Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history

Abstract

ObjectivesModern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabian depending on which dispersal route out of Africa was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.Materials and MethodsWe analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared those data to populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.ResultsWe find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.DiscussionWe infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.

Past human expansions shaped the spatial pattern of Neanderthal ancestry

“…Instead, our results reveal that the current geographical heterogeneity of NE ancestry is due to dynamics that occurred during the more recent Neolithic expansion ~10,000 BP. The early FA populations, which are probably related to the previously identified basal Eurasian lineage 18,19,49 , admixed with HG, leading to a progressive increase in HG ancestry and consequently NE ancestry in the expanding FA populations. The partial replacement of HGs by FAs 31,32 thus contributed to reducing the level of NE ancestry in western Eurasia more than in eastern Eurasia.…”

“…5). Note that it was recently found that modern Levantine and southern Arabian populations still have lower NE ancestry than northern Eurasian populations 49 .…”