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Angela
03-03-17, 06:08
See:
http://www.biorxiv.org/content/early/2017/03/02/112714?%3Fcollection=

Extensive farming in Estonia started through a sex-biased migration from the Steppe
"Farming-based economies appear relatively late in Northeast Europe and the extent to which they involve genetic ancestry change is still poorly understood. Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry, but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry."

Well, that should clarify things quite a bit from whatever confusion came out of the Latvian paper. Interesting also that Comb Ceramic was EHG like. It's nice to see the X included, and it seems to be Anatolian farmer.

"The first signs of crop cultivation in Estonia appeared 6,000 yr BP, 2000 years after the first 56 evidence of farming in Southern Europe, while the transition to the intensive cultivation and animal husbandry is estimated to have taken place much later, between 4,800–4,000 yr BP26 57 . 58 This change is associated with a gradual shift from the primarily hunting-gathering-based Comb 59 Ceramic Culture (CCC) to the farming-based Corded Ware Culture (CWC)."

"Conversely, the rise of CWC around 4,800 yr BP30 66 has been associated with the late spread of farming. CWC later reached 67 Finland, Sweden and Norway in the North (Fig 1), Tatarstan in the East, Switzerland and Ukraine in the South, and Belgium and France in the West31–33 68 ."

"CWC in Estonia is, among other traits, characterized by clay vessels often decorated with cord impressions, boat-shaped stone axes clear evidence of cultivation and animal husbandry ( i.e. bones of sheep/goat, pig, and cattle)."

Interestingly, no mention of metals of any kind, and no horses.

MtDna:
8527

YDna:
8528

" These data support the assignment of Kudruküla3 into an156 early offshoot branch R1a5 of hg R1a. Our finding is further supported by the report of similarcases of R1a43 157 lineages which are derived at M459 but ancestral at M198 SNPs in two Easternhunter-gatherer genomes, one from Karelia and the other from near Samara."

"...findings suggest that various subclades of R1a may have been common in hunter-gatherer populations of Eastern Europe and that just one of them, R1a-M417, was later amplified to highfrequency by the Late Neolithic/Bronze Age expansion. The fact that two Latvian huntergathererY chromosomes have been characterized as belonging to R1b-M269 suggests that both sub-clades of R1 were present in the Baltic area before the expansion of the CWC."

The Admixture chart is on page 13.
Blue is WHG,SHG,and EHG like, Orange peaks in Anatolian farmers, Green peaks in CHG and Iranian farmers, and Red in eastern Siberia.

"Interestingly, modern Estonians showed a bigger proportion of the blue component than CWC individuals. Comparing to CCC individuals, modern Estonians lack the red component. This, together with the absence of Y chromosome hg N in CCC and CWC, points to further influx and change of genetic material after the arrival of CWC."

"Consistent with the ADMIXTURE results, both SHG and EHG were the closest to EstonianCCC samples also in outgroup f3 and Patterson’s D analyses."

"both Estonian ancient groups were most similar to extant Lithuanians (Fig 5B). Also, modern populations speaking Uralic (including Finnic) languages of Europe and Siberia along with all other Siberians were more similar to Estonian CCC than to CWC (Fig 5). These results were confirmed by D statistic in the form D(Yoruba, CCC/CWC;256 Estonian, Y) (S7 Figure; S7 Table). This points to extant Siberians and European Uralic speakers having less Steppe ancestry than Estonian CWC did."

"Contrasting allele frequency patterns on autosomal (S9 Table) vs X chromosome(s) (S10 Table) in outgroup f3 analyses revealed that on X chromosome CWC is strikingly more similar to early farmer populations of both Anatolia/Levant and Europe. Accordingly, on the autosomes we see the opposite – most of the European hunter-gatherer/Steppe Eneolithic, EMBA Steppe and CHG/ancient Iranian populations tend to have higher f3 values (Fig 6). These results suggest that the gene flow associated with the spread of the CWC to Estonia may have been sex- specific, being biased toward Steppe ancestry in the male and early farmers on the female side. This finding is consistent with broader sex-specific patterns of admixture detected in EuropeanBronze Age populations."

This last part I'm not sure that I understand. How could the small amounts of "EEF" or Anatolian farmer like admixture have led to such dominance on the X.

Maybe I'm too tired and it will be clearer in the morning.

bicicleur
03-03-17, 09:57
The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent.

Did they investigate both X and Y in Yamna?
I wouldn't be surprised if they'd come to more or less the same conclusion. There is Anatolian mtDNA in Yamna (and in Khvalynsk and Dnjepr-Donets) , but not in early EHG.
In that case the whole XY combination could have come to the Baltic area in 1 single package from Yamna-related people.

Fire Haired14
03-03-17, 11:27
Great Summary. The Latvian Hunter Gatherer outlier; Latvia_MN2, was apart of the Comb Ceramic culture and mostly EHG as these Comb Ceramic individuals from Estonia are. Comb Ceramic then must be an example of a hunter gatherer culture/nation migrating en masse many miles from their home.

Maciamo
03-03-17, 12:49
So in summary, Comb Ceramic people were apparently typical Eastern Hunter-Gatherers (Y-DNA R1a, mtDNA U2e, U4, U5a), and farming was brought by Corded Ware people (whose genetic make-up we already knew). The most interesting point here is the absence of Y-haplogroups I and N1c among those Estonian Comb Ceramic samples. That doesn't mean that other samples from regions in the vast territory they covered won't have them. Ceramic is supposed to have arrived to Northeast Europe from China/Mongolia via Siberia with haplogroup N1c. In fact, Mazurkevich et al. 2014 (https://www.academia.edu/9452168/Archaeology_of_lake_settlements_IV-II_mill._BC_Mazurkevich_A._Polkovnikova_M._Dolbuno va_E._ed) confirmed the presence of N1c in the Comb Ceramic culture with a sample from the Late Neolithic site of Serteya II in the Smolensk region of Russia, near the Belarussian border.

I have only browsed quickly though the paper, and apparently the CCC Estonians possessed 5-10% of East Asian/Siberian admixture. This could only mean that the absence of N1c is simply due to a sampling bias. On page 12 the authors explain that the red component found in CCC Estonians (but lacking in modern Estonians) peaks in East Siberian populations. The admixture chart shows that Neolithic Europeans and Middle Easterners completely lacked it, but Afanasievo, Yamna and CWC people had 1-2% of it, which is consistent with the recurrent presence of Siberian mtDNA C4a and C5 in the Pontic-Caspian Steppe from the Neolithic to the Bronze Age.

bicicleur
03-03-17, 12:51
many believed haplo N arrived with combed ware, as the oldest combed ware has been detected in Northern China
appearantly pots moved faster or spread wider than DNA

Ukko
03-03-17, 13:25
So in summary, Comb Ceramic people were apparently typical Eastern Hunter-Gatherers (Y-DNA R1a, mtDNA U2e, U4, U5a), and farming was brought by Corded Ware people (whose genetic make-up we already knew). The most interesting point here is the absence of Y-haplogroups I and N1c among those Estonian Comb Ceramic samples. That doesn't mean that other samples from regions in the vast territory they covered won't have them. Ceramic is supposed to have arrived to Northeast Europe from China/Mongolia via Siberia with haplogroup N1c. In fact, Mazurkevich et al. 2014 (https://www.academia.edu/9452168/Archaeology_of_lake_settlements_IV-II_mill._BC_Mazurkevich_A._Polkovnikova_M._Dolbuno va_E._ed) confirmed the presence of N1c in the Comb Ceramic culture with a sample from the Late Neolithic site of Serteya II in the Smolensk region of Russia, near the Belarussian border.

I have only browsed quickly though the paper, and apparently the CCC Estonians possessed 5-10% of East Asian/Siberian admixture. This could only mean that the absence of N1c is simply due to a sampling bias. On page 12 the authors explain that the red component found in CCC Estonians (but lacking in modern Estonians) peaks in East Siberian populations. The admixture chart shows that Neolithic Europeans and Middle Easterners completely lacked it, but Afanasievo, Yamna and CWC people had 1-2% of it, which is consistent with the recurrent presence of Siberian mtDNA C4a and C5 in the Pontic-Caspian Steppe from the Neolithic to the Bronze Age.

I have to give you credit, you are persistent in your beliefs.


N1c and I1 are the opposite ends of peoples that moved in the Baltic Sea region to control the long distance trade, these people merged and clashed in different points in time.

Angela
03-03-17, 15:46
The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent.

Did they investigate both X and Y in Yamna?
I wouldn't be surprised if they'd come to more or less the same conclusion. There is Anatolian mtDNA in Yamna (and in Khvalynsk and Dnjepr-Donets) , but not in early EHG.
In that case the whole XY combination could have come to the Baltic area in 1 single package from Yamna-related people.

I think that's the answer to the seeming contradiction I noticed.

Angela
03-03-17, 16:57
I think that's the answer to the seeming contradiction I noticed.

Now I'm going to back track a little. :) Even if Anatolian farmer like mtDna and X were picked up on the steppe or during their travels, for there to be such a sweep on the X you'd think there would be more autosomal admixture. Could they be having problems differentiating between Anatolian Neolithic and "CHG"/Iranian ancestry?

I'm no longer a real fan of Admixture, and this isn't the first time I've found Admixture runs done by the Willerslev group rather odd in some ways.

Perhaps it's because CHG in their analysis has a lot of Anatolian/Levantine elements in it.

8536

berun
03-03-17, 17:55
So in summary, Comb Ceramic people were apparently typical Eastern Hunter-Gatherers (Y-DNA R1a, mtDNA U2e, U4, U5a), and farming was brought by Corded Ware people (whose genetic make-up we already knew). The most interesting point here is the absence of Y-haplogroups I and N1c among those Estonian Comb Ceramic samples. That doesn't mean that other samples from regions in the vast territory they covered won't have them. Ceramic is supposed to have arrived to Northeast Europe from China/Mongolia via Siberia with haplogroup N1c. In fact, Mazurkevich et al. 2014 (https://www.academia.edu/9452168/Archaeology_of_lake_settlements_IV-II_mill._BC_Mazurkevich_A._Polkovnikova_M._Dolbuno va_E._ed) confirmed the presence of N1c in the Comb Ceramic culture with a sample from the Late Neolithic site of Serteya II in the Smolensk region of Russia, near the Belarussian border.

I have only browsed quickly though the paper, and apparently the CCC Estonians possessed 5-10% of East Asian/Siberian admixture. This could only mean that the absence of N1c is simply due to a sampling bias. On page 12 the authors explain that the red component found in CCC Estonians (but lacking in modern Estonians) peaks in East Siberian populations. The admixture chart shows that Neolithic Europeans and Middle Easterners completely lacked it, but Afanasievo, Yamna and CWC people had 1-2% of it, which is consistent with the recurrent presence of Siberian mtDNA C4a and C5 in the Pontic-Caspian Steppe from the Neolithic to the Bronze Age.

If no R1a is found in Europe before 8000 BC I would say that R1a ALSO is Siberian. In the Baltics they would overcome the old R1b HG.

Maciamo
03-03-17, 18:53
If no R1a is found in Europe before 8000 BC I would say that R1a ALSO is Siberian. In the Baltics they would overcome the old R1b HG.

Maybe, but Europid, not Mongoloid.

Angela
03-03-17, 19:52
Now I'm going to back track a little. :) Even if Anatolian farmer like mtDna and X were picked up on the steppe or during their travels, for there to be such a sweep on the X you'd think there would be more autosomal admixture. Could they be having problems differentiating between Anatolian Neolithic and "CHG"/Iranian ancestry?

I'm no longer a real fan of Admixture, and this isn't the first time I've found Admixture runs done by the Willerslev group rather odd in some ways.

Perhaps it's because CHG in their analysis has a lot of Anatolian/Levantine elements in it.

8536

I think the ADMIXTURE analysis is part of Willerslev maintaining that most of the components in modern Europeans were in Europe or in "Europid" people from the most ancient time periods. So, he's got the green component which peaks in the CHG in Mal'ta, as well as the red Siberian and an ASI like component, everything except Anatolia/Levant Neolithic. Kostenki, however, even has that.

This may be the source of this comment: "Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe. "

I would think some people would be thrilled with that interpretation, and instead they seem to be flipping out over it.

He's not saying, in my opinion, that this particular group of CWC Estonians didn't come from the direction of the steppe; he's just saying CHG was already all over northern and eastern Europe. Color me skeptical. Has anyone checked if their d-stats confirm this?

Ed. Uh oh, double negative, but it's what I meant to convey, so the heck with it. :)

LeBrok
03-03-17, 21:22
Great Summary. The Latvian Hunter Gatherer outlier; Latvia_MN2, was apart of the Comb Ceramic culture and mostly EHG as these Comb Ceramic individuals from Estonia are. Comb Ceramic then must be an example of a hunter gatherer culture/nation migrating en masse many miles from their home. It was interesting to see that Latvian WHG were pushed out by EHG just before CW came. What a dynamic situation in this area.

LeBrok
03-03-17, 21:52
I think the ADMIXTURE analysis is part of Willerslev maintaining that most of the components in modern Europeans were in Europe or in "Europid" people from the most ancient time periods. So, he's got the green component which peaks in the CHG in Mal'ta, as well as the red Siberian and an ASI like component, everything except Anatolia/Levant Neolithic. Kostenki, however, even has that.It is not Siberian admixture, it is American. Siberian came much later during Steppe BA. On the chart is the last one to the right, some sort of fuchsia. Forgive my eyes.


This may be the source of this comment: "Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe. "

I would think some people would be thrilled with that interpretation, and instead they seem to be flipping out over it.

He's not saying, in my opinion, that this particular group of CWC Estonians didn't come from the direction of the steppe; he's just saying CHG was already all over northern and eastern Europe. Color me skeptical. Has anyone checked if their d-stats confirm this?

Ed. Uh oh, double negative, but it's what I meant to convey, so the heck with it. :)
Can't wait for these in gedmatch

Angela
03-03-17, 22:02
It is not Siberian admixture, it is American. Siberian came much later during Steppe BA. On the chart is the last one to the right, some sort of fuchsia. Forgive my eyes.


Can't wait for these in gedmatch

I agree with you. I should have clarified that it's just what they're calling "Siberian".

arvistro
03-03-17, 22:09
No N in Latvia/Lithuania found in study covering time period until 200 BCE...
http://biorxiv.org/content/biorxiv/early/2017/03/03/113241.full.pdf

The Genetic History of Northern EuropeAlissa Mittnik

LeBrok
03-03-17, 22:15
I agree with you. I should have clarified that it's just what they're calling "Siberian". Yes, as per my favorite HarappaWorld admixture. ;), its hotspot is in Northern Siberia today at 90%, also 40% in Mongolia and 6% in Finland. On other hand American admixture is almost all gone from Eurasia today, at 1% and less.

berun
03-03-17, 22:23
in the paper:


However the remains associated with the Yamnaya Culture, which is considered to be ancestral to CWC, have been found with predominantly R1b-Z2105 and no R1a lineages

But even so they stick on the steppes... even if recent papers are pointing to male-biased migrations. By the way the paper about Y-DNA in Afanasievo is providing R1b that surely are realted to those of Yamna, being such cultures realy related. And don't forget to add up the westwards expansion of R1b-L51 from the Pontic steppes: truly the steppes were the womb of the European nations (please take it as irony).

Other inconsitencies taking Yamnayans as the source pop is that they supposedly provide the first EEF mtDNA into the Baltic CWC, but admixtures are not displaying any EEF signal in Yamna! What is wrong about following logics instead of following holy cows?

Angela
03-03-17, 22:41
Yes, as per my favorite HarappaWorld admixture. ;), its hotspot is in Northern Siberia today at 90%, also 40% in Mongolia and 6% in Finland. On other hand American admixture is almost all gone from Eurasia today, at 1% and less.

I know it's your favorite. :) I just hope relative newcomers realize that these "modern" clusters like "North-east Euro" harbor older alleles, including EEF and CHG like alleles, and not just WHG or EHG like alleles. That explains why "CHG" percentages in these academic papers are higher than what shows in Harappa, not that I think those results are necessarily the "gold standard".

johen
03-03-17, 22:54
No N in Latvia/Lithuania found in study covering time period until 200 BCE...
http://biorxiv.org/content/biorxiv/early/2017/03/03/113241.full.pdf

The Genetic History of Northern EuropeAlissa Mittnik

This finnish scholar’s opinion would be correct:

[quote]Juha Janhunen has repeatedly argued that the Ural-Altaic typological complex is an areally distinct unit with clear-cut boundaries in every direction against languages of different typology, and that the Ural-Altaic typology must have had one original centre of expansion. As the earliest protolanguages of the Altaic language families (Proto-Turkic, Proto-Mongolic and Proto-Tungusic) can be traced back to Greater Manchuria (up to Mongolia; Janhunen 1996: 216), this view requires that Pre-Proto-Uralic must also have been present somewhere adjacent to them. According to Janhunen there is no significant chance that Pre-Proto-Uralic could have developed a structural typology so similar to the Altaic languages without being in close contact with them.”[quote]
http://s155239215.onlinehome.us/turkic/40_Language/JanhunenJUralicFig1.htm.gif

I think samoyedic N1b and east scythian N1b is clearly related with Okuneo NO(XO) 2,500bc.
And Yakut N1c also came from Altai.
Problem is where the N originated in? Manchuria or Altai. The altai bronze was archaeologically connected to Gansu Yangshao. And Yangshao N had something to do with Hongshan N in Manchu of northern China, where ancient Egypt-type pyramid is located.

piratica
30-03-17, 22:21
hi
wonder why was Naakamäe left out from the mt data? :samurai:

Rethel
01-04-17, 13:47
Yes, as per my favorite HarappaWorld admixture. ;), its hotspot is in Northern Siberia today at 90%, also 40% in Mongolia and 6% in Finland. On other hand American admixture is almost all gone from Eurasia today, at 1% and less.

What? Harappian were mongoloids?

LeBrok
01-04-17, 16:39
You shouldn't comment on things you don't understand. It just make you look silly.

Rethel
01-04-17, 17:26
You shouldn't comment on things you don't understand. It just make you look silly.

I just asked. It is not comment, but question. If you do not understand the difference, it is not my fault.

LeBrok
01-04-17, 17:40
I just asked. It is not comment, but question. If you do not understand the difference, it is not my fault.Knowing you, I'm sure this question was rhetorical and sarcastic, lol.
In case I'm wrong, please prove us wrong, learn something and discuss it later:
http://www.eupedia.com/forum/threads/32877-HarappaWorld-Gedmatch-post-and-compare-your-admixtures-to-ancient-and-contemporary/page17?p=503238#post503238