People from Oceania
© Michael Coyne/Getty ImagesPeople from Oceania have a higher percentage of genes from ancient humans called Denisovans.
Scars in our genetic landscape have revealed the fertility costs of breeding with different groups of our early ancestors.

Researchers have analysed the DNA of 257 individuals from 120 different non-African populations around the world to look for traces of ancestry from Neanderthals and Denisovans — another group of ancient humans that lived at the same time — in the modern human genome.

Previous studies have shown that almost all present-day non-African people possess some Neanderthal DNA, while some people, particularly people from Oceania, also have Denisovan DNA.

The new analysis, published in Current Biology, indicated that modern humans interbred with Denisovans around 100 generations after their trysts with Neanderthals.

But hybridisation may have reduced male fertility according to evidence of significantly lower Denisovan and Neanderthal ancestry on the X chromosome and near genes more highly expressed in the testes than other tissues.

"They're exactly the parts of the genome that we would expect them to be deficient in if there was infertility in males who were hybrids," said study co-author Professor David Reich of Harvard Medical School.

"What they would reflect is that the males who happened to carry Denisovan or Neanderthal DNA in these sections were not as successful in terms of producing offspring as others, and because of that those sections were removed in that first handful of generations after the mixture occurred."

But even though we can see the "scars of infertility" in the genetic history, it is not relevant to the fertility of populations that contain that mix of ancestry today, Professor Reich said.

'Surprisingly high' Denisovan ancestry in south Asia

As well as showing a peak of Denisovan ancestry around New Guinea — confirming what has been found in recent studies — Professor Reich and colleagues found a surprisingly high concentration of Denisovan genes in individuals from south Asia, around the Himalayas and south-central India.

"We thought that perhaps their Denisovan ancestry should be somewhere intermediate between east Asians and west Eurasians because their ancestry is a mix of that, but we didn't find that," Professor Reich said.

This unexpected result has forced researchers to rethink how Denisovans may have moved around Asia and Eurasia.
Denisovan genome map
© Sankararaman et al/Current BiologyMap showing proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans (with red the highest proportion.)
Professor Reich said there were now two theories emerging to explain the new finding of Denisovan ancestry in south Asia.

"One is that there is actually an independent encounter of modern humans with Denisovan somewhere on the Eurasian mainland that contributed extra Denisovan ancestry to people who live today in south Asia," he said.

The other theory proposes that all the Denisovan DNA seen in modern humans comes from one single encounter at some point in history, and the hybrids of that encounter have since spread across the region, from east and south Asia all the way to New Guinea and Australia.

"That subsequent mixture diluted the Denisovan ancestry on the mainland, but the dilution occurred to different extents, explaining the variability we see today," Professor Reich said.

The team's genetic analysis also added to our understanding of the impact of Denisovan ancestry, with the suggestion that some Denisovan genes are linked to a more subtle sense of smell.