Abstract
BackgroundIn the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history.ResultsHere, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens.ConclusionsSignals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.
Highlights
In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role
We assessed the statistical significance of the scores by defining a critical value of the test, after performing extensive neutral simulations, as corresponding to the 99.99th percentile of the neutral distribution; the threshold is different for each population
We find in all Afroasiatic populations, except Wolayta, an excess of African ancestry in windows under selection containing among other genes FADS1 and FADS2, two enzymes that participate in the omega-3 and omega-6 biosynthesis and found to be under positive selection in other human populations (Fig. 5b) [86, 87]
Summary
In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. African populations are genetically more diverse than any other human population, holding the highest amount of genetic variation, low linkage disequilibrium (LD), and deep population structure [10,11,12,13]. They carry high cultural and phenotypic diversity, speak almost one-third of the world’s languages [14], live in a wide variety of environments including deserts, tropical rainforests and mountain highlands, and follow many subsistence strategies, including pastoralism, agriculture and hunter-gathering [15]. Additional African-specific studies are needed to counterbalance this historical bias [13, 19]
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