Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations.

OBJECTIVES: The aim of this study was to characterize the genetic relationships within and among four neighboring ethnolinguistic groups in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. MATERIALS AND METHODS: We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. RESULTS: Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. DISCUSSION: Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.

Revisiting the notion of deleterious sweeps.

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites-both in the presence and absence of interference amongst deleterious mutations-and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of FST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.