Genetic evidence for archaic admixture in Africa

TLDR

The fate of archaic Homo—whether they went extinct or interbred with modern humans—has been debated, with most focus on their genetic contribution outside Africa. The study tests models of African archaic admixture using DNA sequence data from 61 noncoding autosomal regions in three sub‑Saharan populations. Two complementary approximate‑likelihood methods were applied to a human‑evolution model incorporating recent population structure, with and without archaic gene flow. Simulation results reject a no‑admixture null and indicate that about 2 % of contemporary African genomes derive from an archaic population that split from modern humans ~700 kya and introgressed ~35 kya, with several candidate loci—including a >31 kb segment on chromosome 4—supporting recent interbreeding with a now‑extinct hominin.

Abstract

A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (≈ 2%) that introgressed ≈ 35 kya from an archaic population that split from the ancestors of anatomically modern humans ≈ 700 kya. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.