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. [Neanderthals Had Sex With Humans]

"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.

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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.)

The researchers discovered especially strong evidence for such genetic mixing in the Biaka and San, in the form of a trio of unusual haplotypes. By comparing these sets of genes with those from comparable modern human ones, the investigators estimated the unusual genes may have come from a lineage that first diverged from the ancestors of modern humans about 700,000 years ago. For context, the Neanderthal lineage diverged from ours within the past 500,000 years, while the first signs of anatomically modern human features appeared only about 200,000 years ago.

"The populations that interbred in Africa were on a similar scale of divergence as the expanding modern population and Neanderthals were outside of Africa," Hammer said. "They were similar enough biologically so that they were able to produce fertile offspring, thus allowing genes to flow from one population to the other."

The length of the exotic haplotypes from this extinct lineage suggests interbreeding might still have occurred until as recently as 35,000 years ago.

"We think there were probably thousands of interbreeding events," Hammer said. "It happened relatively extensively and regularly."

Homeland of extinct lineage

A broader survey of where this trio of exotic haplotypes from this extinct lineage might now be found revealed they could be seen in modern human groups across sub-Saharan Africa, but apparently just one central African population of Pygmies, the Mbuti, had all three. Since this group is relatively isolated from other modern human populations, including other Pygmies, the scientists conjecture that central Africa may have been the homeland of this extinct lineage.

In the future, Hammer's team wants to look at the entire genome sequences of several modern human groups in Africa to get a better picture of how interbreeding might have occurred.

"Did it occur in a single burst in a single locale, or was admixture an ongoing process such that genes were flowing over large geographic distances and long periods of time?" Hammer asked. "This has many implications for how modern humans acquired the features that make them unique." [10 Things That Make Humans Special]

The researchers also want to look for ancient DNA from this extinct lineage that might have conferred some evolutionary advantage to hybrids with modern humans. This process of modern humans interbreeding with other lineages as they expanded across the world "may have accelerated the evolutionary process by allowing genes that are beneficial in one locale to spread to a new population that has not yet had time to adapt to those new conditions," Hammer said. "This may be a major mode of acquiring novel characteristics and one of the ways that we became the species that we are today."

So far no traces of the haplotypes from this newfound lineage have been seen in modern human groups outside of Africa. However, "we can't be sure until we do a better job of searching for them," Hammer said. "Another question for the future."

The scientists detailed their findings online Sept. 5 in the Proceedings of the National Academy of Sciences.

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