denisova cave altai mountains
© Ruslan Olinchuk / Alamy Stock Photo
Denisova Cave in the Altai mountains, Siberia, where the only known Denisovan remains were found.
Our ancestors mated with another species of ancient hominins, the Denisovans, on at least two occasions. The discovery suggests that Denisovans were widely across Asia, and apparently co-existed happily with modern humans, to the point of having children with them in two different parts of the ancient world.

The Denisovans were unknown until 2010, when researchers described a fragment of a girl's finger bone found in Denisova cave in Siberia. Soon afterwards, researchers sequenced its genome from the surviving DNA. The DNA did not belong to any known hominins, such as Neanderthals, so it had to be something new.

What's more, around 5 per cent of the DNA of some Australasians - particularly people from Papua New Guinea - is Denisovan. Humans evidently mated with Denisovans 50,000 or more years ago.

But this posed a puzzle: why were the present-day descendants of Denisovans so far from the Denisovans' Siberian home? The simplest explanation was that Denisovans lived throughout much of Asia, including South East Asia, not just Siberia.

Sharon Browning of the University of Washington in Seattle and her colleagues have now found evidence of a second instance of human-Denisovan interbreeding - on the Asian mainland.

Hidden in the genes

Browning's team used a new technique to trawl for segments of ancient DNA in the genomes of 5600 living humans from Europe, Asia, America and Oceania. The chunks of older DNA stand out because they are unusually rich in mutations, which would have built up for hundreds of thousands of years in the genomes of Denisovans, but would not have been present in the human lineage. So when humans and Denisovans mated, their children would inherit these mutation-rich regions of DNA.

After Browning had isolated the ancient DNA, she then used the reference genomes of Denisovans and Neanderthals to establish where it came from. She found that some East Asians carry Denisovan DNA, especially Han Chinese, Chinese Dai and Japanese people.

But this Denisovan DNA is distinct from that carried by Australasians. It is more closely related to the Denisovan sample. "Although the Papuans ended up with more Denisovan ancestry, it turns out to be less similar to the sequenced Denisovan," says Browning.

The upshot is that Denisovans bred with modern humans in at least two places: in east Asia, and further south-east in Indonesia or Australasia. "Our research demonstrates that there were at least two distinct populations of Denisovans living in Asia, probably somewhat geographically distant," says Browning.
world map denisova gene
Even more interbreeding

"The fact that two episodes of interbreeding occurred suggests that at least in some instances, Denisovans and modern humans were willing to live in proximity and interact," says Browning.

As well as mating with Denisovans, there is strong evidence that humans interbred with Neanderthals, which were a sister species to the Denisovans.

"This new work is important because for the first time it unambiguously demonstrates a third interbreeding [of modern with ancient hominins]," says David Reich of Harvard Medical School in Boston. "Up to this point, we only had data for two." There have been claims of a second, earlier instance of interbreeding with Neanderthals, but not everyone is convinced.

Tantalisingly, breeding with Neanderthals and Denisovans may not be the end of our ancestors' promiscuity. A quarter of the chunks of ancient DNA that Browning found in living humans didn't match either Neanderthal or Denisovan DNA. So we may have also had children with other, unidentified hominins.

"At this point, we have no way of knowing if these derive from an as-yet-unknown archaic group, or are simply false positives," says Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Journal reference: Cell, DOI: 10.1016/j.cell.2018.02.031