BenzigerodeHeimburg_LN Bell Beaker LN Benzingerode-Heimburg, Germany; BZH4, grave 7, feature 4607 2283-2146 cal BCE (MAMS 21491) Germany F H1e 246728
I0171 BenzigerodeHeimburg_LN Bell Beaker?

Shaikorth
02-16-2015, 12:13 PM
The results are out of the samples they have. It would have been interesting if they had collected samples from Kashmir, Punjab, and other places. But they have not.

They have samples from many more Caucasus and S-C Asian groups but decided to include just a few non-European populations in the fst-comparison.

rms2
02-16-2015, 12:34 PM
Very nice work.

It's especially interesting to me to see where Beaker falls.



1-Corded_Ware_LN 0.011
2-Unetice_EBA 0.012
3-BenzigerodeHeimburg 0.013
4-Bell_Beaker_LN 0.016
5-Mordovian 0.018
6-Lezgian/Russian 0.019
7-Czech/Belarusian/Estonian/Hungarian/Icelandic 0.020
8-Norwegian/English 0.021
9-Croatian/French/Lithuanian/Orcadian 0.022
10-Bulgarian 0.023

parasar
02-18-2015, 07:39 PM
Out of curiosity why do the Sindhi show up? Among south asian and central asian groups Tajiks, Pamiris, Pashtuns, Burusho, dardic speakers (including the Kalash), Nuristanis, Kashmiris, Punjabis should al be higher up.

They have the data for the others from Moorjani, but used only a subset.
Their stat showing inflow into the Armenians was most negative using Sindhis.

However, the lowest Z-score of statistics of the form f3(Armenian; X, Y) involves the (X, Y) = (LBK_EN, Sindhi) pair (value -0.00575, Z=-15.3), so the signal of admixture from the Yamnaya is not the strongest one for Armenians. Moreover, as shown in SI 7, the Yamnaya have a negative f3-statistic with (X, Y) = (Karelia_HG, Armenian). A negative statistic for both Armenians and Yamnaya with each other as a reference population may suggest that a third (unsampled) population admixed into both the Yamnaya and to Armenians.


It would be interesting to see if Pakhtoons would give even a higher negative stat! The inflow into the Armenians then could even be from a historical period.
Herodotus posits that the origin of Armenians was from the Balkans via Anatolia, but also puts an odd people near them - the Pactyans.

Herodotus has two nations of Pactyans, one inhabiting a portion of Armenia, and the other adjoining upon India...


https://books.google.com/books?id=bKICAAAAQAAJ&pg=PA207

MasterRoshi
02-20-2015, 11:46 PM
They have samples from many more Caucasus and S-C Asian groups but decided to include just a few non-European populations in the fst-comparison.

To be honest I smell Eurocentrism in this decisionl. I can't explain otherwise why you wouldn't include non European populations who would obviously appear as close to Yamna as most Europeans.

newtoboard
02-21-2015, 12:14 AM
To be honest I smell Eurocentrism in this decisionl. I can't explain otherwise why you wouldn't include non European populations who would obviously appear as close to Yamna as most Europeans.

I wouldn't go as far as accuse them of having an agenda but it does seem to be strange to include the most southern group in NW South Asia. Punjabis, Kashmiris, Pahari speakers, Dardic speakers, Pashtuns, the Nuristanis, Pamiris, and Tajiks would have all been better choices. Also seems weird to include Armenians but somehow leave out Ossetians, Kurds, and Iranians. I think it was just a poor choice. But yea we should expect to see those groups much higher on the list.

Arbogan
02-21-2015, 11:03 AM
I wouldn't go as far as accuse them of having an agenda but it does seem to be strange to include the most southern group in NW South Asia. Punjabis, Kashmiris, Pahari speakers, Dardic speakers, Pashtuns, the Nuristanis, Pamiris, and Tajiks would have all been better choices. Also seems weird to include Armenians but somehow leave out Ossetians, Kurds, and Iranians. I think it was just a poor choice. But yea we should expect to see those groups much higher on the list.

Well some geneticists do seem to have preconceived intellectual ideation that christian-ethnic groups in middle-east are somehow the only resvoir of ancient middle-east, meanwhile everyone else is diluted and admixed. I see that idea coming up whenever I see the name pierre zalloua listed in genetic studies. As much as I like to imagine otherwise, most studies do have a research bias. It's ludicrous that you'd include iraqi-jews in this study but disclude populations with obvious cultural/linguistic links to pontic steppe peoples. It's almost deliberate neglect on their part.

newtoboard
02-21-2015, 03:58 PM
Well some geneticists do seem to have preconceived intellectual ideation that christian-ethnic groups in middle-east are somehow the only resvoir of ancient middle-east, meanwhile everyone else is diluted and admixed. I see that idea coming up whenever I see the name pierre zalloua listed in genetic studies. As much as I like to imagine otherwise, most studies do have a research bias. It's ludicrous that you'd include iraqi-jews in this study but disclude populations with obvious cultural/linguistic links to pontic steppe peoples. It's almost deliberate neglect on their part.

You know what is funny though? A South Asian ethnic group with significant South Eurasian ancestry is closer to the Yamnaya samples than Armenians and Sicilians. This means modern Indo-Iranian speakers likely do have a good amount of Yamnaya ancestry for them to be higher up that list than any West Asian or European group and not that much more distant from quite a few other groups.

I think West Asians, Central Asians, NW South Asians will be similarly close to Yamnaya. West Asians likely have less Yamnaya ancestry but Central Asian and NW South Asian groups should have East Eurasian and South Eurasian ancestry pushing them away from Yamnaya. We will have to wait and see though.

newtoboard
02-21-2015, 04:01 PM
Well some geneticists do seem to have preconceived intellectual ideation that christian-ethnic groups in middle-east are somehow the only resvoir of ancient middle-east, meanwhile everyone else is diluted and admixed. I see that idea coming up whenever I see the name pierre zalloua listed in genetic studies. As much as I like to imagine otherwise, most studies do have a research bias. It's ludicrous that you'd include iraqi-jews in this study but disclude populations with obvious cultural/linguistic links to pontic steppe peoples. It's almost deliberate neglect on their part.

If that bias does exist it is pretty funny especially given the long history of the Roman Empire, Ottoman Empires, the known migrations of Greeks, and the Crusades. They likely have more recent admixture.

parasar
02-24-2015, 07:06 PM
I wouldn't go as far as accuse them of having an agenda but it does seem to be strange to include the most southern group in NW South Asia. Punjabis, Kashmiris, Pahari speakers, Dardic speakers, Pashtuns, the Nuristanis, Pamiris, and Tajiks would have all been better choices. Also seems weird to include Armenians but somehow leave out Ossetians, Kurds, and Iranians. I think it was just a poor choice. But yea we should expect to see those groups much higher on the list.

While yes, I too would have liked to see more populations, especially the Kalash, Burusho, Brahui, and Baloch who are off the Indian cline, but Sindhi should serve our purpose as they have lot of ANI ("18 groups that formed tight clusters along the Indian Cline, and included the Pathan and Sindhi" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/table/T2/ ), plus hopefully the Sindhi are not prone to small population artifacts.

ADW_1981
02-24-2015, 07:22 PM
If that bias does exist it is pretty funny especially given the long history of the Roman Empire, Ottoman Empires, the known migrations of Greeks, and the Crusades. They likely have more recent admixture.

Crusades vs Muslim conquest? No comparison whatsoever. It's like saying an apple and an orange are the same fruit.

newtoboard
02-24-2015, 11:40 PM
Crusades vs Muslim conquest? No comparison whatsoever. It's like saying an apple and an orange are the same fruit.

What is more like an apple of orange is what I said and what you think I said. I said it was silly to leave out Iranians, Kurds, and Ossetians out (ie Indo-European and Indo-Iranian speakers) because of some possible bias that they have more recent admixture than Christian groups because of their most Islamic faith (of course non muslim Iranians, Kurds, and Ossetians exist as well).

You know what else is like an apple and an orange? The amount of geneflow Muslim conquest contributed to the Levant/Anatolia vs the amount that it contributed to the Kurdistan and the Iranian plateau. No need for those conquests and their resulting changes on the native population to be mentioned in the same breath.

newtoboard
02-24-2015, 11:43 PM
While yes, I too would have liked to see more populations, especially the Kalash, Burusho, Brahui, and Baloch who are off the Indian cline, but Sindhi should serve our purpose as they have lot of ANI ("18 groups that formed tight clusters along the Indian Cline, and included the Pathan and Sindhi" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/table/T2/ ), plus hopefully the Sindhi are not prone to small population artifacts.

ANI just means whatever West Eurasian ancestry. Why are we still using the term when we know ANI in one place is not the same as in another place. It is pretty clear that the ANE/WHG or EHG components that dominated among Yamnaya and HGs from Eastern Europe will have their South Asian peaks in more Northern groups whereas the Basal Eurasian or ENF peak will be among more southern groups like the Sindhis.

parasar
02-24-2015, 11:54 PM
ANI just means whatever West Eurasian ancestry. Why are we still using the term when we know ANI in one place is not the same as in another place. It is pretty clear that the ANE/WHG or EHG components that dominated among Yamnaya and HGs from Eastern Europe will have their South Asian peaks in more Northern groups whereas the Basal Eurasian or ENF peak will be among more southern groups like the Sindhis.

Ancestral ANI is West Eurasian.
ANI is a mix which is the mystery input into Yamna.

newtoboard
02-25-2015, 12:03 AM
Ancestral ANI is West Eurasian.
ANI is a mix which is the mystery input into Yamna.

No. Just no. Please tell me how West Eurasian ancestry arrived In Eastern Europe from South Asia without any South Eurasian ancestry. I am one of the few to think West Eurasian components (associated with y H and mt R/U) were in South Asia first and South Eurasian components arrived later (primarily with mt M but also y O) but there is no doubt South Eurasian ancestry was present in South Asia in the Neolithic. That is way too late.

And how could ANI contribute to Yamnaya ancestry when it is likely ANI is composed heavily of Yamnaya ancestry. ANI is such an primitive concept to use in population genetics at this point especially since we know what i breaks down into (I would argue that the old Northern European, West Asian, Mediterranean and SW Asian breakdown isn't very valuable either although to a lesser degree).

The mystery input into Yamnaya will likely just be a population from the Caucasus or less likely, a population from the East Caspian.

parasar
02-25-2015, 01:34 AM
No. Just no. Please tell me how West Eurasian ancestry arrived In Eastern Europe from South Asia without any South Eurasian ancestry. I am one of the few to think West Eurasian components (associated with y H and mt R/U) were in South Asia first and South Eurasian components arrived later (primarily with mt M but also y O) but there is no doubt South Eurasian ancestry was present in South Asia in the Neolithic. That is way too late.

And how could ANI contribute to Yamnaya ancestry when it is likely ANI is composed heavily of Yamnaya ancestry. ANI is such an primitive concept to use in population genetics at this point especially since we know what i breaks down into (I would argue that the old Northern European, West Asian, Mediterranean and SW Asian breakdown isn't very valuable either although to a lesser degree).

The mystery input into Yamnaya will likely just be a population from the Caucasus or less likely, a population from the East Caspian.

The south or likely east Eurasian input is very old (splitting from ASI 1700 generations back and entering ancestral ANI+W. Eurasian 600 generations back).

"600 gens ago Gene flow from ‘proto-East Asia’ into the ancestral population of ANI and West Eurasians"
http://genetics.med.harvard.edu/reich/Reich_Lab/Publications_files/2009_Nature_Reich_India_Supplementary.pdf
http://www.gnxp.com/blog/uploaded_images/indiaMODEL-783101.png

As far as the southern South Asian admixture is concerned, that had not yet admixed into ANI. That happened earliest 4200ybp and for some populations such as northern Indian Brahmans just a couple of thousand years back which implies that as late as ~1900ybp potentially there was an un-admixed ANI population.
http://www.sciencedirect.com/science/article/pii/S0002929713003248

Our analysis documents major mixture between populations in India that occurred 1,900–4,200 years BP, well after the establishment of agriculture in the subcontinent. We have further shown that groups with unmixed ANI and ASI ancestry were plausibly living in India until this time.


As far as proximate input into Yamna, of your two choices, east of Caspian and the Caucasus, IMO the former is very likely and the latter highly unlikely.

Sein
02-25-2015, 04:27 AM
You know what is funny though? A South Asian ethnic group with significant South Eurasian ancestry is closer to the Yamnaya samples than Armenians and Sicilians. This means modern Indo-Iranian speakers likely do have a good amount of Yamnaya ancestry for them to be higher up that list than any West Asian or European group and not that much more distant from quite a few other groups.

I think West Asians, Central Asians, NW South Asians will be similarly close to Yamnaya. West Asians likely have less Yamnaya ancestry but Central Asian and NW South Asian groups should have East Eurasian and South Eurasian ancestry pushing them away from Yamnaya. We will have to wait and see though.

For what it's worth, I quickly collated fst results from the paper, for the HGDP Sindhi population.

1) Turkish=0.013
2) Lezgin, Mala=0.014 (HGDP Pashtun vs Lezgin=0.010, HGDP Pashtun vs Mala=0.017)
3) Armenian=0.016 (HGDP Pashtun=0.012)
4) Bulgarian, Greek, Iraqi_Jew=0.020
5) Russian, Hungarian, Mordovian, Sicilian=0.021 (HGDP Pashtun vs Russian=0.016).
6) Croatian, Czech, French=0.022 (HGDP Pashtun vs French=0.018)
7) Belarusian, Bergamo, English=0.023
8) Unetice_EBA, Norwegian, Spanish=0.024
9) Estonian, Icelandic=0.025
10) Bell_Beaker_LN, Orcadian=0.026
11) HungaryGamba_BA=0.027
12) Yamnaya, BenzigerodeHeimburg_LN, Lithuanian=0.028
13) Corded_Ware_LN=0.029
14) Basque=0.032
15) Sardinian=0.035 (HGDP Pashtun=0.031)
16) HungaryGamba_EN=0.042
17) BedouinB=0.043 (HGDP Pashtun=0.038)
18) Baalberge_MN=0.047
19) LBK_EN=0.049
20) Spain_MN=0.052
21) EHG=0.057
22) Spain_EN=0.058
23) SwedenSkoglund_NHG=0.074
24) Han=0.081 (HGDP Pashtun=0.082)
25) WHG=0.087
26) Motala_HG=0.088
27) Yoruba=0.133 (HGDP Pashtun=0.141)
28) Onge=0.142
29) Papuan=0.162 (HGDP Pashtun=0.166)

I checked the Sindhi fst distances found in Metspalu et al., and I can't see any real differences when it comes down to the same populations (for example, Sindhi vs Han fst is 0.081 in both papers). So, I added the HGDP Pashtun results from Metspalu et al., to compare with the Sindhis. I modified a few numbers for the HGDP Pashtuns when distances weren't perfectly identical between papers, in relation to the Sindhis (with the Mala, I looked at the difference between Sindhis and South Indian groups, in relation to the HGDP Pashtuns).

Be that as it may, the Sindhis are very close to all West Eurasian groups, and obviously closest to people from the Caucasus/northern West Asia.

Hando
02-25-2015, 11:28 AM
The south or likely east Eurasian input is very old (splitting from ASI 1700 generations back and entering ancestral ANI+W. Eurasian 600 generations back).

"600 gens ago Gene flow from ‘proto-East Asia’ into the ancestral population of ANI and West Eurasians"
http://genetics.med.harvard.edu/reich/Reich_Lab/Publications_files/2009_Nature_Reich_India_Supplementary.pdf
http://www.gnxp.com/blog/uploaded_images/indiaMODEL-783101.png

As far as the southern South Asian admixture is concerned, that had not yet admixed into ANI. That happened earliest 4200ybp and for some populations such as northern Indian Brahmans just a couple of thousand years back which implies that as late as ~1900ybp potentially there was an un-admixed ANI population.
http://www.sciencedirect.com/science/article/pii/S0002929713003248


As far as proximate input into Yamna, of your two choices, east of Caspian and the Caucasus, IMO the former is very likely and the latter highly unlikely.

I'm still having a really hard time understanding the whole ASI ANI split. What confuses me is the use of Europe Asia split at the top and then proto-East Asia and Proto Europe below. Why are Europe and Asia splitting more than once?

Kurd
02-25-2015, 12:04 PM
For what it's worth, I quickly collated fst results from the paper, for the HGDP Sindhi population.

1) Turkish=0.013
2) Lezgin, Mala=0.014 (HGDP Pashtun vs Lezgin=0.010, HGDP Pashtun vs Mala=0.017)
3) Armenian=0.016 (HGDP Pashtun=0.012)
4) Bulgarian, Greek, Iraqi_Jew=0.020
5) Russian, Hungarian, Mordovian, Sicilian=0.021 (HGDP Pashtun vs Russian=0.016).
6) Croatian, Czech, French=0.022 (HGDP Pashtun vs French=0.018)
7) Belarusian, Bergamo, English=0.023
8) Unetice_EBA, Norwegian, Spanish=0.024
9) Estonian, Icelandic=0.025
10) Bell_Beaker_LN, Orcadian=0.026
11) HungaryGamba_BA=0.027
12) Yamnaya, BenzigerodeHeimburg_LN, Lithuanian=0.028
13) Corded_Ware_LN=0.029
14) Basque=0.032
15) Sardinian=0.035 (HGDP Pashtun=0.031)
16) HungaryGamba_EN=0.042
17) BedouinB=0.043 (HGDP Pashtun=0.038)
18) Baalberge_MN=0.047
19) LBK_EN=0.049
20) Spain_MN=0.052
21) EHG=0.057
22) Spain_EN=0.058
23) SwedenSkoglund_NHG=0.074
24) Han=0.081 (HGDP Pashtun=0.082)
25) WHG=0.087
26) Motala_HG=0.088
27) Yoruba=0.133 (HGDP Pashtun=0.141)
28) Onge=0.142
29) Papuan=0.162 (HGDP Pashtun=0.166)

I checked the Sindhi fst distances found in Metspalu et al., and I can't see any real differences when it comes down to the same populations (for example, Sindhi vs Han fst is 0.081 in both papers). So, I added the HGDP Pashtun results from Metspalu et al., to compare with the Sindhis. I modified a few numbers for the HGDP Pashtuns when distances weren't perfectly identical between papers, in relation to the Sindhis (with the Mala, I looked at the difference between Sindhis and South Indian groups, in relation to the HGDP Pashtuns).

Be that as it may, the Sindhis are very close to all West Eurasian groups, and obviously closest to people from the Caucasus/northern West Asia.

Any idea where Iranians or Kurds would fit into the stack (vs. Sindhi population)

Shaikorth
02-25-2015, 12:24 PM
Any idea where Iranians or Kurds would fit into the stack (vs. Sindhi population)

They would probably top the list, I assume they are closer to Sindhi than Anatolian Turks and Lezgins.

Augustus
02-25-2015, 09:17 PM
Has anyone considered the possibility that West Yamnaya might be somewhat similar but still noticeably different from Samara autosomally speaking? I personally think the Yamnaya component is overstated in these samples, and they're probably mixing up WHG and ANE from Eastern Europe as Yamna.

Also, the Cucuteni culture might be representative of later neolithic farming migrations with "recent" middle eastern DNA.

R.Rocca
02-25-2015, 09:32 PM
Has anyone considered the possibility that West Yamnaya might be somewhat similar but still noticeably different from Samara autosomally speaking? I personally think the Yamnaya component is overstated in these samples, and they're probably mixing up WHG and ANE from Eastern Europe as Yamna.

Also, the Cucuteni culture might be representative of later neolithic farming migrations with "recent" middle eastern DNA.

The likelihood of Western Yamnaya being similar to Samara is likely quite high considering that the Samara Yamnaya already had farmer mixture. I don't see how one can think that the Yamnaya component is overstated when the authors of the paper ran ADMIXTURE analysis. The beauty of programs like ADMIXTURE is they take personal feelings and biases out of the equation. Furthermore, they will release the raw data and would be lambasted and if they fudged it.

Augustus
02-25-2015, 09:47 PM
I'm talking about the way they calculate Yamnaya component. Don't forget Northern and Western Europe were mostly WHG just a year ago, until they changed it up with this paper.

lgmayka
02-26-2015, 12:46 AM
Has anyone considered the possibility that West Yamnaya might be somewhat similar but still noticeably different from Samara autosomally speaking? I personally think the Yamnaya component is overstated in these samples, and they're probably mixing up WHG and ANE from Eastern Europe as Yamna.
I have suggested that, but in the opposite direction. Various posters are hypothesizing that the Yamnaya horizon included a region of R1b-Z2103 concentration (the one tested and described in the published paper), a region of R1b-L51 concentration, and a region of R1a-M417 concentration. My own hypothesis is that these three regions may be slightly different autosomally, so that comparisons only with the R1b-Z2103 region do not fully capture the breadth of Yamnaya's influence.

Let's hypothesize that Corded Ware was primarily R1a-M417. Let's also say that the next aDNA investigation of Yamnaya happens to hit its R1a-M417 region. Then according to my hypothesis, Corded Ware will appear to be more than 75% R1a-Yamnaya.

newtoboard
02-26-2015, 12:55 AM
I have suggested that, but in the opposite direction. Various posters are hypothesizing that the Yamnaya horizon included a region of R1b-Z2103 concentration (the one tested and described in the published paper), a region of R1b-L51 concentration, and a region of R1a-M417 concentration. My own hypothesis is that these three regions may be slightly different autosomally, so that comparisons only with the R1b-Z2103 region do not fully capture the breadth of Yamnaya's influence.

Let's hypothesize that Corded Ware was primarily R1a-M417. Let's also say that the next aDNA investigation of Yamnaya happens to hit its R1a-M417 region. Then according to my hypothesis, Corded Ware will appear to be more than 75% R1a-Yamnaya.

Why should R1a-Z93+ and R1a-Z282+ have no separation?

parasar
02-26-2015, 01:18 AM
I'm still having a really hard time understanding the whole ASI ANI split. What confuses me is the use of Europe Asia split at the top and then proto-East Asia and Proto Europe below. Why are Europe and Asia splitting more than once?

It looks complex because there are multiple back and forth even under this simple model!

The first split is African YRI about 4000 generations back though obviously we have had crossovers since then.

Among non-Africans, even under a simplistic ancestral ANI and ancestral ASI split (2000 generations back) scenario, we have a prong Cp splitting from the ASI side (1700 generations back) and merging into the ancestral ANI side about 600 generations back. An then that combination of ancestral ANI Ep and Cp splits into ANI and Adygei about 400 generations back, and the ANI part merges into ASI about 200 generations back.

R.Rocca
02-26-2015, 02:03 AM
I have suggested that, but in the opposite direction. Various posters are hypothesizing that the Yamnaya horizon included a region of R1b-Z2103 concentration (the one tested and described in the published paper), a region of R1b-L51 concentration, and a region of R1a-M417 concentration. My own hypothesis is that these three regions may be slightly different autosomally, so that comparisons only with the R1b-Z2103 region do not fully capture the breadth of Yamnaya's influence.

Let's hypothesize that Corded Ware was primarily R1a-M417. Let's also say that the next aDNA investigation of Yamnaya happens to hit its R1a-M417 region. Then according to my hypothesis, Corded Ware will appear to be more than 75% R1a-Yamnaya.

This I agree with this, that there will be an R1a pocket that will plot even closer to another area of Yamnaya. If I had to guess, it would be closer to the north/north-west part of the Forest-Steppe...

http://biomodel.info/wp-content/uploads/2009/11/Forest-steppe_ua.png

Sein
02-26-2015, 03:19 AM
Any idea where Iranians or Kurds would fit into the stack (vs. Sindhi population)

I think Shaikorth is right, Iranians or Kurds would definitely top the list. Based on the results provided in Metspalu et al., Sindhi vs Iranian fst is 0.009.

jesus
02-26-2015, 05:19 AM
For what it's worth, I quickly collated fst results from the paper, for the HGDP Sindhi population.

1) Turkish=0.013
2) Lezgin, Mala=0.014 (HGDP Pashtun vs Lezgin=0.010, HGDP Pashtun vs Mala=0.017)
3) Armenian=0.016 (HGDP Pashtun=0.012)
4) Bulgarian, Greek, Iraqi_Jew=0.020
5) Russian, Hungarian, Mordovian, Sicilian=0.021 (HGDP Pashtun vs Russian=0.016).
6) Croatian, Czech, French=0.022 (HGDP Pashtun vs French=0.018)
7) Belarusian, Bergamo, English=0.023
8) Unetice_EBA, Norwegian, Spanish=0.024
9) Estonian, Icelandic=0.025
10) Bell_Beaker_LN, Orcadian=0.026
11) HungaryGamba_BA=0.027
12) Yamnaya, BenzigerodeHeimburg_LN, Lithuanian=0.028
13) Corded_Ware_LN=0.029
14) Basque=0.032
15) Sardinian=0.035 (HGDP Pashtun=0.031)
16) HungaryGamba_EN=0.042
17) BedouinB=0.043 (HGDP Pashtun=0.038)
18) Baalberge_MN=0.047
19) LBK_EN=0.049
20) Spain_MN=0.052
21) EHG=0.057
22) Spain_EN=0.058
23) SwedenSkoglund_NHG=0.074
24) Han=0.081 (HGDP Pashtun=0.082)
25) WHG=0.087
26) Motala_HG=0.088
27) Yoruba=0.133 (HGDP Pashtun=0.141)
28) Onge=0.142
29) Papuan=0.162 (HGDP Pashtun=0.166)

I checked the Sindhi fst distances found in Metspalu et al., and I can't see any real differences when it comes down to the same populations (for example, Sindhi vs Han fst is 0.081 in both papers). So, I added the HGDP Pashtun results from Metspalu et al., to compare with the Sindhis. I modified a few numbers for the HGDP Pashtuns when distances weren't perfectly identical between papers, in relation to the Sindhis (with the Mala, I looked at the difference between Sindhis and South Indian groups, in relation to the HGDP Pashtuns).

Be that as it may, the Sindhis are very close to all West Eurasian groups, and obviously closest to people from the Caucasus/northern West Asia.

HGDP Pashtuns seem to be 0.004 closer to Lezgians/Armenians/French/Sardinian than Sindhis. The distance between Yamnaya and Sindhis is 0.0028, that would probably mean that the distance between HGDP Pashtuns and Yamnaya is around 0.0024.

Sein
02-26-2015, 07:40 AM
HGDP Pashtuns seem to be 0.004 closer to Lezgians/Armenians/French/Sardinian than Sindhis. The distance between Yamnaya and Sindhis is 0.0028, that would probably mean that the distance between HGDP Pashtuns and Yamnaya is around 0.0024.

That seems very reasonable.

If so, the HGDP Pashtuns are about as close to Yamnaya as the Orcadian, French, Bulgarian, Croatian, and HungaryGamba_BA populations are to Yamnaya (which is striking, considering the lack of WHG among the HGDP Pashtuns).

Arbogan
02-26-2015, 07:02 PM
That seems very reasonable.

If so, the HGDP Pashtuns are about as close to Yamnaya as the Orcadian, French, Bulgarian, Croatian, and HungaryGamba_BA populations are to Yamnaya (which is striking, considering the lack of WHG among the HGDP Pashtuns).

Probably closer than 0.24. They haven't added pamirs or tajiks.

newtoboard
02-27-2015, 12:41 AM
This I agree with this, that there will be an R1a pocket that will plot even closer to another area of Yamnaya. If I had to guess, it would be closer to the north/north-west part of the Forest-Steppe...

http://biomodel.info/wp-content/uploads/2009/11/Forest-steppe_ua.png

It seems strange that most of us are expecting both R1a and R1b pockets to be so separated from each other.

Augustus
02-27-2015, 12:55 AM
No signs of R1a and R1b together so far occuring in ancient sites.

A question I have is when did Yamna go from pastoralists and hunter gatherers to warriors?

newtoboard
02-27-2015, 01:03 AM
No signs of R1a and R1b together so far occuring in ancient sites.

A question I have is when did Yamna go from pastoralists and hunter gatherers to warriors?

If you mean charioteers (warriors) then sometime after the chariot was invented in Asia. There is a map about the diffusion of the chariot that can be found on the internet.

Augustus
02-27-2015, 01:04 AM
Well that and adopting bronze weapons. All the steppe and Russian samples appear primitive so far.

Megalophias
02-27-2015, 01:09 AM
A question I have is when did Yamna go from pastoralists and hunter gatherers to warriors?

Well, they were "warriors" all along, like most people on the planet. Could you clarify what you are asking?

Chariots were not invented until after Yamnaya (as far as is known).

Augustus
02-27-2015, 04:47 AM
It's interesting that in the paper, there are non-R, non-steppe-Y-Dna bearing (presumably), central European folks who have the autosomal Yamna component. Even Otzi had some, and the Hungary samples had them as well.

I'm wondering how they were able to obtain the Yamna autosomal component without it being reflected to Y-Dna, since the Corded Ware culture was a foreign imposed one, and largely replaced people, rather than intermingled gently.

parasar
03-07-2015, 10:15 PM
Posted by Sergey at Eurogenes blog:
Yamnaya IBD map http://s019.radikal.ru/i606/1503/2d/e97903629173.png
http://s019.radikal.ru/i606/1503/2d/e97903629173.png

Srkz said...
BR2 77,11 ---//Confidence: very low
Moksha 67,05 ---//Confidence: low
Estonian 64,63 ---//Confidence: high
German 63,96 ---//Confidence: medium
Finnish 63,93 ---//Confidence: low
Balt 63,66 ---//Confidence: high
Swedish 63,16 ---//Confidence: high
Kosovar 62,21 ---//Confidence: medium
Ukrainian-East-and-Center 61,45 ---//Confidence: high
Russian-West 60,92 ---//Confidence: very high
Croatian 58,96 ---//Confidence: very high
Udmurt 58,96 ---//Confidence: high
Russian-North-Kargopol 58,86 ---//Confidence: very high
Ukrainian-West-and-Center 58,48 ---//Confidence: high
Norwegian 57,6 ---//Confidence: high
Russian-South 57,14 ---//Confidence: very high
Hungarian 56,87 ---//Confidence: very high
Belarusian 56,64 ---//Confidence: very high
British 55,98 ---//Confidence: very high
Chechen 55,85 ---//Confidence: very high
Karelian 55,53 ---//Confidence: high
Tatar-Volga 55,53 ---//Confidence: high
Russian-North-East 54,99 ---//Confidence: very high
Greek_Azov 54,58 ---//Confidence: low
Veps 54,14 ---//Confidence: medium
Tatar-Crimean 53,56 ---//Confidence: low
Polish 53,08 ---//Confidence: very high
Erzya 52,91 ---//Confidence: medium
Bosnian 51,94 ---//Confidence: medium
Adygei 51,29 ---//Confidence: high
French 51,29 ---//Confidence: very high
Italian 50,92 ---//Confidence: very high
Komi 50,89 ---//Confidence: high
Balkarian 49,52 ---//Confidence: very high
Macedonian 49,13 ---//Confidence: medium
Gagauz 48,62 ---//Confidence: medium
Bulgarian 48,55 ---//Confidence: high
Chuvash 48,54 ---//Confidence: very high
Serbian 48,42 ---//Confidence: high
Uttar-Pradesh-HC 48,26 ---//Confidence: high
Ashkenazi 47,61 ---//Confidence: high
Spanish 47,58 ---//Confidence: very high
Kumyk 47,06 ---//Confidence: high
Lezgin 46,5 ---//Confidence: very high
Ossetian 46,33 ---//Confidence: high
Sicilian 46,26 ---//Confidence: very high
Abkhazian 46,26 ---//Confidence: very high
Nogay 46,25 ---//Confidence: high
Mari 46,14 ---//Confidence: high
Turkish 45,74 ---//Confidence: very high
Italian-South 45,22 ---//Confidence: high
Romanian 44,11 ---//Confidence: medium
Turkmen 43,4 ---//Confidence: very high
Montenegrian 42,92 ---//Confidence: medium
Greek 42,75 ---//Confidence: very high
Burusho 42,34 ---//Confidence: very high
Basque 42,26 ---//Confidence: very high
Saami 41,25 ---//Confidence: medium
Armenian 41,24 ---//Confidence: high
Syrian 40,37 ---//Confidence: high
Sindhi 39,74 ---//Confidence: very high
Kalash 39,67 ---//Confidence: very high
Tadjik 39,45 ---//Confidence: high
Uygur 39,13 ---//Confidence: medium
Uzbek 39,05 ---//Confidence: high
Pathan 38,99 ---//Confidence: very high
Bashkir 38,82 ---//Confidence: very high
Azerbaijani 38,74 ---//Confidence: high
Ust-Ishim 38,57 ---//Confidence: very low
Georgian 38,44 ---//Confidence: very high
Sephard 38,32 ---//Confidence: high
Iranian 38,32 ---//Confidence: very high
Balochi 37,46 ---//Confidence: very high
Sardinian 36,96 ---//Confidence: very high
Brahui 36,81 ---//Confidence: very high
Shor 35,77 ---//Confidence: very low
Kurd 35,39 ---//Confidence: low
Makrani 34,67 ---//Confidence: very high
Jordanian 34,14 ---//Confidence: very high
Yemenite 33,91 ---//Confidence: medium
Cypriot 33,19 ---//Confidence: medium
Tatar_Lithuanian 33,07 ---//Confidence: very low
Hazara 32,26 ---//Confidence: very high
Kanjar 32,07 ---//Confidence: low
Druze 32,02 ---//Confidence: very high
Mansi 31,98 ---//Confidence: low
Hakas 30,72 ---//Confidence: medium
Palestinian 30,6 ---//Confidence: very high
Gujarati 30,54 ---//Confidence: very high
Saud 30,3 ---//Confidence: very high
Kazah 30,02 ---//Confidence: high
Bedouin 29,33 ---//Confidence: very high
Uttar-Pradesh 29,12 ---//Confidence: very high
UAE 28,09 ---//Confidence: medium
Kirgiz 27,82 ---//Confidence: very high
Tunisian 27,16 ---//Confidence: medium
Selkup 25,93 ---//Confidence: high
Moroccan 25,82 ---//Confidence: very high
Altaian 25,6 ---//Confidence: high
Egyptian 25,57 ---//Confidence: medium
Ket 25,06 ---//Confidence: low
Andhra-Pradesh 24,81 ---//Confidence: medium
Kol 24,61 ---//Confidence: high
Dolgan 23,82 ---//Confidence: medium
Karnataka 23,48 ---//Confidence: medium
LBK 23,07 ---//Confidence: very low
Kalmyk 22,67 ---//Confidence: medium
Nenets 22,17 ---//Confidence: medium
Tamil-Nadu 21,21 ---//Confidence: high
Mongol 20,7 ---//Confidence: medium
NE1 19,73 ---//Confidence: very low
Loschbour 19,07 ---//Confidence: very low
Tuvinian 18,99 ---//Confidence: high
Maya 18,05 ---//Confidence: very high
Nivh 17,13 ---//Confidence: very low
Kerala 16,91 ---//Confidence: medium
Evenk 16,73 ---//Confidence: high
Yakut 15,65 ---//Confidence: very high
Buryat 15,11 ---//Confidence: very high
Nganassan 14,41 ---//Confidence: medium
Munda 14,37 ---//Confidence: very high
Burmese 14,26 ---//Confidence: high
Mongola 14,01 ---//Confidence: medium
Japanese 13,13 ---//Confidence: very high
Oroqen 13 ---//Confidence: low
Xibo 12,24 ---//Confidence: low
Even 12,17 ---//Confidence: medium
Naxi 11,71 ---//Confidence: low
Han-North 10,64 ---//Confidence: medium
Dai 10,56 ---//Confidence: low
Yi 10,55 ---//Confidence: low
Han 9,71 ---//Confidence: very high
Ethiopian 9,67 ---//Confidence: high
Karitiana 9,63 ---//Confidence: medium
Tu 9,54 ---//Confidence: low
She 9,34 ---//Confidence: medium
Tujia 9 ---//Confidence: medium
Lahu 8,41 ---//Confidence: low
Cambodian 8,09 ---//Confidence: medium
Naga 7,7 ---//Confidence: very low
Daur 6,84 ---//Confidence: low
Hezhen 6,81 ---//Confidence: low
Miao 6,76 ---//Confidence: medium
MbutiPygmy 5,82 ---//Confidence: very low
Melanesian 5,7 ---//Confidence: low
BiakaPygmy 4,4 ---//Confidence: very low
BantuKenia 4,36 ---//Confidence: low
Yoruba 3,76 ---//Confidence: low
Papuan 2,66 ---//Confidence: low

parasar
03-07-2015, 10:26 PM
Posted by Sergey at Eurogenes blog:
Yamnaya/Karelian_EHG difference
http://s018.radikal.ru/i513/1503/79/b6aac3f9e73f.png
http://s018.radikal.ru/i513/1503/79/b6aac3f9e73f.png

jesus
03-07-2015, 10:49 PM
[QUOTE=parasar;73207]Posted by Sergey at Eurogenes blog:
Yamnaya IBD map http://s019.radikal.ru/i606/1503/2d/e97903629173.png
http://s019.radikal.ru/i606/1503/2d/e97903629173.png

Syrian 40,37 ---//Confidence: high
Sindhi 39,74 ---//Confidence: very high
Kalash 39,67 ---//Confidence: very high
Tadjik 39,45 ---//Confidence: high
Uygur 39,13 ---//Confidence: medium
Uzbek 39,05 ---//Confidence: high
Pathan 38,99 ---//Confidence: very high
Bashkir 38,82 ---//Confidence: very high
Azerbaijani 38,74 ---//Confidence: high
Ust-Ishim 38,57 ---//Confidence: very low
Georgian 38,44 ---//Confidence: very high
Sephard 38,32 ---//Confidence: high
Iranian 38,32 ---//Confidence: very high
Balochi 37,46 ---//Confidence: very high
Sardinian 36,96 ---//Confidence: very high
Brahui 36,81 ---//Confidence: very high
Shor 35,77 ---//Confidence: very low
Kurd 35,39 ---//Confidence: low
Makrani 34,67 ---//Confidence: very high
Jordanian 34,14 ---//Confidence: very high
Yemenite 33,91 ---//Confidence: medium
Cypriot 33,19 ---//Confidence: medium/QUOTE]

Interesting that most Iranic speakers(Or people with a long history with Iranics like Azeris and Brahuis) have fairly similar results.

newtoboard
03-07-2015, 11:54 PM
Strange how Uttar-Pradesh-HC 48,26 ---//Confidence: high appears above many European, North Caucasian (Lazgin, Ossetian etc), Central Asian and NW South Asian groups.

parasar
03-08-2015, 02:08 AM
Strange how Uttar-Pradesh-HC 48,26 ---//Confidence: high appears above many European, North Caucasian (Lazgin, Ossetian etc), Central Asian and NW South Asian groups.

UP Brahmans were one the last ANI rich populations to mix with ASI - calculated at ~1885 years by Moorjani et al.
So perhaps less time to recombine.