Fan S., Kelly D.E., Beltrame M.H., Hansen M.E.B., Mallick S., Ranciano A., Hirbo J., Thompson S., Beggs W., Nyambo T.B., Omar S.A., Meskel D.W., Belay G., Froment Alain, Patterson N., Reich D., Tishkoff S.A. (2019). African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations [plus Correction]. Genome Biology, 20, art. 82 [14 p. + 1 p.]. ISSN 1474-760X.
Titre du document
African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations [plus Correction]
Année de publication
2019
Auteurs
Fan S., Kelly D.E., Beltrame M.H., Hansen M.E.B., Mallick S., Ranciano A., Hirbo J., Thompson S., Beggs W., Nyambo T.B., Omar S.A., Meskel D.W., Belay G., Froment Alain, Patterson N., Reich D., Tishkoff S.A.
Source
Genome Biology, 2019,
20, art. 82 [14 p. + 1 p.] ISSN 1474-760X
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]
;
Démographie [108]
Description Géographique
AFRIQUE
Localisation
Fonds IRD [F B010075637]
Identifiant IRD
fdi:010075637
