Human DNA carries hints of unknown extinct ancestor | Science News for Students

Human DNA carries hints of unknown extinct ancestor

New analyses suggest ancestors of modern Pacific Islanders bred with an extinct species still unknown to science
Nov 11, 2016 — 7:00 am EST
Papua New Guinea trio

These men live in Papua New Guinea, one of four nations making up Melanesia. Some people from their region appear to carry remnant genes from an unknown ancestral species.


Anselmo Lastra/ Flickr CC BY 2.0

VANCOUVER, British Columbia — The human family tree may be even more tangled than scientists had thought. A new computer analysis has turned up evidence pointing to some long-lost human cousins. That evidence was found hiding in the DNA — genetic instruction book — of some people alive today.

Ryan Bohlender led the new study. This statistical geneticist works at the University of Texas MD Anderson Cancer Center in Houston. He and his colleagues pored over DNA from people living in Melanesia. This part of the South Pacific includes Papua New Guinea and nearby islands. And here, the new study finds, people inherited genes that appear to come from an unknown extinct hominid. (Hominids are a group of species that includes humans and our ancient relatives.)

Melanesia location
Melanesia is a part of Oceania comprising the nations of Papua-New Guinea, Vanuatu, the Solomon Islands and Fiji.
Lillian Steenblik Hwang/Source: Wikimedia Commons (CC BY-SA 3.0)

Bohlender reported his team’s new conclusions here in Canada, on October 20. It was at the annual meeting of the American Society of Human Genetics.

Earlier research had shown that the ancestors of Melanesians mated with two groups of extinct hominids. One group, Neandertals, left behind fossils in Europe and Asia. The other group had been distant cousins of the Neandertals. Known as Denisovans (Deh-NEES-oh-vuns), this group is known only from DNA found in a finger bone and a couple of teeth. Their fossils came from a cave in Siberia.

The new study found some mysterious DNA in Melanesians that was very old. But it didn’t seem to come from either Neandertals or Denisovans. The mystery DNA likely comes from a third hominid species. Scientists have not yet found fossil evidence for such a species, Bohlender notes.

Other scientists also have dug into the DNA of present-day people and found traces of unknown species. In 2012, another group of researchers suggested some Africans carry heirloom DNA from an unknown extinct hominid. Again, no bones with that particular DNA have yet turned up.

Accounting for missing DNA

After ancestors of humans began migrating out of Africa, they mixed with Neandertals in Europe and Asia. As a result, people whose ancestors came from outside of Africa still carry a small amount of Neandertal DNA. Bohlender and his colleagues calculate that Europeans and Chinese people carry a similar amount of this Neandertal ancestry — some 2.8 percent.

Europeans have no sign of Denisovan ancestry. People in China do, but the amount is very small, just 0.1 percent, according to calculations by Bohlender’s group. But 2.74 percent of the DNA in people in Papua New Guinea comes from Neandertals. And Bohlender estimates the Denisovan DNA in Melanesians at about 1.1 percent. That’s far less than the 3 to 6 percent Denisovan DNA that other researchers have reported in the Melanesians.

PNG boy
This boy lives in a fishing village within Papua-New Guinea (a part of Melanesia). People from his part of the world have genes that may trace back millennia to some unknown ancestral species.
Nomad Tales/ Flickr (CC BY-NC-ND 2.0)

But Melanesians carry other bits of old DNA too. These bits may have come from a relative of Neandertals and Denisovans. If true, that would make a third species of extinct hominid that has mixed with human ancestors.

“Human history is a lot more complicated than we thought it was,” Bohlender now says.

Another team recently concluded much the same thing. Eske Willerslev, who led this group, is an evolutionary geneticist. He works at the Natural History Museum of Denmark in Copenhagen. Willerslev’s group examined DNA from 83 aboriginal Australians. They also probed the DNA of 25 people from native populations in Papua New Guinea. DNA similar to Denisovans showed up in the study volunteers. But that DNA didn’t match that of the Denisovans precisely. In fact, it may be from another extinct hominid. That's what these researchers reported in the October 13 Nature. “Who this group is we don’t know,” Willerslev points out.

Fossils from other extinct human relatives have been found in the South Pacific. Scientists have not yet gotten DNA out of those bones. It’s possible that the not-quite-Denisovan DNA that Willerslev’s team found comes from one those unknown hominids. If researchers can get DNA from the old bones, they’ll try to match it to what’s in people today.


A possible confounder

It’s hard to know for sure whether such a third group mated with the ancestors of the South Pacific islanders. One reason is that within any group, DNA will vary from person to person. Some groups have quite a bit of this genetic diversity.

Researchers don’t know much about Denisovans, says Mattias Jakobsson. He’s an evolutionary geneticist at Uppsala University in Sweden. But it’s possible that Denisovans formed distant communities. These might have been separated from each other for a long time. If true, those groups could have developed many genetic differences. If there were enough such changes to their DNA, this might have fooled scientists into thinking the groups were different species.

Still, Jakobsson says he wouldn’t be surprised if other groups of extinct hominids mixed with humans. Modern and ancient humans, he observes, “have met many times and had many children together.”

Power Words

(more about Power Words)

annual     Adjective for something that happens in every year. (in botany) A plant that lives only one year, so it usually has a showy flower and produces many seeds.

colleague     Someone who works with another; a co-worker or team member.

Denisovans     An ancient humanlike population whose existence is known only because of a few fossils discovered in a cave in Siberia.

DNA     (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

evolutionary     An adjective that refers to changes that occur within a species over time as it adapts to its environment. Such evolutionary changes usually reflect genetic variation and natural selection, which leave a new type of organism better suited for its environment than its ancestors. The newer type is not necessarily more “advanced,” just better adapted to the conditions in which it developed.

extinct     An adjective that describes a species for which there are no living members.

fossil     Any preserved remains or traces of ancient life. There are many different types of fossils: The bones and other body parts of dinosaurs are called “body fossils.” Things like footprints are called “trace fossils.” Even specimens of dinosaur poop are fossils. The process of forming fossils is called fossilization.

gene     (adj. genetic) A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

genetic     Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.

genetic diversity     The range of genes types — and traits — within a population.

hominid     A primate of an animal family that includes humans and their ancient, fossil relatives.

native     Associated with a particular location; native plants and animals have been found in a particular location since recorded history began. These species also tend to have developed within a region, occurring there naturally (not because they were planted or moved there by people). Most are particularly well adapted to their environment.

Neandertal     A species ( Homo neanderthalensis ) that lived in Europe and parts of Asia from about 200,000 years ago to roughly 28,000 years ago.

Pacific     The largest of the world’s five oceans. It separates Asia and Australia to the west from North and South America to the east.

population     (in biology) A group of individuals from the same species that lives in the same area.

Siberia     A region in northern Asia, almost all of which falls within Russia. This land takes its name from the language of the Tatar people, where Siber means sleeping land. This region is vast. It has become famous for its long, harsh winters, where temperatures can fall to −68° Celsius (−90° Fahrenheit).

species     A group of similar organisms capable of producing offspring that can survive and reproduce.

statistics     The practice or science of collecting and analyzing numerical data in large quantities and interpreting their meaning. Much of this work involves reducing errors that might be attributable to random variation. A professional who works in this field is called a statistician.


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

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

Journal: L. Pagani et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. Vol. 538, October 13, 2016, p. 238. doi: 10.1038/nature19792.