In 2010 when the Neandertal sequence paper was published the word was that all non-Africans had the same proportion of ancestry from this population, a few percent. Over the past few years researchers have looked closer, and come to the conclusion that that was wrong. In particular, East Asians seem to have ~20 percent greater Neandertal ancestry than Europeans. Why? A simple solution is that there were several admixture events with Neandertals on the way out of Africa as modern humans settled the world. But there are other options, making recourse to standard population genetic theories. So last year in The genomic landscape of Neanderthal ancestry in present-day humans proposed that the higher fraction in East Asians in Neandertals was a function of the weaker efficacy of purifying selection, which removes deleterious alleles from the genetic background, in populations which went through bottlenecks. As you may know, East Asians seem to have gone through more bottlenecks in the out of Africa migration, probably because of several choke points from west to east Eurasia.
Two new papers in The American Journal of Human Genetics seem to suggest that this explanation is unlikely. First, in Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations, the authors use simulation frameworks to suggest that the extent of the bottleneck difference can not account for the difference in ancestry fractions. In other words, there isn’t that much variation in purifying selection. In the second paper the authors explicit test the ‘two pulse’ model vs. the ‘single pulse’ model. To remove the confound of selection they looked at neutral regions, and the difference persisted. Though the authors could not rule out the possibility that Europe received an influx of African-like individuals who reduced the Neandertal fraction in western Eurasian, the three ancestral populations which fused to form Europeans (i.e., hunter-gatherers, first farmers, and the steppe invaders) all had about the same Neandertal fraction. This leaves then the possibility that East Asians received a second dollop of Neandertal ancestry, ergo, the two pulse model.
A few years back Jeff Wall published a paper that showed that the Complete Genomes Gujarati samples were in between the Europeans and East Asians in Neandertal fraction. We know that the “Ancestral South Indian” (AS) fraction of Gujarati ancestry is closer to East Asians than to West Eurasian groups. To me this suggests that the second admixture may have occurred in the eastern zone of the Middle East, seem it seems basal to the eastern lineages of humans.
The topology of the human phylogenetic graph is getting somewhat more complex. But there are diminishing returns. We’re arguing over tenths of a percent now, as opposed to percents. In the near future this book will be probably be closed.
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