Humans Had Sex Regularly With Mysterious Extinct Relatives in Africa

A new study of the human genome reveals modern humans interbred not only with Neanderthals but also with an extinct group of relatives in Africa. CREDIT: NASA/JPL-Caltech

Our species may have bred with a now extinct lineage of humanity before leaving Africa, scientists say.

Although we modern humans are now the only surviving lineage of humanity, others once roamed the Earth, making their way out of Africa before our species did, including the familiar Neanderthals in West Asia and Europe and the newfound Denisovans in East Asia. Genetic analysis of fossils of these extinct lineages has revealed they once interbred with modern humans, unions that may have endowed our lineage with mutations that protected them as we began expanding across the world about 65,000 yeas ago.

Now researchers analyzing the human genome find evidence that our species hybridized with a hitherto unknown human lineage even before leaving Africa, with approximately 2 percent of contemporary African DNA perhaps coming from this lineage. In comparison, recent estimates suggest that Neanderthal DNA makes up 1 percent to 4 percent of modern Eurasian genomes and Denisovan DNA makes up 4 percent to 6 percent of modern Melanesian genomes.

“We need to modify the standard model of human origins in which a single population transitioned to the anatomically modern state in isolation — a garden of Eden somewhere in Africa — and replaced all other archaic forms both within Africa and outside Africa without interbreeding,” researcher Michael Hammer, a population geneticist at the University of Arizona in Tucson, told LiveScience. “We now need to consider models in which gene flow occurred over time.”

Haplotype hints

Hammer and his colleagues gathered DNA samples from the Center for the Study of Human Polymorphisms in Paris and sequenced about 60 regions of the human genome that apparently have no function. These genes are less subject than functional DNA to change as a result of recent evolutionary pressures driving the survival of the fittest; in such a way, they can give a clearer view of how populations might have mixed or not in the past.

The investigators focused on three populations that presented a good sample of the geographic and cultural diversity of sub-Saharan Africa — Mandenka farmers in western Africa, Biaka Pygmies in west-central Africa, and San Bushmen of southern Africa — looking for unusual patterns that suggested ancient interbreeding with other lineages. This included a hunt for long haplotypes, or sets of DNA sequences, not seen in other modern human groups, the idea being that while short haplotypes could potentially be explained by a few chance mutations within these modern human populations, comparatively long haplotypes were instead likely inherited from a significantly different lineage.

“If interbreeding occurs, it’s going to bring in a whole chromosome,” Hammer explained. Although this genetic contribution would have dwindled over time, remnants would still exist as shorter, unusual fragments, and “by looking at how long they are, we can get an estimate of how far back the interbreeding event happened.” (The longer these odd haplotypes are, the more recently they occurred, having less time to get diminished by other genetic inputs.)