Genome of Kostenki-14, an Upper Paleolithic European

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A new paper in Science reports on the genome of Kostenki-14 (K14), an Upper Paleolithic European from Russia. This is now the third oldest Homo sapiens for which we have genetic data, after Ust'-Ishim (Siberia, 45 thousand years), Tianyuan (China, 40 thousand years), and now Kostenki (European part of Russia, 37 thousand years). Of these three genomes, the Ust'-Ishim is both the highest coverage and earliest (Siberia is the gift that keeps on givin'), Tianyuan only has its chromosome 21 known, and K14, a complete 2.42x coverage sequence (and, apparently, good teeth, after all these years; left).

The publication of the Tianyuan genome showed that populations related to East Asians and Oceanians existed in the world 40 thousand years ago. So, models based on modern humans that put the split of East Asians from Europeans to a much more recent time period were basically wrong (more on this a little below). The Ust'-Ishim genome showed that populations basal to both East Asians and Europeans existed in the world 45 thousand years ago. So, either East Asians and Europeans hadn't gone along their different paths yet, or, if they had, Ust'-Ishim happened to be a side branch and not the major East Asian and European lineages.

K14 may not be the older Upper Paleolithic human, but as of this writing it is the only Upper Paleolithic European that has been published so far, the next ones being the Loschbour, Motala, and La Brana Mesolithic Europeans who who have about 1/5 of its age. The new paper shows that K14 was definitely European (or more correctly West Eurasian or Caucasoid), as it was more similar to modern Europeans than to East Asians or other non-West Eurasian populations. Thus, the morphological description of the sample as "Australoid" by some early anthropologists did not reflect its ancestral makeup. Also, this proves that Caucasoids existed 37,000 years ago, which most physical anthropologists would believe, but it is nice to have direct confirmation. This pushes the lower bound from 24,000 years ago (because MA-1 was West Eurasian according to the results of Raghavan et al.). It will be nice to push the lower bound further to the past as there are much older bones (and plenty of teeth) from earlier Upper Paleolithic Europeans.

But there is a slight kink in the story, as K14 also belonged to Y-haplogroup C which is predominantly East Asian/Ocenian/Native American today. So, maybe there is some distant link to these populations in its ancestry. But, there is definitely a link to much more recent Europeans: the tiny percentage of living Europeans who have preserved K14's Y-chromosomal type (some of which were doubtlessly told a few years back that they were descendants of Genghis Khan, before the phylogenetic structure of C was known), the La Brana hunter-gatherer from Mesolithic Spain, as well as Neolithic Europeans from Hungary.

The authors of the current paper also date the date of Neandertal admixture to 54 thousand years. This seems very compatible with the finding of between 50 and 60 thousand years by Fu et al. (2014) based on the Ust'-Ishim genome (which is both earlier and better, so the chunks of Neandertal ancestry in it are probably be longer and more well-defined).

The authors propose the following model for how various populations are related to each other:

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This model is not formally tested, but at least it seems to derive Europeans as a 3-way mixture that is basically identical to that of Lazaridis et al., with some relabeling of populations (MHG=WHG and NEOL=EEF).

The model also includes Yeniseian Siberians as a mixture of MHG and East Asians (although it does not include actual East Asians). It's strange that Yeniseians apparently are given no ANE ancestry but only WHG/MHG. Both Raghavan et al. and Lazaridis et al. mentioned that ancestry related to MA-1 in living Siberians is diminished, but none at all?

The major new finding of this paper, however, is that K14 had Basal Eurasian ancestry, which was first proposed for EEF from Germany 7,000 years ago, so now it postulated for Russian hunter-gatherers 37,000 years ago. I don't think many archaeologists would derive European farmers from Russia (Russia is actually one of the last places in Europe that became agricultural). So, maybe the hunter-gatherers from Russia had Basal Eurasian ancestry and this wasn't limited to the ancestors of the EEF? If they did, it's strange that Loschbour, La Brana, MA-1, Ust'-Ishim, Swedish Mesolithic (and maybe KO1?) didn't have it. So, either Kostenki was very unique or there is an alternative explanation for its strangeness.

The evidence for the Basal Eurasian ancestry in K14 is summarized in the figure above in bullet point (b).
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* The statistic D(Mbuti, East Asia; HG, K14) is less than 0. So, there's some link between HG and East Asians. Is this because of Basal Eurasian admixture in K14 or due to some admixture between Caucasoids and Mongoloids after the time of K14? (this might cause the lower dates of European-East Asian splits alluded to above).

  • The statistic D(Mbuti, East Asia; NEOL, K14) is 0. So, East Asians don't "prefer" either Neolithic Europeans (NEOL) or K14. I guess the value of this statistic depends on how much Basal Eurasian the different populations have and what's the relationship between East Asians, K14, and the non-Basal Eurasian part in K14.

  • Finally, "NEOL component for K14 in ADMIXTURE". I think they are referring to the "Middle East" component (right). This may be Basal Eurasian ancestry, or maybe because K14 is so old, it pre-dates the European/Middle Eastern divide and its ancestry isn't attracted to either Europe or the Middle East, so it gets ancestry from both (and many other colors besides).

It is fascinating how many new questions are both answered and raised each time a new genome gets published (and there has been a constant stream of these over the last couple of years). 

Science DOI: 10.1126/science.aaa0114

Genomic structure in Europeans dating back at least 36,200 years

Andaine Seguin-Orlando1,*, Thorfinn S. Korneliussen1,*, Martin Sikora1, et al.

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.