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previously unknown kind of human—the Denisovans—likely roamed Asia for thousands of years, probably interbreeding occasionally with humans like you and me, according to a new genetic study.
In fact, living Pacific islanders in Papua New Guinea may be distant descendants of these prehistoric pairings, according to new analysis of DNA from a girl's 40,000-year-old pinkie bone, found in Siberian Russia's Denisova cave.
This "new twist" in human evolution adds substantial new evidence that different types of humans—so-called modern humans and Neanderthals, modern humans and Denisovans, and perhaps even Denisovans and Neanderthals—mated and bore offspring, experts say.
"We don't think the Denisovans went to Papua New Guinea," located at the northwestern edge of the Pacific region called Melanesia, explained study co-author Bence Viola, an anthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
"We think the Denisovan population inhabited most of eastern Eurasia in the same way that Neanderthals inhabited most of western Eurasia," Viola said. "Our idea is that the ancestors of Melanesians met the Denisovans in Southeast Asia and interbred, and the ancestors of Melanesians then moved on to Papua New Guinea."
(See "Interspecies Sex: Evolution's Hidden Secret?")
Interbreeding Common Among Various Types of Humans?
Taken together with a May DNA study that found Neanderthals also interbred with modern human ancestors, the Denisovan finding suggests there was much more interbreeding among different human types than previously thought, Stanford University geneticist Brenna Henn said.
"In the actual archaeological record, people have been talking about this for a long time. ... But before six months ago, there was no genetic evidence for any admixture between archaic humans and modern humans," said Henn, who co-authored an article accompanying the study in tomorrow's issue of the journal Nature.
"Then these two papers come out, and I won't say they've turned the field on its head, but they certainly support a view that has not been well recognized for years" by geneticists, said Henn, who wasn't part of the study.
Brian Richmond, a paleoanthropologist at George Washington University, said he expects the new study to spark much interest and excitement.
"Nothing is more intriguing than learning new twists about our origins," said Richmond, who also didn't participate in the Denisovan-genetics research. "And this is another new twist."
Fossil Finger Points to New Human Type
The centerpiece of the DNA study is a Denisovan fossil finger bone discovered in 2008. The fossil is thought to be from a young girl—dubbed X-woman—who was between 5 and 7 years old when she died.
For a previous Nature study, released in March 2010, the team had collected and sequenced mitochondrial DNA, or mtDNA, from X-woman's finger. But mtDNA—inherited only from mothers—contains far less information about a person's genetic makeup than DNA found in the nucleus of a cell, or nuclear DNA (see a quick genetics overview).
In the new study the team reports successfully extracting and sequencing nuclear DNA from the bone.
Then, using DNA-comparison techniques, the scientists were able to determine that Denisovans were distinct from both modern humans and Neanderthals, yet closely related to the latter.
The team estimates Denisovans split from the parent group of Neanderthals about 350,000 years ago.
(Related: "Oldest Skeleton of Human Ancestor Found.")
New Humans Had Huge Teeth
Along with the finger bone, archaeologists from the Russian Academy of Sciences, who excavated the site, discovered a single tooth that belonged to a Denisovan adult.
The tooth, a molar, is bigger than any modern human tooth and is even bigger than the biggest Neanderthal tooth. This could suggest Denisovans were "comparable in size to Neanderthals, maybe a little bit bigger," said George Washington University's Richmond.
(See a picture of the first model of a Neanderthal based in part on ancient DNA evidence.)
Richmond cautioned, however, that tooth size isn't always a good indicator of body size. A hominin "can have big teeth and not be a giant," he said.
(See "Face of Ancient Human Drawn From Hair's DNA.")
Denisovans a New Human Species?
The team has been careful not to call Denisovans a new species, opting instead to label them as a Neanderthal "sister group."
If modern humans and Denisovan humans were separate species, their hybrid children probably wouldn't have been able to reproduce. But the hybrids apparently were able to have babies, otherwise the Denisovan DNA couldn't have been passed down to today's Papua New Guineans. Therefore, study co-author Viola reasoned, Denisovans and modern humans probably weren't separate species.
Scientifically, though, it matters little whether Denisovan is ultimately recognized as a new species, said Terry Brown, a geneticist at the University of Manchester in the U.K., who wasn't involved in the study.
"This whole species thing is a red herring, something that makes a nice headline but does not in my view contribute much to the scientific debate," Brown said in an email.
"We really don't know how to equate differences in genome sequences with the species concept," he said. "You could have two genuine species, whose members cannot interbreed, but whose genomes are very similar.
"So really the nuclear DNA does not help us decide if Denisovans are a new species, though the evidence for interbreeding with modern humans suggests they are not."
Given the mounting evidence that modern humans interbred with Neanderthals and now Denisovans, some evolutionary biologists have even suggested dropping the species designation for Neanderthals and modern humans.
As scientists "produce evidence that Denisovans interbred with modern humans (as did Neanderthals) then the implication is that modern humans, Denisovans and Neanderthals are all subspecies of Homo sapiens," he said.
It's indisputable, though, that each of these groups was genetically distinct, said George Washington University's Richmond.
"Whether you call them subspecies or species, it is clear that modern humans, Neanderthals, and now Denisovans were separated for hundreds of thousands of years, and only later did some of them meet and interbreed."
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30,000-year-old finger bone found in a cave in southern Siberia came from a young girl that was neither an early modern human nor Neanderthal, but instead belonged to a previously unknown group of human relatives who may have lived throughout much of Asia during the late Pleistocene epoch, according to new research (Reich, D. et al. Nature 468, 1053-1060 2010.
The fossil evidence consists of just a bone fragment and one tooth but DNA extracted from the bone has yielded a draft 3-billion-letter nuclear genome sequence (Krause, J. et al. Nature 464, 894-897 2010), enabling the scientists to make some conclusions about this extinct branch of the human family tree, called "Denisovans" after the cave where the fossils were found.
By comparing the Denisovan genome sequence with the genomes of Neanderthals and modern humans, the researchers determined that the Denisovans were a sister group to the Neanderthals, descended from the same ancestral population that had separated earlier from the ancestors of present-day humans. The study also found evidence of Denisovan gene sequences in modern-day Melanesians, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians, just as Neanderthals appear to have interbred with the ancestors of all modern-day non-Africans.
"The story now gets a bit more complicated," said co-author Richard Green of the University of California, Santa Cruz, an assistant professor of biomolecular engineering in the Baskin School of Engineering. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neanderthals, we now see these very intertwined story lines with more players and more interactions than we knew of before."
The Denisovans appear to have been quite different both genetically and morphologically from Neanderthals and modern humans. The tooth found in the same cave as the finger bone shows a morphology that is distinct from Neanderthals and modern humans and resembles much older human ancestors, such as Homo habilis and Homo erectus. DNA analysis showed that the tooth and the finger bone came from different individuals in the same population.
The finger bone was found in 2008 by Russian scientists in Denisova Cave, an archaeological site in southern Siberia. Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, who had worked with the Russian scientists before, obtained the bone for his research on ancient DNA. In Leipzig, researchers extracted DNA from the bone and sequenced the mitochondrial genome, a smaller DNA sequence separate from the chromosomal DNA and easier to obtain from ancient samples. The results, published earlier this year (Green, R. E. et al. Science 328, 710-722 2010), showed a surprising divergence from the mitochondrial genomes of Neanderthals and modern humans, and the team quickly began working to sequence the nuclear genome.
"It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome, because we already had the team assembled and ready to do another similar analysis," Green said. "This is an incredibly well-preserved sample, so it was a joy to work with data this nice. We don't know all the reasons why, but it is almost miraculous how well-preserved the DNA is."
The relationship between Denisovans and present-day Melanesians was an unexpected finding, he said. The comparative analysis, which included genome sequences of individuals from New Guinea and Bougainville Island, indicates that genetic material derived from Denisovans makes up about 4 to 6 percent of the genomes of at least some Melanesian populations. The fact that Denisovans were discovered in southern Siberia but contributed genetic material to modern human populations in Southeast Asia suggests that their population may have been widespread in Asia during the late Pleistocene, said David Reich of Harvard Medical School, who led the population genetic analysis.
It is not clear why fossil evidence had not already revealed the existence of this group of ancient human relatives. But Green noted that the finger bone was originally thought to be from an early modern human, and the tooth resembles those of other ancient human ancestors. "It could be that other samples are misclassified," he said. "But now, by analyzing DNA, we can say more definitively what they are. It's getting easier technically to do this, and it's a great new way to extract information from fossil remains."
In the light of the Neanderthal and Denisovan genomes, a new, more complex picture is emerging of the evolutionary history of modern humans and our extinct relatives. According to Green, there was probably an ancestral group that left Africa between 300,000 and 400,000 years ago and quickly diverged, with one branch becoming the Neanderthals who spread into Europe and the other branch moving east and becoming Denisovans. When modern humans left Africa about 70,000 to 80,000 years ago, they first encountered the Neanderthals, an interaction that left traces of Neanderthal DNA scattered through the genomes of all non-Africans. One group of humans later came in contact with Denisovans, leaving traces of Denisovan DNA in the genomes of humans who settled in Melanesia.
"This study fills in some of the details, but we would like to know much more about the Denisovans and their interactions with human populations," Green said. "And you have to wonder if there were other populations that remain to be discovered. Is there a fourth player in this story?"
