New Study Details Interbreeding of Ancient Humans With Evolutionary Cousins

Genetic analysis shows multiple periods of inbreeding—trysts that may have given ancient humans the genetic tools they needed to survive

Figure from the Neanderthal Museum in Mettmann, Germany Iain Masterton/incamerastock/Corbis

Scientists have known for a while that early humans interbred with their ancient Neanderthal and Denisovan cousins. Chunks of their DNA can still be found in most non-African populations. But just how often and where this interbreeding took place has remained a mystery—until now.

A new study published in the journal Science is starting to unravel that timeline, showing that the periods of mating between evolutionary cousins took place multiple times over a 60,000 year period on several different continents.

Cari Romm at The Atlantic reports that researchers analyzed the DNA from 1,523 modern people of various ethnic backgrounds. Using a new statistical method, the team classified which DNA came from Neanderthals or Denisovans and whether that ancient DNA came from one encounter or separate periods of interbreeding.

The study led to an interesting chronology, writes Ann Gibbons for Science MagazineIt revealed that most of the ancient DNA in Melanesians—the people who live in Papua New Guinea and the surrounding islands in the South Pacific—came from Denisovans, a close cousin of the Neanderthal known from some molars and a single pinky bone found in a cave in Siberia.

While researcher knew Melanesians had Denisovan DNA, they did not think the percentage would be so high, roughly 1.9 to 3.4 percent of their total genome. Melanesians also have Neanderthal DNA from one encounter period, which probably took place soon after Homo sapiens left Africa. It’s thought the Melanesian ancestors then moved on, picking up the Denisovan DNA somewhere in Asia.

“That's pretty strange,” Joshua Akey, a population geneticist at the University of Washington in Seattle and a lead author on the study tells Charles Q. Choi at LiveScience. “What we know of Denisovans comes from a pinky bone from a cave in northern Siberia, yet the only modern human population with appreciable levels of Denisovan ancestry is a couple of thousand miles away from that cave, in Melanesia.”

A second tryst with Neanderthals is recorded in the DNA of Europeans, South Asians and East Asians, which likely took place somewhere in the Middle East. The genome also shows that East Asians had a third dalliance with Neanderthals sometime after breaking away from Europeans and South Asians.

“The most exciting new thing about the paper is that it confirms that there have been multiple Neanderthal introgression events independently on several different human evolutionary lineages," Rasmus Nielsen, a researcher at the University of California, Berkeley, not involved in the project, tells Eva Botkin-Kowaki at The Christian Science Monitor. “Instead of thinking of Neanderthal admixture as something that happened just once or twice, we are now forced to consider the possibility that there has been extensive admixture between Neanderthals and humans in the entire range in which they overlapped.”

The interspecies breeding may have also helped Homo sapiens gain a few useful genes as they radiated out of Africa reports Gibbons. As early humans moved north and east, they encountered new climates, new food sources, and new diseases. Mating with Neanderthals and Denisovans may have given them the genetic tools to survive. In fact, the researchers identified 21 chunks of ancient DNA in modern humans which include genes that recognize viruses, help handle blood glucose and code for proteins that break down fat.

“The immune system is a pretty frequent target of evolution,” Akey tells Choi. “As our ancestors were spreading to new environments all over the world, hybridization would have provided an efficient way to pick up copies of genes adapted to local environmental conditions, and immune-related genes probably helped our ancestors handle new pathogens they were exposed to.”

Needless to say the human gene pool is getting deeper and over the next couple years scientists may learn that it is even more jumbled than we thought. Carl Zimmer at The New York Times points out a report released last month in Genome Research indicating that pieces of DNA in African pygmies come from an unknown ancestor that mated with humans within the last 30,000 years.

Akey’s team will soon take a look at that too, adding another unexpected branch to the increasingly full human family tree.

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