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, 29 (10), 2987-95

Ancient Structure in Africa Unlikely to Explain Neanderthal and non-African Genetic Similarity


Ancient Structure in Africa Unlikely to Explain Neanderthal and non-African Genetic Similarity

Melinda A Yang et al. Mol Biol Evol.


Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.


F<sc>IG</sc>. 1.
FIG. 1.
Demographic models relating Neanderthals and modern humans. At time tH in the past (t = 0 being the present), non-African humans (Non-Afr) split from African humans (Afr). After they split, Non-Afr and Afr may exchange migrants at rate mt. At time tN, Neanderthals (Neand) split from the ancestors of modern humans. (a) Recent admixture model. At time tGF < tH, Neand admixed with non-Afr at rate f. The variables used in the derivation of the dcfs are shown in parantheses. (b) Ancient structure model. The ancestral population of modern humans is structured in two subpopulations exchanging migrants at rate m. The substructure continues in the ancestral population of Neanderthals and modern humans.
F<sc>IG</sc>. 2.
FIG. 2.
The dcfs for recent admixture (a, c, e) and ancient structure (b, d, f) for parameters shown in table 1, including no ongoing gene flow (a, b), ongoing gene flow of 4Nmt = 1 (c, d), and ongoing gene flow of 4Nmt = 5 (e, f). The time of admixture in the recent admixture model was 4NtGF = 0.05. The admixture rate simulated was 0.05.

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