Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

Nyambo, Thomas B.

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.

dc.contributor.author	Nyambo, Thomas B.
dc.date.accessioned	2023-09-08T06:03:01Z
dc.date.available	2023-09-08T06:03:01Z
dc.date.issued	2023
dc.description.abstract	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.	en_US
dc.identifier.citation	Fan, S., Spence, J.P., Feng, Y., Hansen, M.E., Terhorst, J., Beltrame, M.H., Ranciaro, A., Hirbo, J., Beggs, W., Thomas, N. and Nyambo, T., 2023. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell, 186(5), pp.923-939.	en_US
dc.identifier.other	https://doi.org/10.1038/nature22336
dc.identifier.uri	http://hdl.handle.net/123456789/1175
dc.language.iso	en	en_US
dc.publisher	Cell	en_US
dc.subject	African genomics	en_US
dc.subject	Local adaptation	en_US
dc.subject	African demographic history	en_US
dc.title	Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.	en_US
dc.type	Article	en_US