Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals
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Date
2023-10-13
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Current Biology
Abstract
Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history
of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Af-
rica to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neander-
thals that descend from this introgression. Regions of the genome with Neanderthal similarities have
also been identified in sub-Saharan African populations, but their origins have been unclear. To better
understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and
what their distribution within the genome tells us about early AMH and Neanderthal evolution, we
analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse
sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African
ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by
recent migration, and subsequent admixture, of AMH populations originating from the Levant and North
Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate
from migration of AMH populations from Africa to Eurasia 250 kya, and subsequent admixture with
Neanderthals, resulting in 6% AMH ancestry in Neanderthals. These results indicate that there have
been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has
been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal
introgression are also regions where Neanderthal genomes show a depletion of AMH introgression
points to deleterious interactions between introgressed variants and background genomes in both
groups—a hallmark of incipient speciation.
Description
Keywords
Genomes, African, Neanderthals
Citation
Harris, D.N., Platt, A., Hansen, M.E., Fan, S., McQuillan, M.A., Nyambo, T., Mpoloka, S.W., Mokone, G.G., Belay, G., Fokunang, C. and Njamnshi, A.K., 2023. Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. Current Biology.