To oversimplify, the main reason that Europeans have lower percentages of Neanderthal admixture than Asians is African migration to Europe in the last 20,000 years, and not natural selection against Neanderthal variants or "basal European" admixture from Southwest Europe. This is encouraging as the notion of "basal Europeans" with little or no Neanderthal admixture in Southwest Europe never made much sense to me.
Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans due to deleterious alleles that had accumulated in the Neandertals after they split from the modern human lineage. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45 thousand years. Here we show that this apparent decline is an artifact caused by gene flow between West Eurasians and Africans, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When applying a more robust statistic that takes advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Western Europe over the past 45 thousand years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters, and find that negative selection is not expected to cause a significant long- term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular a depletion of Neandertal ancestry in conserved genomic regions that are likely to be of functional importance. Thus, we find that negative selection against Neandertal ancestry has not played as strong a role in recent human evolution as had previously been assumed.Martin Petr, Svante Pääbo, Janet Kelso, Benjamin Vernot, "The limits of long-term selection against Neandertal introgression" bioRxiv (July 4, 2018) doi: https://doi.org/10.1101/362566
UPDATE: A comment suggests that I have misinterpreted the paper somewhat and I am looking into that possibility.
To oversimplify, the main reason that Europeans have lower percentages of Neanderthal admixture than Asians is African migration to Europe in the last 20,000 years
You must have misread the paper since the paper concludes that the earlier findings of lower Neanderthal admixture percentages in modern West Eurasians than East Eurasians and early West Eurasians were due to West Eurasian gene flow to Africans in the last 20,000 years, and not due to any African gene flow to West Eurasians. They come to this conclusion because they find that modern West Eurasians actually have virtually the same amount of Neanderthal admixture percentages as East Eurasians and early West Eurasians and the previous tests found lower Neanderthal admixture percentages in modern West Eurasians than East Eurasians and early West Eurasians because their samples and methodologies were not sufficient enough to discern the effects of West Eurasian gene flow to Africans on the estimations of Neanderthal admixture percentages.
and not natural selection against Neanderthal variants or "basal European" admixture from Southwest Europe. This is encouraging as the notion of "basal Europeans" with little or no Neanderthal admixture in Southwest Europe never made much sense to me.
There is no such thing as Basal European, there is Basal Eurasian. The paper does not refute the idea of Basal Eurasian, it just finds that Basal Eurasians were virtually no different from other Eurasians in their percentages of Neanderthal ancestry. So that means early Basal Eurasians may well have lived in the territories of the Near East with Neanderthal admixture and there is no reason to locate their place of origin in North Africa or East Africa.
Thanks. I'll take another look at the paper. I may have skimmed it too quickly.
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