A new preprint on the genetic history of North Eurasia has just appeared at bioRxiv. Here's the abstract:
Siberia and Western Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups. Yet, genetic variation of peoples from this region is largely uncharacterized. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We combine these datasets with additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees. Our results provide new links between modern and ancient inhabitants of Eurasia. Siberians share 38% of ancestry with descendants of the 45,000-year-old Ust-Ishim people, who were previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to the Ancient North Eurasians, represented by the 24,000-year-old Siberian Malta boy. In addition, Siberians admixtures are present in lineages represented by Eastern European hunter-gatherers from Samara, Karelia, Hungary and Sweden (from 8,000-6,600 years ago), as well as Yamnaya culture people (5,300-4,700 years ago) and modern-day northeastern Europeans. These results provide new evidence of ancient gene flow from Siberia into Europe.
My initial thought was that the MA1 or Mal'ta boy-related admixture estimate of 57% for Western Siberians (in fact, Mansis) was way too high. However, I checked it using qpAdm and the Mansis from the Human Origins dataset, and apparently it does make sense as a three-way model including MA1, Han Chinese and Georgians. The full qpAdm output is available here.
chisq 0.278, tail prob 0.870155
Curiously, I get a very similar result with Eastern European hunter-gatherers (EHG) in place of MA1, and the fit is almost as good. The full output is here.
chisq 0.916, tail prob 0.632459
In any case, we can safely assume that Mansis harbor a lot of MA1/EHG-related ancestry. Perhaps as much as ~60%. However, I have to say that this quote from the paper makes no sense whatsoever:
Our findings also point to Western Siberians Mansi as a likely source of the ANE [aka MA1-related] ancestry among northeastern Europeans.
Really? Mansis? Not even proto-Mansis, or some sort of Mansi-related population?
Also, as far as I can see, the authors consider Y-haplogroup N1c1 as an EHG paternal marker, simply because they dated its main expansion to 7,100-4,900 BP based on present-day samples. Please note that Karelia_HG and Samara_HG are classified as EHG.
The Western Siberian admixture into the Eastern Europeans likely began before the Yamnaya culture period (5.3-4.7 kya), since the admixtures with Mansi are also very strong among hunter gatherers from Northeastern Europe from 6.6-8 kya (Karelia HG, Samara HG and to lesser degree Motala HG and Hungary Gamba HG; Fig. S21f-q) that predated the Yamnaya people. Therefore Western Siberian admixtures into northeastern Europe likely began prior to 6,600 years ago, coinciding with the expansion of Y-DNA haplogroup N1c1 among Siberians and northeastern Europeans (7,100-4,900 years ago). Since haplogroup N likely originates in Asia or Siberia, its presence among eastern Europeans likely reflects ancient gene flows from Siberia into Eastern Europe.
The problem is that this isn't yet supported by any direct evidence from ancient DNA. Thus far, we know that EHG carried Y-haplogroups J, R1a and R1b, but no N1c1. Later populations, with significant EHG ancestry, such as Corded Ware, Khvalynsk and Yamnaya, carried mostly R1a and R1b, as well as I2a and Q1a, but again, no N1c1.
That's not to say that N1c1 won't ever turn up in EHG remains. But in my opinion the major subclades of N1c1 can't be associated with EHG, but rather with later populations of more complex origin, such as early Uralic-speakers with significant levels of East Eurasian admixture.
By the way, the claims about Ust-Ishim in the paper are interesting, but in my opinion not very parsimonious based on the data we have at the moment. I could be wrong though. Let's wait and see.
Valouev et al., Reconstructing Genetic History of Siberian and Northeastern European Populations, bioRxiv preprint, Posted October 18, 2015, doi: http://dx.doi.org/10.1101/029421