CLARE WILSON | New Scientist
LONDON - Our species may have been interbreeding with Denisovans as recently as 15,000 years ago, according to a detailed analysis of the DNA of people living in Indonesia and Papua New Guinea.
We already know that, after Homo sapiens first migrated out of Africa, our species repeatedly interbred with a number of now-extinct hominin species, including the Neanderthals and Denisovans.
The signs are in our DNA today – all people of non-African descent carry some Neanderthal DNA, while some Asian people also have Denisovan DNA.
Not much is known about the mysterious Denisovans. Their only physical remnants discovered so far are a few teeth and fragments of bone unearthed in a cave in Siberia.
But DNA analyses have found that the Denisovans must have lived much further east and south of Siberia too. Genetic evidence suggested our species interbred with Denisovans at least twice, in Asia and Australasia, and that the genomes of people from Papua New Guinea may be up to 5% Denisovan.
Until now, such genetic studies have generally looked at only a small fraction of people’s DNA to draw these conclusions.
To get a fuller picture, Murray Cox of Massey University, New Zealand, and his colleagues have done the first large-scale study of whole genomes from people living in Indonesia and Papua New Guinea, sequencing all the DNA of 161 different people.
This reveals that our ancestors in this part of the world seem to have interbred with at least two distinct groups of Denisovans – one group about 50,000 years ago, as previously thought, and a second group much more recently.
The genetic analysis suggests this occurred sometime between 50,000 to 15,000 years ago. There’s reason to think it happened at the most recent end of that range, says Cox.
The genes from the second interbreeding are much more common in people living in the Papua New Guinea mainland than in people living on nearby islands, suggesting the mixing happened with the mainlanders after the islanders’ ancestors had left.
Archaeological evidence suggests this migration to the islands happened 30,000 years ago. But, by comparing the genomes of mainlanders and islanders, Cox’s team calculates that it was later, at around 15,000 years ago.
The only explanation for the data is that there was an extra bout of mainlanders interbreeding with Denisovans, says Cox, who presented the data at the American Association of Physical Anthropology Conference in Cleveland last week.
Cox doesn’t think any last remaining Denisovans could still be hiding out on an island. “It’s isolated, but it still has too much contact for something like that not to be noticed.”
The new data also reveals considerable genetic diversity among the Denisovans – the group involved in the earlier PNG interbreeding are almost as genetically different to a Denisovan bone found in Siberia as they are to the Neanderthals, a completely different branch of the hominin family tree.
“This study is giving us insight into the real pattern of human diversity,” says John Hawks of the University of Wisconsin-Madison. “It opens a window to the fact that there was once a population that was as rich and diverse as modern humans that’s now gone.”
At the same conference, Bence Viola of the University of Toronto and colleagues revealed a newly identified piece of Denisovan bone, the first skull fragment to be discovered. “It indicates it was a pretty large individual,” says Viola.
The fragment is small, and raises more questions than it answers, says Viola. “But look at how our knowledge has exploded over the past nine years from a tiny fragment of finger bone.”