African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations.
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Date
2019-04-26
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Genome Biology
Abstract
Background: Africa is the origin of modern humans within the past 300 thousand years. To infer the complex
demographic history of African populations and adaptation to diverse environments, we sequenced the genomes
of 92 individuals from 44 indigenous African populations.
Results: Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography
and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range
migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all
modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged
by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza
hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120–100 kya. Niger-Congo, Nilo-Saharan,
and Afroasiatic lineages diverged more recently by ~ 54–16 kya. Eastern and western CRHG lineages diverged by ~ 50–
31 kya, and the western CRHG lineages diverged by ~ 18–12 kya. The San and CRHG populations maintained the
largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of
positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy
metabolism, and cell signaling, which may contribute to local adaptation of African populations.
Conclusions: We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated
with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
Keywords: African populations, Genomic variation, Human evolution, Local adaptation, Demographic history, Effective
population size, Whole genome sequencing
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Keywords
African populations, Genomic variation, Human evolution
Citation
Fan, S., Kelly, D.E., Beltrame, M.H., Hansen, M.E., Mallick, S., Ranciaro, A., Hirbo, J., Thompson, S., Beggs, W., Nyambo, T. and Omar, S.A., 2019. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biology, 20(1), pp.1-14.