Intra-African variation in Neandertal admixture is due to non-African admixture

I haven't read this, but the idea seems to be that variation between Africans in Neandertal admixture can be wholly explained by recent admixture with Eurasians (who already had this type of admixture). This is not very surprising, given that Neandertals were a Eurasian-distributed species, so that admixture with them cannot have taken place in Africa.

The finding that Africans don't vary in their Neandertal admixture suggests that the source cannot have been an unknown African hominin related of Neandertals (in which case we'd expect to see variation in Africans). I don't know of any anthropologically plausible African cousin of the Neandertals, but, of course, the lack of anthropological evidence does not mean non-existence (cf. Denisovans as an anthropologically invisible Neandertal relative in Eurasia).

Genome Biol Evol. 2013 Oct 25. [Epub ahead of print]

Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations.

Wang S, Lachance J, Tishkoff S, Hey J, Xing J.

Abstract

Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and the modern humans descended from the Out-of-Africa (OOA) migration. Here we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression while others do not. To test this alternative model we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like SNP alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern human and Neanderthal-like hominid within Africa.

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