Modern humans interbred with Denisovans twice in history

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Modern humans co-existed and interbred not only with Neanderthals, but also with another species of archaic humans, the mysterious Denisovans. While developing a new genome-analysis method for comparing whole genomes between modern human and Denisovan populations, researchers unexpectedly discovered two distinct episodes of Denisovan genetic intermixing, or admixing, between the two. This suggests a more diverse genetic history than previously thought between the Denisovans and modern humans.

Modern humans interbred with Denisovans twice in history
New research suggests a more diverse genetic history than previously thought between
the Denisovans and modern humans [Credit: Rebecca Handler/Getty Images]

In a paper published in Cell, scientists at the University of Washington in Seattle determined that the genomes of two groups of modern humans with Denisovan ancestry — individuals from Oceania and individuals from East Asia — are uniquely different, indicating that there were two separate episodes of Denisovan admixture.

“What was known already was that Oceanian individuals, notably Papuan individuals, have significant amounts of Denisovan ancestry,” says senior author Sharon Browning, a research professor of biostatistics, University of Washington School of Public Health. The genomes of modern Papuan individuals contain approximately 5% Denisovan ancestry.”

Researchers also knew Denisovan ancestry is present to a lesser degree throughout Asia. The assumption was that the ancestry in Asia was achieved through migration, coming from Oceanian populations. “But in this new work with East Asians, we find a second set of Denisovan ancestry that we do not find in the South Asians and Papuans,” she says. “This Denisovan ancestry in East Asians seems to be something they acquired themselves.”

After studying more than 5,600 whole-genome sequences from individuals from Europe, Asia, America, and Oceania and comparing them to the Denisovan genome, Browning and colleagues determined that the Denisovan genome is more closely related to the modern East Asian population than to modern Papuans. “We analyzed all of the genomes searching for sections of DNA that looked like they came from Denisovans,” says Browning, whose team relied on genomic information from the UK10K project, the 1000 Genomes Project, and the Simons Genome Diversity Project.

Modern humans interbred with Denisovans twice in history
This graphical abstract shows two waves of Denisovan ancestry have shaped
present-day humans [Credit: Browning et al./Cell]

“When we compared pieces of DNA from the Papuans against the Denisovan genome, many sequences were similar enough to declare a match, but some of the DNA sequences in the East Asians, notably Han Chinese, Chinese Dai, and Japanese, were a much closer match with the Denisovan,” she says.

What is known about Denisovan ancestry comes from a single set of archaic human fossils found in the Altai mountains in Siberia. That individual’s genome was published in 2010, and other researchers quickly identified segments of Denisovan ancestry in several modern-day populations, most significantly with individuals from Oceania but also in East and South Asians.

“The assumption is that admixing with Denisovans occurred fairly quickly after humans moved out of Africa, around 50,000 years ago, but we do not know where in terms of location,” Browning says. She theorizes that perhaps the ancestors of Oceanians admixed with a southern group of Denisovans while the ancestors of East Asians admixed with a northern group.

Going forward, the researchers plan on studying more Asian populations and others throughout the world, including Native Americans and Africans. “We want to look throughout the world to see if we can find evidence of interbreeding with other archaic humans,” says Browning. “There are signs that intermixing with archaic humans was occurring in Africa, but given the warmer climate no one has yet found African archaic human fossils with sufficient DNA for sequencing.”

Source: Cell Press [March 15, 2018]

3 COMMENTS

  1. I'm wondering if the research really did take place with Papuans – or with New Guineans? Not presuming for a single moment to comment on the scholarship here – but the nomenclature.

    I have noticed in more than one American publication – as well as in televised lectures – that American scholars are not equally confident or consistent when discussing the independent country of Papua New Guinea.

    This might not matter other than as a matter of pride, or courtesy, were it not for the fact that Papua New Guineans are composed of two completely different groups, with completely different origins. Until Independence in 1975, Australia administered the Protectorate of the two separate countries of Papua (Southern coastal fringe) and New Guinea (the Northern Mountain ranges).

    The Papuans are descendants of the people from Samoa, Tahiti, and even Hawaii. Whether they set off deliberately, were blown of course, were following a known water way through the Pacific, is not yet established, They are relative newcomers. They are tall, pale brown skin, with straight hair.

    The New Guineans are the original inhabitants with a history in the country which reaches far back. They are very dark brown/black, very short & powerfull, with tight, curly hair, and some live in hunter-gatherer groups to this day.Their Art, Religions, History,Diet, – their entire culture – is sharply, demonstrably, and recordedly, in direct contrast to that of the sensuous Papuans.

    Thus any connection to Denisovans and Papuans would not simply be truly astonishing, but would therefore have repercussions throughout all the Pacific Islands as all inhabitants of the several hundreds of island and countries, then, that share the same DNA as the Papuans, would also carry Denisovan DNA.

    Were it, on the other hand, the original inhabitants – the New Guineans – found to have Denisovan DNA it would be a further peeling back of the layers which Anthropologists have been studying for decades: where did the New Guineans come from, who were their ancestors, what are their origins?

    As I stressed, this isn't mere pedantry about continually getting the name of a country wrong-
    but of these findings being completely misinterpreted.

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