ASHG 2010 abstract on archaic admixture in modern humans

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Evidence for archaic admixture in contemporary non-African human populations. J. Long, R. Ferrucci, S. Joyce, K. Hunley Dept of Anthropology, Univeristy of New Mexico, Albuquerque, NM.

Analyses of large-scale genetic data sets show evidence for a series of founder effects that occurred as modern humans left Africa and settled the rest of the world. Nonetheless, research on modern humans has not ruled out the possibility that other processes, such as local gene flow, or mixing between archaic and modern humans, have also contributed to modern human diversity. Recent analyses of the Neanderthal genome make archaic admixture a salient issue because they show evidence for mixing between Neanderthals and out-of-Africa migrants. The present study examines evidence for archaic admixture in genotypes for 619 microsatellite loci collected from over 2,000 individuals from 100 human populations. We obtained these data from the Marshfield Clinic collection. The populations analyzed represent all inhabited continents of the world. In our analysis, we formulate the serial founder effects (SFE) model as a special case of a phylogenetic model promoted by Cavalli-Sforza and his associates. In this light, the SFE process makes four predictions: 1) A tree of descent according to the pattern of fissions. 2) The root of the tree lies in Africa. 3) The length of each branch is proportional to ratio of evolutionary time to effective population size. 4) The gene identity between all pairs of populations that share the same most recent common ancestor is equal in expectation. Using hypothesis tests based on generalized hierarchical statistical models, we find good agreement between the SFE predictions and diversity within and between African populations, and we find good agreement between the SFE predictions and diversity between non-African populations. However, there is more diversity within the non-African populations than the SRE model can account for. This makes for greater genetic distance between Africans and non-Africans than otherwise expected. How and where did the non-Africans obtain this diversity? A simple explanation for the finding is that the earliest migrants out-of-Africa mixed with an archaic population such as Neanderthals prior to their expansion throughout Europe and Asia. Coalescent based computer simulations of the SFE model with mixing support our interpretation. The time and place that we detect mixing coincides perfectly with that detected in a recent examination of Neanderthal genome sequences. Our study shows that genomic diversity in modern humans still reflects ancient events and processes.