Peer-reviewed
Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation
Shaohua Fan, Jeffrey P. Spence, Yuanqing Feng, Matthew E.B. Hansen, Jonathan Terhorst, Marcia H. Beltrame, Alessia Ranciaro, Jibril Hirbo, William Beggs, Neil Thomas, Thomas Nyambo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Alfred K. Njamnshi, Charles Fokunang, Dawit Wolde Meskel, Gurja Belay, Yun S. Song, Sarah A. Tishkoff
We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from “ghost” populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.
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• Whole-genome sequencing of 180 Africans identifies millions of unreported variants • Complex African demographic history with ancient structure, admixture, and introgression • Southern and Central African hunter-gatherers share a unique ancient common ancestry • Signatures of local adaptation for skin color, immune response, height, and metabolism
Fan et al. studied the complex demographic history and the genetic basis of local adaptation for traits related to skin color, immune response, and metabolic processes across African populations using high-coverage whole-genome sequencing data of 180 individuals from 12 indigenous African populations
• Whole-genome sequencing of 180 Africans identifies millions of unreported variants • Complex African demographic history with ancient structure, admixture, and introgression • Southern and Central African hunter-gatherers share a unique ancient common ancestry • Signatures of local adaptation for skin color, immune response, height, and metabolism
Fan et al. studied the complex demographic history and the genetic basis of local adaptation for traits related to skin color, immune response, and metabolic processes across African populations using high-coverage whole-genome sequencing data of 180 individuals from 12 indigenous African populations
Article, 2023