Genetic evidence for archaic admixture in Africa

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 (z2%) that introgressed z35 kya from an archaic population that split from the ancestors of anatomically modern humans z700 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.H. sapiens | hybridization I t is now well accepted that anatomically modern humans (AMH) originated in Africa and eventually dispersed to all inhabited parts of the world. What is not known is the extent to which the ancestral population that gave rise to AMH was genetically isolated, and whether archaic hominins made a genetic contribution to the modern human gene pool. Answering these questions has important implications for understanding the way in which adaptations associated with modern traits were assembled in the human genome: do the genes of AMH descend exclusively from a single isolated population, or do our genes descend from divergent ancestors that occupied different ecological niches over a wider geographical range across and outside of the African Pleistocene landscape?The introgression debate is typically framed in terms of interbreeding between AMH and Neandertals in Europe or other archaic forms in Asia. The opportunity for such hybridizations may have existed between 90 and 30 kya, after early modern humans dispersed from Africa and before archaic forms went extinct in Eurasia (1-5). Recent genome-level analyses of ancient DNA suggest that a small amount of gene flow did occur from Neandertals into the ancestors of non-Africans sometime after AMH left Africa (6) and that an archaic "Denisovan" population contributed genetic mat...

Variability in the Middle Stone Age of Eastern Africa

“…The early fossils of H. sapiens and the populations they represent are highly variable, and there is as yet no consensus on how to partition this variability (Gunz et al 2009;Pearson 2008;Trinkaus 2005). Given the possible presence of ancestral and sister taxa in the region (e.g., Hammer et al 2011;Lachance et al 2012), a more cautious reading of the available evidence would be that the variability among MSA sites likely encapsulates the behavioral outcomes of multiple hominin populations of varying taxonomic affinities. Direct linkage between particular hominins and specific archaeological entities is beyond the resolution of our data, a problem that arises in other regions such as the Levant (cf.…”

Neanderthals had outsize effect on human biology

“…The genomes of most Europeans and Asians are 2-4% Neanderthal 1 , with Denisovan DNA making up about 5% of the genomes of Mela nesians 2 and Aboriginal Australians 3 . DNA slivers from other distant relatives probably pepper a variety of human genomes 4 .…”

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

“…Furthermore, there is growing evidence that archaic introgression occurred also within Africa (Labuda et al, 2000;Hammer et al, 2011;Lachance et al, 2012;Hsieh et al, 2016;Xu et al, 2017;Zanolli et al, 2017), raising the exciting possibility that other unknown archaic groups may have contributed to human genetic diversity. Therefore, recent work suggests that apparently distinct species can exchange the genetic material along their evolutionary history (Mallet et al, 2016).…”