Our Ancestors Interbred With At Least Four Archaic Human Populations


Stephen Luntz

Stephen has a science degree with a major in physics, an arts degree with majors in English Literature and History and Philosophy of Science and a Graduate Diploma in Science Communication.

Freelance Writer


Throughout what is now island Southeast Asia modern humans interbred with archaic populations, and even though we don't have the genetic sequence or fossils from these people, we can detect the genetic sequences they left behind. Teixeira and Cooper/Proceedings of the National Academy of Sciences

It's not long since we learned most of us carry DNA from Neanderthals and Denisovans, but that was only the beginning. A new study indicates the genetic legacy of at least four archaic human populations survives today from five or six rounds of interactions. Prejudice against sex between races looks pretty laughable when you consider our ancestors didn't seem to care too much about the species they were having sex with.

To identify Neanderthal and Denisovan influences in modern genomes, scientists use DNA from fossil members of each. It’s much harder to identify the presence of gene variations from populations whose DNA we don’t have, but some teams have developed methods allowing us to do this. Dr João Teixeira of the University of Adelaide put this work together in the Proceedings of the National Academy of Sciences to create a picture of approximately where and when this intermixing occurred.


Teixeira explained to IFLScience that Neanderthal genes account for about 2 percent of the genome of everyone, other than those of recent African descent. Other archaic humans' legacies are more concentrated in people from particular regions.

“Geneticists have come up with methods to screen the genome for deviations that look old,” Teixeira said. “The trick is to look for a set of variants that segregate together and are not found in Africa. After we match these with those from Neanderthals and Denisovans there are several left over.”

Archaic sequences in modern populations help us draw a picture of where we met these archaic populations.

One encounter, with a population dubbed Extinct Hominin 1, probably happened in India soon after humanity spread out of Africa and the ancestors of modern Asians and Europeans separated.





Our encounters with Neanderthals came not long after we left Africa, followed by Extinct Hominin 1, and Denisovans (3). Teixeira and Cooper PNAS

Another took place in the last ice age when sea levels were far lower and the Sunda Shelf united Borneo, Java, and Sumatra to the Asian mainland. Teixeira describes this as a “Denisovan-like event.” The population we mated with clearly had a lot in common with Denisovans, but their geographic isolation from their Siberian home makes it likely they were distinct.


The indigenous people of the Philippines have an extra helping of Denisovan-like genetics, suggesting a separate encounter there.

Perhaps most intriguing of all is the presence of genetic sequences in people from Flores. This was identified in a Science paper, but not highlighted, perhaps because the authors considered the findings tentative.

Teixeira told IFLScience the romantic notion some part of the “hobbits” (Homo floresiensis) survives within us is unlikely. The hobbits are believed to descend from Homo erectus. The Flores sequence appears to come from more closely related relatives, which the paper calls Extinct Hominin 2, on the island, and it is their genes that survive today.

We know that Neanderthals affected our immune systems and Denisovans gave Tibetans altitude adaptation. Teixeira said we haven’t been able to identify if the descendants of Extinct Hominins 1 and 2 have benefited.


Nevertheless, these long-gone people helped us become who we are. “Each of us carry within ourselves the genetic traces of these past mixing events,” Teixeira said in a statement. “These archaic groups were widespread and genetically diverse, and they survive in each of us. Their story is an integral part of how we came to be.”