In the post below Martin Sikora, an author on the K14 ancient DNA paper, has responded. The whole thing is worth reading:
Hi Razib,
after reading your post it I thought it would not hurt to chime in with a bit of perspective from my side, as I don’t entirely agree with some of your criticisms. Some of the reactions to our paper have caught me a little by surprise, but in retrospect it probably reflects the complexity of the story, which is something I also struggled with (and still am!).
Part of the confusion seems to be that it is assumed that since we find that K14 somehow relates to all three European ancestral proposed by Lazaridis et al., that it necessarily also has contributed these components to modern Europeans. In your post you also seem to imply that, i.e we don’t “acknowledge the possibility that K14 did not leave modern descendants, and was part of an early population which did not end up flourishing”. I actually agree with the early population part, and we also acknowledge that in our suggested model in Figure 2, which does not have a K14-related population directly contributing to modern Europeans. What one can say with reasonable certainty though is that K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians, so things are complex. Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent.
Regarding your take on the PCA results, I would disagree and say that these are very much what you would expect for an individual of that age. K14 is after all ~36,000 years closer to the East Asia / West Eurasia split, so it lacks a substantial amount of drift on the European branch. It is nevertheless shifted towards Europe on PC1 from the origin as expected (a bit more so than MA1 actually). Pontus Skoglund had a nice recent paper in MBE that demonstrates the same effect (see Figure 9 in doi:10.1093/molbev/msu1920). As you say, using modern variation to infer affinities of ancient samples has limitations, and PCs are often hard to interpret. In the same spirit I would also not interpret the different admixture components in K14 as itself being admixed with all those components, but rather reflecting ancestral relationship with modern populations represented by these components. The same is obviously true for the “Middle East” component, but it still implies that K14 somehow relates ancestrally to those populations whereas all other HGs including MA1 do not.
Overall, I do think that migrations played an important role, e.g. I don’t think that “Basal Eurasian” came with K14 to Central Europe or was already present back then in another way, that seems pretty clear. I would also not say that our results are necessarily a refutation of the Lazaridis et al model, but I do think they show that it seems to have been already quite complicated in the Upper Paleolithic. If you need a new migration/component for every new individual, to me this questions at least to a some extent whether one can really talk about three or any other number of discrete ancestral populations for all modern Europeans. Personally I would expect ancient samples from the Caucasus or Central Asia to yet again spring some surprises. The cool thing is that we’ll probably know soon, since many groups are adding more and more samples to the picture.
Anyways, I just wanted to share my thoughts, hope this clears up things a bit.
Btw regrading your subsequent ANE post, I can confirm that those are the Kalash. Interesting also that the correspondingly the Kalash ADMIXTURE component shows up in MA1, but is almost absent in K14 (see our Figure S20).
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