Now-Extinct Relative Had Sex with Humans Far and Wide
A molar tooth belonging to a Denisovan, thought to be a new branch of ancient humans.
Credit: David Reich et al., Nature.

A mysterious extinct branch of the human family tree that once interbred with ours apparently lived in a vast range from Siberia to Southeast Asia, mating with just as widely spread a group of modern humans, scientists find.

This new research also demonstrates that contrary to the findings of the largest previous genetic studies, modern humans apparently settled Asia in multiple waves of migration, investigators added.

These lost relatives, known as the Denisovans, were discovered from at least 30,000-year-old bones and teeth unearthed in the Siberian Denisova cave in 2008. Analysis of DNA taken from these fossils suggested they shared a common origin with Neanderthals, but were nearly as genetically distinct from Neanderthals as Neanderthals were from living people.

Although we modern humans are the only surviving members of our lineage, other now-extinct human groups once lived alongside our ancestors, including Neanderthals, Denisovans and an as-yet- unnamed lineage recently discovered in Africa.  Modern humans even occasionally interbred with these relatives, with estimates suggesting that Neanderthal DNAmakes up1 percent to 4 percent of modern Eurasian genomesand Denisovan DNA 4 percent to 6 percent of modern New Guinean and Bougainville Islander genomes in the islands of Melanesia. [See images of mysterious human ancestor]

Now, using state-of-the-art genome analysis methods, an international team of scientists confirmed that Denisovans must have roamed widely, from Siberia to tropical Southeast Asia. They apparently left a genetic footprint not only in present-day Melanesia, but also in Australia, the Philippines and elsewhere.

"They must have extended over a large geographic range," researcher David Reich, an evolutionary geneticist at Harvard Medical School, told LiveScience. Indeed, these findings suggest "Denisovans were spread more widely geographically and ecologically than any other hominin, with the exception of modern humans," said molecular anthropologist Mark Stoneking at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. (Hominins include those species after the human lineage Homo split from that of chimpanzees.)

Tracing Denisovan genes

The new study was initiated byStoneking, an expert on genetic variation in Southeast Asia and Oceania who has assembled diverse samples from that region. Stoneking, Reich and their colleagues analyzed DNA from 33 present-day populations in south Asia, Southeast Asia and Oceania, including Borneo, Fiji, Indonesia, Malaysia, Australia, the Philippines, Papua New Guinea and Polynesia.

"Denisovan DNA is like a medical imaging dye that traces a person's blood vessels — it is so recognizable that you can detect even a little bit of it in one individual," Reich said. "In a similar way, we were able to trace Denisovan DNA in the migrations of people."

Their analysis shows that, in addition to Melanesians, Denisovans contributed DNA to Australian aborigines, a Philippine "Negrito" group called Mamanwa, and several other populations in eastern Southeast Asia and Oceania. However, groups in the west or northwest, including other Negrito groups such as the Onge in the Andaman Islands and the Jehai in Malaysia, as well as mainland East Asians, did not interbreed with Denisovans.

Overall, this suggests that Denisovans interbred with modern humansin Southeast Asia at least 44,000 years ago, before the time of the separation of the Australians and New Guineans.

"The fact that Denisovan DNA is present in some aboriginal populations of Southeast Asia but not in others shows that there was a checkerboard of populations with and without Denisovan material more than 44,000 years ago," Stoneking said, adding the discrepancy could be explained if the Denisovans lived in Southeast Asia. [Top 10 Mysteries of the First Humans]

"We often think of population mixtures as a kind of recent phenomenon in human history, such as in the Americas, but what the genetic data is telling us more and more with the Neanderthals and Denisovans is that it happened over many times in history as a common feature of our evolution," Reich said.

"There might be a tendency to think that mating between modern humans and archaic humans such as Neanderthals and Denisovans is a very strange behavior and therefore there must be something unusual or different about populations that engaged in such behavior," Stoneking added. "Instead, I think the picture we are getting from both this work as well as from analyses of genetic data from all modern human populations is that there are two things humans like to do — migrate and mate — and the product of these two is going to be admixture."

"The prediction I would make, which is already largely fulfilled, is that every human population shows signs of admixture, either with other modern human populations and-or with archaic humans, and that this is very normal behavior for humans," Stoneking told LiveScience.

Waves of migration

In addition, the patterns the scientists found can only be explained by at least two waves of migration of modern humans into Asia. The first gave rise to the aboriginal populations that currently live in Southeast Asia and Oceania, and later migrations gave rise to relatives of East Asians who now are the primary population of Southeast Asia.

"This shows the power of sequencing ancient DNA as a tool for understanding human history," Reich said. [History's Most Overlooked Mysteries]

Such findings support the idea of modern humans dispersing eastward to Asia by a southern route through India to Australia and Melanesia. This concept was previously supported by archaeological evidence, but never had strong genetic support until now.

"The archaeological evidence suggested that the first people got to Australia and New Guinea incredibly early, with tools that were less advanced technologically than later seen in the Middle East, Europe and Asia," Reich said. "The genetic work now supports that, showing there were multiple waves of migration to Asia and Oceania, with some quite earlier than others."

The researchers now want to pinpoint the time at which interbreeding with Denisovans occurred, "and to figure out if the genes that modern humans received from Denisovans have contributed anything of importance," Stoneking said.

The scientists detailed their findings online Sept. 22 in the American Journal for Human Genetics.

Follow LiveScience for the latest in science news and discoveries on Twitter @livescience and on Facebook.