Human Ancestors Interbred with Related Species

Our ancestors bred with other species in the Homo genus, according to a study published today in the Proceedings of the National Academy of Sciences. The authors say that up to 2% of the genomes of some modern African populations may originally come from a closely related species.

Palaeontologists have long wondered whether modern humans came from a single, genetically isolated population of hominins or whether we are a genetic mix of various hominin species.

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It has been a mystery whether similar genetic mixing [to that of non-Africans and Neanderthals] took place among Homo species even earlier, before the populations that became modern humans left Africa.

To find out, evolutionary biologist Michael Hammer at the University of Arizona in Tucson and his colleagues studied DNA from two African hunter-gatherer groups, the Biaka Pygmies and the San, as well as from a West African agricultural population known as the Mandenka.

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To find signs of infiltration from other Homo species, the researchers looked at 61 non-coding DNA regions in all three groups. Because direct comparison to archaic specimens wasn’t possible, the authors used computer models to simulate how infiltration from different populations might have affected patterns of variation within modern genomes.

Then they looked for such patterns of variation in the DNA of the three African populations. On chromosomes 4, 13 and 18, the researchers found genetic regions that were more divergent on average than known modern sequences at the same locations, hinting at a different origin.

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Hammer and his colleagues argue that roughly 2% of the genetic material found in these modern African populations was inserted into the human genome some 35,000 years ago. They say these sequences must have come from a now-extinct member of the Homo genus that broke away from the modern human lineage around 700,000 years ago.

Hammer says this disproves the conventional view that we are descended from a single population that arose in Africa and replaced all other Homo species without interbreeding. “We need to modify the standard model of human origins,” he says.

Geneticist Sarah Tishkoff, who studies population genetics and human evolution at the University of Pennsylvania in Philadelphia, is more cautious. “This raises the possibility that there may have been ancient admixture with archaic populations,” she says.

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Michael F. Hammer et al., PNAS, September 6, 2011

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.