Thursday, November 6, 2014
Kostenki14: first genome of an Upper Paleolithic European
At last, we have an ancient genome from pre-LGM Europe: Kostenki14 (K14) from the famous Kostenki Upper Paleolithic site in southern Russia. The paper, Seguin-Orlando et al. 2014, is locked away behind a paywall, but at least the supplementary materials are open access.
K14 is dated at 38,700-36,200 cal BP and belongs to Y-chromosome haplogroup C-M130, a basal and widespread paternal marker that has already been reported in three other ancient European genomes: La Brana-1 from Mesolithic Spain and NE5 and NE6 from Neolithic Hungary. It also belongs to mitochondrial (mtDNA) haplogroup U2, but we've actually known this since 2010 (see here).
The shared drift stats of the form f3(Mbuti;K14,X), where X is the test population, reveal that from among present-day Eurasians, this early European is most similar to Northeast Europeans, such as Lithuanians, Estonians and Belarusians, and some Western Europeans, like Basques and Orcadians (ie. people from the Orkney Isles). This is also what we've seen from other indigenous European hunter-gatherer genomes sequenced to date.
As far as Eurasians are concerned, Papuans and Melanesians are the most distinct from K14, somewhat paradoxically so, considering the ancient genome's Oceanian-like Y-haplogroup. The authors speculate that this might be because they carry ancestry from a very basal lineage that went its own way before the split between West Eurasians and East Asians. But I'm wondering whether this result can't simply be explained by the inflated Denisovan admixture among Oceanians (usually reported at around 5%)?
Indeed, there's no mention anywhere in the paper that K14 has Denisova ancestry. However, much like the recently published Ust'-Ishim genome, it shows significantly larger genomic tracts of Neanderthal origin than present-day Eurasians. The implication of this is obvious, and well covered elsewhere, so I won't go into it here.
Arguably the most controversial outcome of the study is that it shows K14 to be partly of Basal Eurasian origin. This is a highly divergent Eurasian clade first described in Lazaridis et al. (see here), and associated with Neolithic farmers. Seguin-Orlando et al. came to their conclusion via two sets of D-statistics and an ADMIXTURE run, which showed K14 to carry a component specific to the Middle East.
If true, then this finding debunks one of the main premises in Lazaridis et al., which is that Basal Eurasian admixture first arrived in Europe from the Middle East with Neolithic farmers. However, it doesn't debunk this paper's model of the formation of the modern European gene pool. Basically, for that to happen we'd need the Basal Eurasian component to show up in pre-Neolithic samples from Western and Central Europe.
Nevertheless, David Reich (one of the co-authors of Lazaridis et al.) seemed so taken aback by the news that he suggested K14 might be contaminated. Or at least, he was reported to have made this suggestion (scroll down to the last paragraph here)
This is interesting because Reich is currently working on a paper that includes ancient genomes from the Samara Valley, which isn't too far away from the Kostenki site (see here). Judging by his reaction to K14's purported Basal Eurasian admixture, we can probably assume that the pre-Neolithic genomes he's analyzed from Russia don't show any signals of this type of ancestry.
In any case, the model devised by Seguin-Orlando et al., set out in the figure below, is actually very similar to the one in Lazaridis et al., with NEOL basically standing in for EEF (Early European Farmer) and MHG for WHG and SHG (Western European Hunter-Gatherer and Scandinavian Hunter-Gatherer, respectively).
However, the suggestion that the Yenisei Siberians carry MHG rather than ANE doesn't look right to me. Why would Siberians carry European rather than Siberian hunter-gatherer ancestry? I suspect the problem is that MHG is a composite of WHG and ANE (because, as we know, SHG are partly ANE). Thus, if the Yenisei Siberians do carry both ANE and WHG, because they might indeed harbor some ancient European admixture, then perhaps this is simply being classified as MHG? If so, then I suppose it's not technically wrong, but it does look confusing.
Seguin-Orlando et al., Genomic structure in Europeans dating back at least 36,200 years, Published Online November 6 2014, Science, DOI: 10.1126/science.aaa0114