Positive selection in admixed populations from Ethiopia

BMC Genetics

Luca Pagani¹  Sandra Walsh²  Jaume Bertranpetit²  Hafid Laayouni³  Yali Xue⁴  Chris Tyler-Smith⁴ 

[1]Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia

[2]Department of Biology, University of Padova, 35131, Padova, Italy

[3]Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain

[4]Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain

[5]Bioinformatics Studies, ESCI-UPF, Barcelona, Catalonia, Spain

[6]The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK

关键词: Positive selection;    Selective sweeps;    Human population genetics;    Genomics;    Admixture;    African populations;    Ethiopia;    West Asia;   

DOI  :  10.1186/s12863-020-00908-5

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY