A new paper by Federico Sánchez-Quinto and colleagues reports on comparisons of North African population samples with the Neandertal DNA project data [1]. The paper shows that North African populations also carry a substantial trace of Neandertal ancestry, like living populations outside of Africa, much more than populations of sub-Saharan Africa.

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

The interesting aspect of the paper is that the authors attempted to separate the ancestry of North African samples into a pre-Neolithic indigenous African component, and a residual component that represents more recent gene flow into North Africa, from all sources. The historic movement into North Africa has been fairly cosmopolitan, involving sub-Saharan Africans, Arabs, Medieval Europeans, Romans, Carthaginians and many other peoples. Sánchez-Quinto and colleagues used the ADMIXTURE program to try to sort out a pre-Neolithic indigenous component and analyze that specifically for Neandertal similarity.

Unsurprisingly, the fraction of estimated sub-Saharan African ancestry in each population sample was inversely correlated with the estimated Neandertal ancestry. That is, the more a population looks like sub-Saharan Africans, the less Neandertal it has.
Here's what's surprising: When they sorted out parts of the genome in Tunisians that ADMIXTURE determines to be most likely from pre-Neolithic North Africans, they found these parts of the genome hadmore Neandertal ancestry than typical of the CEU sample of northern European ancestry. Is it possible that ancient North Africans had more Neandertal similarity than today's Europeans?
Sánchez-Quinto and colleagues suggest that the Neandertal ancestry in this population came in Upper Paleolithic times from the Near East. That is possible, or some of the Neandertal similarity may reflect ancient African population structure. Really I think we will have to do a finer analysis of chromosome blocks to examine the subset of shared Neandertal derived alleles that reflect introgression versus incomplete sorting from the ancestral African population. It will be very interesting to examine more closely the mixture of population history within Egypt, through which most Near Eastern pre-Neolithic population movement must have come.
The authors note that the distribution of Neandertal similarity outside Africa increases with distance from Africa.

A previous study [26] observed that the similarity to Neandertals increases with distance from Africa and suggested this could be explained by SNP ascertainment bias plus a strong genetic drift in East Asian populations. Nonetheless more complex, population-biased, ascertainment schemes might have additional effects (i.e bottlenecks), but these are not expected to significantly increase the rate of false positives in admixture tests [31]. The Tunisian population has been reported to be a genetic isolate [17] so it is plausible that part of the signal detected is actually due to genetic drift. However, this should not affect the other North African groups in our study. Finally, given that SNP arrays are based on common alleles and probably the relevant admixture information is encoded within the rare and very rare alleles, the potential bias, if anything, will underestimate ancient hominid admixture signals, as shown in previous studies [2],[3].

This pattern was also observed by Meyer and colleagues earlier this year [2], and I discussed it in my post on that paper ("Denisova at high coverage"). Both papers note that ascertainment bias may contribute to this pattern. I added that Meyer and colleagues had assumed that genes found in sub-Saharan African populations could not have come from Neandertals, which greatly biased their estimates against Europe and West Asia, considering historical and prehistoric gene flow across the Sahara and along the Indian Ocean coast. So I'm not yet accepting the relative numbers of Neandertal ancestry from different populations, as we don't know that they have all come from consistent assumptions. In particular, an elevated amount of Neandertal ancestry in China -- this paper puts it almost as double the amount of Neandertal ancestry in northern Europeans -- is unlikely. There is no pattern of bottlenecks that can give rise to that excess without additional population mixture, and hard to see where such population mixture would have happened without also affecting the ancestors of Europeans. Instead, we have some work to do in reducing the biases on these comparisons.