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Aberdeen
07-06-14, 22:28
Eurogenes Blog has a link to an abstract relating to a discussion paper for an upcoming conference. The authors sequenced mtDNA but apparently not Y DNA, from a location that's part of the assumed IE homeland. The abstract reads as follows.

"Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppeDavid Reich 1 ,2, Nadin Rohland1 ,2, Swapan Mallick1 ,2, Iosif Lazaridis1, Eadaoin Harney1, Susanne Nordenfelt1, Qiaomei Fu3, Matthias Meyer3, Dorcas Brown4, David Anthony4, Nick Patterson2
1Harvard Medical School, Boston, MA, USA, 2Broad Institute of Harvard and MIT, Cambridge, MA, USA, 3Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 4Hartwick College, Oneonta, NY, USA
A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:


Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages."

LeBrok
07-06-14, 23:07
Eurogenes Blog has a link to an abstract relating to a discussion paper for an upcoming conference. The authors sequenced mtDNA but apparently not Y DNA, from a location that's part of the assumed IE homeland. The abstract reads as follows.

"Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppeDavid Reich 1 ,2, Nadin Rohland1 ,2, Swapan Mallick1 ,2, Iosif Lazaridis1, Eadaoin Harney1, Susanne Nordenfelt1, Qiaomei Fu3, Matthias Meyer3, Dorcas Brown4, David Anthony4, Nick Patterson2
1Harvard Medical School, Boston, MA, USA, 2Broad Institute of Harvard and MIT, Cambridge, MA, USA, 3Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 4Hartwick College, Oneonta, NY, USA
A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:
Great find Aberdeen.




Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.

Sweet. Nice to be right again about IE carrying ANE to the whole Europe. :) There was a thread we were discussion ANE incursion?





The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.



What is the area of Northwest Russia they point to?
[/QUOTE]Perhaps it means that Y N1c1 and Q were already in place up north. The East Eurasian down south came later in middle ages' migrations with Huns, Turks, Tatars and Mongols.
http://www.eupedia.com/images/content/East-Asian-admixture.gif



Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.


It looks more and more that the women are behind spreading farming. Farmer's women were taken into HGs societies, and this is how farming genes had spread. I'm wondering if farmers were trading/exchanging women with HGs or HGs/nomads were stealing them? With typical warrior mentality, "kill men - take women"?

Sile
07-06-14, 23:17
Great find Aberdeen.



Sweet. Nice to be right again about IE carrying ANE to the whole Europe. :) There was a thread we were discussion ANE incursion?


What is the area of Northwest Russia they point to?
[QUOTE]
Perhaps it means that Y N1c1 and Q were already in place up north. The East Eurasian down south came later in middle ages' migrations with Huns, Turks, Tatars and Mongols.
http://www.eupedia.com/images/content/East-Asian-admixture.gif






It looks more and more that the women are behind spreading farming. Farmer's women were taken into HGs societies, and this is how farming genes had spread. I'm wondering if farmers were trading/exchanging women with HGs or HGs/nomads were stealing them? With typical warrior mentality, "kill men - take women"?

Maybe you can nudge Maciano to produce his maps for the EEF, WHG and ANE ...............these seem to be the new flavor of the year in genetics


here is mine
EEF 69.21
WHG 20.20
ANE 10.59

Fire Haired14
07-06-14, 23:25
I Emailed David Reich who is one of the authors of the Ust-Ishmin paper and the will be paper on genome wide data from over 40 3,000-9,000YBP indviduals from Samara, Russia in yesterday.

This was his sresponse.


The Ust-Ishim paper is submitted to a journal and under review, while the other is still in preparation.

If anyone here knows how the academic world works please give an estimate of when each should be published. Since the Ust-Ishim paper is finished and under review in a journal(who would reject it?) i bet it'll be published soon.

Angela
08-06-14, 00:21
Thanks, Aberdeen. It will be interesting to see the exact proportions autosomally, and if and how they change over time.

It's great that they got complete mitochondrial results, unlike that very disappointing study on near eastern Neolithic mtDNA. I'm wondering why they didn't mention the yDNA. It would be nice if they managed to get some results.

Aberdeen
08-06-14, 01:34
[QUOTE=LeBrok;433431]Great find Aberdeen.

Sweet. Nice to be right again about IE carrying ANE to the whole Europe. :) There was a thread we were discussion ANE incursion?



[LIST]
What is the area of Northwest Russia they point to?[Quote]

The samples used for the current paper are apparently from somewhere near the banks of the Volga and Samara Rivers. The other study they refer to mentions a discontinuity between Mesolithic and later periods in Northwest Russia, presumably as a result of genetic inflow from Siberia, judging by the change in mtDNA types. An abstract for the other study can be found here.

www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296#pgen-1003296-g006 (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296#pgen-1003296-g006)

epoch
08-06-14, 10:35
[LIST]
What is the area of Northwest Russia they point to?
Perhaps it means that Y N1c1 and Q were already in place up north. The East Eurasian down south came later in middle ages' migrations with Huns, Turks, Tatars and Mongols.


Could they have meant these hunter-gatherers from Karelia? The contain mtDNA haplogroup C, common in Siberia.

http://www.anthrogenica.com/showthread.php?1420-Chronology-of-European-mtDNA/page7

LeBrok
08-06-14, 18:29
Maybe you can nudge Maciano to produce his maps for the EEF, WHG and ANE ...............these seem to be the new flavor of the year in genetics


here is mine
EEF 69.21
WHG 20.20
ANE 10.59
Indeed there are no maps yet, I'm surprised. I gave it a shot a while ago but data was missing for half of European countries.
Perhaps I can open a thread and collect self reporting numbers, and also collect what people report on other sites to fill voids.

6466

polako
09-06-14, 05:32
Indeed there are no maps yet, I'm surprised. I gave it a shot a while ago but data was missing for half of European countries.
Perhaps I can open a thread and collect self reporting numbers, and also collect what people report on other sites to fill voids.

6466


You can always run the EEF/WHG/ANE Excel test on these K13 averages.

https://drive.google.com/file/d/0B9o3EYTdM8lQY2c2RW5hUlNvNzg/edit?usp=sharing

Fire Haired14
09-06-14, 06:24
Indeed there are no maps yet, I'm surprised. I gave it a shot a while ago but data was missing for half of European countries.
Perhaps I can open a thread and collect self reporting numbers, and also collect what people report on other sites to fill voids.

6466

I have a results from all over Europe in an excel document(I'll put them into a public google spreadsheet today), plus you can calculate them straight from the Eurogenes K13 spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0Ato3EYTdM8lQdEUtZjRwTkQxRzBCeHdTaTdWUUY4Z 0E#gid=0). It would be very interesting to see an accurate map of EEF, WHG, ANE percentages. You can probably find an accurate way to find show east Asian and Sub Saharan ancestry percentages, and then subtract them from EEF, WHG, ANE percentages.