Genome-wide patterns of population structure and admixture in West Africans and African Americans

Abstract

West African populations, because previous genetic and historical studies suggest that region was the source for most of the ancestry of present-day African Americans (2, 27, 28). Among the sampled West African populations, Wright’s measure of population differentiation [autosomal FST (29)] was low (1.2%), suggesting quite recent common ancestry of all individuals in our sample or, alternatively, a large effective population size for the structured population from which the sample was drawn, with a large degree of gene flow among subpopulations. Nonetheless, we observed substantial variation in pairwise FST among sampled populations, suggesting genetic heterogeneity among the groups (Table 1). Differences in pairwise FST may reflect variation in effective population size or migration rates among the populations potentially attributable to isolation by distance or heterogeneity in geographical or cultural barriers to gene flow. For example, the Fulani appear to be genetically distinct from all other West African populations we sampled (average pairwise FST = 3.91%). Likewise, we found that the Bulala, Xhosa, and Mada populations consistently exhibited pairwise FST above 1% when compared with any other population, whereas the non-Bantu NigerKordofanian populations of the Igbo, Brong, and Yoruba exhibited little genetic differentiation from one another (average FST <0.4%). These results suggest that there are clear and discernible genetic differences among some of the West African populations, whereas others appear to be nearly indistinguishable even when comparing over 300,000 genetic markers. To investigate whether we could reliably distinguish ancestry among individuals from these populations, we used two approaches tailored for high-density genotype data. One, FRAPPE, implements a maximum likelihood method to infer genetic ancestry of each individual, wherein the individuals are assumed to have originated from K ancestral clusters (26). Fig. 1A and Fig. S2 summarize FRAPPE results when the number of clusters, K, is varied from K = 2 to K = 7. The small number of clusters was