The Population History of Northeastern Siberia

[Angela]

See:
Martin Sikora et al (Willerslev group)

"The population history of northeastern Siberia since the Pleistocene"
https://www.biorxiv.org/content/bior...48829.full.pdf

"Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia."






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The next two graphics are based on fst 3 stats.

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[halfalp]

Omg, we found the ancestor of R and Q and also mtdna U link with Mal'ta? Amazeballs!

[markod]

Awesome, I had hoped the Yana site would get tested. The earliest hunters with Y-DNA P1 and mtDNA U again show that the ANE like individuals were a hybrid of the Sungir-Kostenki clade and an East Eurasian population. They are differentiated from Mal'ta because the latter received additional admixture from a CHG-like population:

Mal’ta and Yana also exhibit a similar pattern of genetic affinities to bothEWE and EEA, consistent with previous studies40,46 (Extended Data Fig. 3e). The ANElineage can thus be considered a descendant of the ANS lineage, demonstrating that by 31.6kya early representatives of this lineage were widespread across northern Eurasia, includingfar northeastern Siberia. Fitting Yana and Mal’ta in an extended admixture graph includingother EWE individuals reveals an increase in complexity of the ANS lineage over time due todifferentiation and admixture with other lineages, with evidence for low levels of earlyCaucasus hunter-gatherer (CHG)–related ancestry in Mal’ta, as well as Western huntergatherer(WHG) and CHG–related ancestry in the individual from Karelia, commonlyreferred to as “Eastern hunter-gatherer” (EHG).

[halfalp]

Awesome, I had hoped the Yana site would get tested. The earliest hunters with Y-DNA P1 and mtDNA U again show that the ANE like individuals were a hybrid of the Sungir-Kostenki clade and an East Eurasian population. They are differentiated from Mal'ta because the latter received additional admixture from a CHG-like population:

y-dna G1b + mtdna X2a ( native american )?

Edit. Never mind the G1b is actually mtdna, i was ready to explode...

[halfalp]

Awesome, I had hoped the Yana site would get tested. The earliest hunters with Y-DNA P1 and mtDNA U again show that the ANE like individuals were a hybrid of the Sungir-Kostenki clade and an East Eurasian population. They are differentiated from Mal'ta because the latter received additional admixture from a CHG-like population:

And it's not any U, it's U2'3'4'7'8'9... If we admit that it was the same for Mal'ta and that we dream it's not Sungir-Kostenki U2, it could be the maternal ancestry lineage from a lot of craziness. U3 and U8,U9 are probably out of map, U8 is so old and absolutely not in that geographical pattern, same for U3, U9 is way too young... It let us U2,U4,U7 maybe even the 3! ( yeah ok i'm going too far here ).

[markod]

y-dna G1b + mtdna X2a ( native american )?

Edit. Never mind the G1b is actually mtdna, i was ready to explode...

I think G1b is typically North Asian & Japanese (presumably Ainu in origin). It's mtDNA.

[halfalp]

I just looked up about Yana RHS because i totally didn't know about and... wow it's totally in the arctic, like very very high in the arctic. Those are some 30'000 years old samples, shouldn't it be covered by ice sheets in those times?

[halfalp]

Interesting also are all the y-dna Q1b wich are found in middle-east and afghanistan in modern times. A potential source for ANE-related in prehistoric Iran?

[markod]

Interesting also are all the y-dna Q1b wich are found in middle-east and afghanistan in modern times. A potential source for ANE-related in prehistoric Iran?

My guess would be that it isn't. The Iranian Neolithic population is the most East Eurasian shifted of all Holocene West Eurasians:



The ANE-like population that entered southern Central Asia and Iran must have had more East Eurasian Ancestry than Mal'ta IMHO. These Siberians too are very West Eurasian (~70%).

[ToBeOrNotToBe]

Did they actually find X2a in NE Siberia? I believed (against the tide, I know) that it was brought by pre-Columbian pre-Viking West Eurasian contact...

By the way, why do we STILL not know what subclade of R1b the Native Americans belonged to? I mean, it can't be that hard, surely. If I had to guess, it would be some rare form of M269 not found among present-day European populations.





I'll just out myself now - I'm a supporter of Thor Heyerdahl's Canary hypothesis (the gist, anyway - as one example, samples of cocaine (a New World crop) found amongst some of the Egyptian mummies (people try to explain it away as "contamination", as if people were doing coke while excavating - it was found in the hair anyway, which is normally enough to rule something like that out, but because this is so incredible people see it as crackpot)).

[holderlin]

Wow, the arctic was being utilized 30k years ago. That is pretty amazing, and the people were a very West Eurasian population of about 500. Can you imagine your entire world being 500 people? I knew these HG populations were small, but it's still amazing to get a quantitative measure of it from so long ago. People had been essentially guessing at all of this stuff until like 10-15 years ago.

[halfalp]

Did they actually find X2a in NE Siberia? I believed (against the tide, I know) that it was brought by pre-Columbian pre-Viking West Eurasian contact...

By the way, why do we STILL not know what subclade of R1b the Native Americans belonged to? I mean, it can't be that hard, surely. If I had to guess, it would be some rare form of M269 not found among present-day European populations.





I'll just out myself now - I'm a supporter of Thor Heyerdahl's Canary hypothesis (the gist, anyway - as one example, samples of cocaine (a New World crop) found amongst some of the Egyptian mummies (people try to explain it away as "contamination", as if people were doing coke while excavating - it was found in the hair anyway, which is normally enough to rule something like that out, but because this is so incredible people see it as crackpot)).

No they didn't found X2a in those samples, i was very excited because i missread a sample y-dna G1b but it is mtdna.

[Angela]

From Razib Khan:

"First, the authors got really high coverage (so high quality) genomes from the Yana RS site. Notice that they’re doing more data-intense analytic methods. Second, they did not find any population with the affinities to Australo-Melanesian that several research groups have found among some Amazonians. Likely they are hiding somewhere…but the ancient DNA sampling is getting pretty good. We’re missing something. Third, I am not sure what to think about the very rapid bifurcation of lineages we’re seeing around ~40,000 years ago.The ANS population, ancestral by and large to ANE, seems to be about ~75% West Eurasian (without much Basal Eurasian) and ~25% East Eurasian. Or at least that’s one model. Did they then absorb other peoples? Or, was there an ancient population structure in the primal ur-human horde pushing out of the Near East? That is, are the “West Eurasians” and “East Eurasians” simply the descendants of original human tribes venturing out of Africa ~50,000 years ago? Also, rather than discrete West Eurasian and East Eurasian components, perhaps there was a genetic cline where the proto-ANS occupied a position closer to the former, as opposed to some later pulse admixture?"

https://www.gnxp.com/WordPress/2018/...medium=twitter

[halfalp]

From Razib Khan:

"First, the authors got really high coverage (so high quality) genomes from the Yana RS site. Notice that they’re doing more data-intense analytic methods. Second, they did not find any population with the affinities to Australo-Melanesian that several research groups have found among some Amazonians. Likely they are hiding somewhere…but the ancient DNA sampling is getting pretty good. We’re missing something. Third, I am not sure what to think about the very rapid bifurcation of lineages we’re seeing around ~40,000 years ago.The ANS population, ancestral by and large to ANE, seems to be about ~75% West Eurasian (without much Basal Eurasian) and ~25% East Eurasian. Or at least that’s one model. Did they then absorb other peoples? Or, was there an ancient population structure in the primal ur-human horde pushing out of the Near East? That is, are the “West Eurasians” and “East Eurasians” simply the descendants of original human tribes venturing out of Africa ~50,000 years ago? Also, rather than discrete West Eurasian and East Eurasian components, perhaps there was a genetic cline where the proto-ANS occupied a position closer to the former, as opposed to some later pulse admixture?"

https://www.gnxp.com/WordPress/2018/...medium=twitter

But if they got high coverage of Yana and its U'2'3'4'7'8'9 but we know that for exemple U2 and U8 already had their proper group by that time. So that Yama U'2'3'4'7'8'9 is actually basal from the one from Sunghir and Kostyonki?

[bicicleur]

But if they got high coverage of Yana and its U'2'3'4'7'8'9 but we know that for exemple U2 and U8 already had their proper group by that time. So that Yama U'2'3'4'7'8'9 is actually basal from the one from Sunghir and Kostyonki?

it's a dead end, but it hints at where they came from or along, 38 ka

[markod]

Samples from the Near East, Europe and North Asia probably won't be very informative as regards the diversification of Eurasian lineages. Summerhayes (2010) gives 49k B.P. for some of the earliest human settlements in Papua. India is unclear, but evidently it must be earlier - same for Sunda.

It is very unlikely that any of the discernible Eurasian Upper Paleolithic populations differentiated in the Middle East (with the possible exception of the Basal Eurasian population which could have stayed in southern Arabia). The region became exclusive Neanderthal territory until a later wave of humans from Asia replaced them ~40k B.P. .

[halfalp]

Samples from the Near East, Europe and North Asia probably won't be very informative as regards the diversification of Eurasian lineages. Summerhayes (2010) gives 49k B.P. for some of the earliest human settlements in Papua. India is unclear, but evidently it must be earlier - same for Sunda.

It is very unlikely that any of the discernible Eurasian Upper Paleolithic populations differentiated in the Middle East (with the possible exception of the Basal Eurasian population which could have stayed in southern Arabia). The region became exclusive Neanderthal territory until a later wave of humans from Asia replaced them ~40k B.P. .

Can you explain more your idea?

[markod]

Can you explain more your idea?

What I mean is that in my opinion DNA evidence favors the Single Wave Dispersal models (blue).

The Multiple Waves Dispersal model (red) seems unlikey due to a lack of archaic ancestry in most Eurasians, no deep bifurcation in Eurasian haploid lineages and the concentration of basal haplogroups around India and the Sunda. The Middle East barely offers anything in the way of basal haplogroups.

An exception to this might be the population of Pestera cu Oase population, which however was unsuccesful.

The evidence for modern humans in South Asia immediately post-Toba is piling up, see for example: https://www.nature.com/articles/natu...tcallback=true

Much of the early diversification of Eurasians must have taken place in this region. Populations must have been small and vulnerable, since the rainforests were unfamiliar terrain for humans. Hence we see rapid differentation in those early humans.

[halfalp]

What I mean is that in my opinion DNA evidence favors the Single Wave Dispersal models (blue).

The Multiple Waves Dispersal model (red) seems unlikey due to a lack of archaic ancestry in most Eurasians, no deep bifurcation in Eurasian haploid lineages and the concentration of basal haplogroups around India and the Sunda. The Middle East barely offers anything in the way of basal haplogroups.

An exception to this might be the population of Pestera cu Oase population, which however was unsuccesful.

The evidence for modern humans in South Asia immediately post-Toba is piling up, see for example: https://www.nature.com/articles/natu...tcallback=true

Much of the early diversification of Eurasians must have taken place in this region. Populations must have been small and vulnerable, since the rainforests were unfamiliar terrain for humans. Hence we see rapid differentation in those early humans.

So ancient modern humans or ancient eurasians would have in a single wave quit Africa, and in India a coherent population of maybe 1000 individuals would go in every direction and rapidly diversified?

[markod]

So ancient modern humans or ancient eurasians would have in a single wave quit Africa, and in India a coherent population of maybe 1000 individuals would go in every direction and rapidly diversified?

That's what I'm thinking. The East Eurasian - West Eurasian split could have occurred maybe with the early migration to Sundaland 73-63k B.P. .

Seems at least much more in line with the evidence than a differentation in the Near East or even Africa as proposed by Razib Khan IMHO. Not even taking into account the genetic data, plains hunters in Africa and the Near East would be much less likely to become isolated and drift from each other than rainforest dwellers seperated by the sea.

[halfalp]

That's what I'm thinking. The East Eurasian - West Eurasian split could have occurred maybe with the early migration to Sundaland 73-63k B.P. .

Seems at least much more in line with the evidence than a differentation in the Near East or even Africa as proposed by Razib Khan IMHO. Not even taking into account the genetic data, plains hunters in Africa and the Near East would be much less likely to become isolated and drift from each other than rainforest dwellers seperated by the sea.

Thing is, i feel such hypothesis have to be back 75k bp like you said and our oldest sample ever is 45k bp so we have a gap of 30k year old between out of india and the first differentiated humans that we have. Also in samples like Vestonice or Goyet we can still see traces of related ancestry with modern Papuan wich mean they are not that more old than 30K no? Maybe the Sundaland that we talk about are maybe more linked with Denisovans?

[markod]

Thing is, i feel such hypothesis have to be back 75k bp like you said and our oldest sample ever is 45k bp so we have a gap of 30k year old between out of india and the first differentiated humans that we have. Also in samples like Vestonice or Goyet we can still see traces of related ancestry with modern Papuan wich mean they are not that more old than 30K no? Maybe the Sundaland that we talk about are maybe more linked with Denisovans?

We can be reasonably sure that the humans from Sumatra were AMH. We do not know whether they actually contributed to the modern Eurasian lineage, however. I think they did since the evidence is piling up. Just recently Dortch et al. (2017) gave ~65k B.P. (though disputed) for the peopling of the northern Sahul for example.

Sadly archaeological research is lacking in the place that is focal to this scenario (India and vicinity).

[halfalp]

We can be reasonably sure that the humans from Sumatra were AMH. We do not know whether they actually contributed to the modern Eurasian lineage, however. I think they did since the evidence is piling up. Just recently Dortch et al. (2017) gave ~65k B.P. (though disputed) for the peopling of the northern Sahul for example.

Sadly archaeological research is lacking in the place that is focal to this scenario (India and vicinity).

But could they be some AMH like the one who contributed a little bit to Denisova but not related to our AMH ancestry?

Well at the speed the results for the India paper is coming. They probably have their next sample, and a middle-age one, only in 10 years sadly.

[markod]

But could they be some AMH like the one who contributed a little bit to Denisova but not related to our AMH ancestry?

Well at the speed the results for the India paper is coming. They probably have their next sample, and a middle-age one, only in 10 years sadly.

Yeah, without aDNA it's impossible to rule out that this was just a failed earlier exodus of humans from Africa.

I've been waiting for more info on this site: https://timesofindia.indiatimes.com/...ow/6622838.cms

[bicicleur]

That's what I'm thinking. The East Eurasian - West Eurasian split could have occurred maybe with the early migration to Sundaland 73-63k B.P. .

Seems at least much more in line with the evidence than a differentation in the Near East or even Africa as proposed by Razib Khan IMHO. Not even taking into account the genetic data, plains hunters in Africa and the Near East would be much less likely to become isolated and drift from each other than rainforest dwellers seperated by the sea.

that is asuming east asians came via sundaland
I don't
hard to tell though