There's a little cave man in all of us: Early human inbreeding

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Story highlights

  • People living in South Asia have DNA from Denisovans, an early hominin, new research finds
  • The genes we borrowed from ancestor cousins may have helped us adapt to new environments but reduced our fertility

(CNN)Your ancestry can reveal a lot about you, including how related you are to cave men.

If you have Chinese heritage, you might have slightly more Neanderthal in your genome, while a new study finds that people from South Asia have more Denisovan, another type of early human, in their DNA.
Evidence started to emerge in 2010 that our distant ancestors interbred with Neanderthals, the Stone Age hominins who populated Europe until around 40,000 years ago. We can all, with the exception of African people, credit Neanderthals for around 2% of our genome. (Our ancestors apparently started hooking up with their stocky cousins after moving out of Africa.)
Now it seems Neanderthals were not the only interbreeding game in town. The new study finds that Denisovans interbred with the distant ancestors of people living in what is now South Asia, including India, Bangladesh and Pakistan. Previously the only people known to have detectable traces of Denisovan DNA were in Papua New Guinea, Australia, China and other parts of East Asia.
The inter-hominin mating, both with Neanderthals and Denisovans, seemed to bestow our ancestors with advantageous traits, such as thicker hair (thanks, Neanderthals) and ability to live at high altitudes (courtesy of Denisovans). However the new study suggests that there could also have been evolutionary downsides to interbreeding, such as reduced fertility.
"The South Asia finding was a bit of a surprise. It is not explainable by what we know about human history," said Sriram Sankararaman, assistant professor of computer science and human genetics at the University of California-Los Angeles. Sankararaman is the lead author of the study, which was published Monday in Current Biology.
Proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans.
Researchers had been thinking that our ancestors could have picked up Denisovan DNA just once, when one population of our ancestors intermingled with one population of Denisovans, and then the descendants moved to East Asia and the Pacific Islands. Although that still could have happened, Sankararaman said these findings also raise the possibility that Homo sapiens made babies with Denisovans in three different areas, including South Asia.
The current study and previous research suggest that we can no longer think of our ancestors as interbreeding with other hominins only once, said John Hawks, professor of anthropology at University of Wisconsin-Madison. "It is happening repeatedly, wherever modern humans are coming into contact with these archaic people," said Hawks, who was not involved in the current study.
Of all the nationalities today, Papua New Guineans and Australians can claim the most Denisovan DNA, about 5% of their genome, followed by South Asians, and then East Asians and Native Americans, all at around 2%. Europeans have no detectable Denisovan DNA.

What's in your caveman genes?

Looking at the kind of Neanderthal or Denisovan DNA we possess "is a first step to understanding the (genomic) regions which might have been important for modern humans," Sankararaman said. We can also learn a lot from the regions of our genome where cave man DNA is glaringly absent.
The current study found some of the most prevalent Neanderthal genes are associated with thicker skin and hair, just as previous research concluded.
"You have humans that lived in Africa, and now they are going into different environments in the world and there are already populations (of Neanderthals and Denisovans) that adapted to those environments. And so, for the modern humans it almost makes sense that they borrow the genes from them," Sankararaman said.
The study also found evidence that our ancestors may not have passed on certain parts of the genome from their hominin cousins, such as a less evolutionarily advanced version of the FOXP2 gene, which is thought to play a role in language and speech.
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"We all agree there has been positive and negative selection. ... It is interesting that similar regions in both Neanderthal and Denisovans, like FOXP2, had negative selection," said Rasmus Nielsen, professor of evolutionary biology at University of California-Berkeley, who was not involved in the current research.
Another group of genes that seems to be avoided by early humans, from an evolutionary standpoint, is involved in reproduction. This finding suggests that the offspring of an early human and Neanderthal or Denisovan pairing could have been less able to procreate and pass on their genes. If interbreeding reduces fertility, Hawks said, "that creates the expectation that maybe (these three hominins) were different species," which has been a matter of debate.