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DNA data offer evidence of unknown extinct human relative

Melanesians carry genetic clues to hominid not revealed by fossils

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4:01pm, October 21, 2016

GENETIC HEIRLOOMS People from Papua New Guinea (shown) and Australia carry small amounts of DNA from extinct human relatives. New research suggests that the DNA may not come from Neandertals or Denisovans, but from a third, previously unknown extinct hominid.

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VANCOUVER — Traces of long-lost human cousins may be hiding in modern people’s DNA, a new computer analysis suggests.

People from Melanesia, a region in the South Pacific encompassing Papua New Guinea and surrounding islands, may carry genetic evidence of a previously unknown extinct hominid species, Ryan Bohlender reported October 20 at the annual meeting of the American Society of Human Genetics. That species is probably not Neandertal or Denisovan, but a different, related hominid group, said Bohlender, a statistical geneticist at the University of Texas MD Anderson Cancer Center in Houston. “We’re missing a population or we’re misunderstanding something about the relationships,” he said.

This mysterious relative was probably from a third branch of the hominid family tree that produced Neandertals and Denisovans, an extinct distant cousin of Neandertals. While many Neandertal fossils have been found in Europe and Asia, Denisovans are known only from DNA from a finger bone and a couple of teeth found in a Siberian cave (SN: 12/12/15, p. 14).

Bohlender isn’t the first to suggest that remnants of archaic human relatives may have been preserved in human DNA even though no fossil remains have been found. In 2012, another group of researchers suggested that some people in Africa carry DNA heirlooms from an extinct hominid species (SN: 9/8/12, p. 9).

Less than a decade ago, scientists discovered that human ancestors mixed with Neandertals. People outside of Africa still carry a small amount of Neandertal DNA, some of which may cause health problems (SN: 3/5/16, p. 18). Bohlender and colleagues calculate that Europeans and Chinese people carry a similar amount of Neandertal ancestry: about 2.8 percent. Europeans have no hint of Denisovan ancestry, and people in China have a tiny amount — 0.1 percent, according to Bohlender’s calculations. But 2.74 percent of the DNA in people in Papua New Guinea comes from Neandertals. And Bohlender estimates the amount of Denisovan DNA in Melanesians is about 1.11 percent, not the 3 to 6 percent estimated by other researchers.

While investigating the Denisovan discrepancy, Bohlender and colleagues came to the conclusion that a third group of hominids may have bred with the ancestors of Melanesians. “Human history is a lot more complicated than we thought it was,” Bohlender said.  

Another group of researchers, led by Eske Willerslev, an evolutionary geneticist at the Natural History Museum of Denmark in Copenhagen, recently came to a similar conclusion. Willerslev’s group examined DNA from 83 aboriginal Australians and 25 people from native populations in the Papua New Guinea highlands (SN: 10/15/16, p. 6). The researchers found Denisovan-like DNA in the study volunteers, the group reported October 13 in Nature. But the DNA is genetically distinct from Denisovans and may be from another extinct hominid. “Who this group is we don’t know,” Willerslev says. They could be Homo erectus or the extinct hominids found in Indonesia known as Hobbits (SN: 4/30/16, p. 7), he speculates.

But researchers don’t know how genetically diverse Denisovans were, says Mattias Jakobsson, an evolutionary geneticist at Uppsala University in Sweden. A different branch of Denisovans could be the group that mated with ancestors of Australians and Papuans.

Researchers know so little about the genetic makeup of extinct groups that it’s hard to say whether the extinct hominid DNA actually came from an undiscovered species, said statistical geneticist Elizabeth Blue of the University of Washington in Seattle. DNA has been examined from few Neandertal fossils, and Denisovan remains have been found only in that single cave in Siberia. Denisovans may have been widespread and genetically diverse. If that were the case, said Blue, the Papuan’s DNA could have come from a Denisovan population that had been separated from the Siberian Denisovans for long enough that they looked like distinct groups, much as Europeans and Asians today are genetically different from each other. But if Denisovans were not genetically diverse, the mysterious extinct ancestor could well be another species, she said.

Jakobsson says he wouldn’t be surprised if there were other groups of extinct hominids that mingled with humans. “Modern humans and archaic humans have met many times and had many children together,” he said.


Editor’s note: This story was updated October 24, 2016, to correct Ryan Bohlender’s estimate of the percentage of Denisovan DNA in people from Papua New Guinea.

Citations

R. Bohlender et al. A complex history of archaic admixture in modern humans. American Society of Human Genetics, Vancouver, October 20, 2016.

A.-S. Malaspinas et al. A genomic history of Aboriginal Australia. Nature. Vol. 538, October 13, 2016, p. 207. doi:10.1038/nature18299

Further Reading

T.H. Saey. Single exodus from Africa gave rise to today’s non-Africans. Science News. Vol. 190, October 15, 2016, p. 6.

B. Bower. Animal hybrids may hold clues to Neandertal-human interbreeding. Science News. Vol. 190, October 15, 2016, p. 22.

B. Bower. Hobbits died out earlier than thought. Science News. Vol. 189, April 30, 2016, p. 7.

B. Bower. Pacific islanders got a double whammy of Stone Age DNA. Science News Online, March 17, 2016.

T.H. Saey. Neandertal DNA may raise risk for some modern human diseases. Science News. Vol. 189, March 5, 2016, p. 18.

B. Bower. DNA puts Neandertal relatives in Siberia for 60,000 years. Science News. Vol. 188, December 12, 2015, p. 14.

T.H. Saey. DNA hints at African cousin to humans. Science News. Vol. 182, September 8, 2012, p. 9.

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