East and West Eurasians separated at least 45,000 years ago, but...

Finally, something interesting. Open access at Molecular Biology and Evolution:

A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.

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In our model, K14 fits well as unadmixed (aside from archaic introgression), but MA1 receives, in addition to its archaic admixture, a component of eastern Eurasian ancestry. The latter gene flow explains the preliminary residual f4 (MA1, K14; Ami, Ust’-Ishim), which is of a similar form to several other relatively poorly fitting statistics from our initial graph, for example f 4 (MA1, K14; Ami, New Guinea) = 2.00 (fitted 0.08; Z = 2.68) and f 4 (MA1, Ust’-Ishim; Ami, New Guinea) = 1.73 (fitted 0.08; Z = 2.49). We added this admixture into our model with its best-fitting source position (near the root of the East Asian lineage) and mixture proportion (17.4% East Asian-related ancestry, 95% CI 7.7–27.4%).

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We note that a recent study (Lazaridis et al., 2016) found a cline of MA1-relatedness among a large number of present-day eastern Eurasian populations and argued for admixture from west to east instead; while the present analysis supports the other direction, an important subject for future work will be to reconcile these results.

Mark Lipson and David Reich, Working model of the deep relationships of diverse modern human genetic lineages outside of Africa, Mol Biol Evol (2017), doi: 10.1093/molbev/msw293