Previously unknown Siberian group left fingerprints in some humans' DNA

By Laura Sanders

Web edition: December 22, 2010
Print edition: January 15, 2011; Vol.179 #2 (p. 10)

Neandertals need to make room for a new kid sister in the early human family. By sequencing the full genome of a girl’s fossil finger bone found in a Siberian cave, researchers conclude that there must have been a closely related sister group of Neandertals living in central Asia about 40,000 years ago. The data also show that, like Neandertals, the mysterious group interbred with modern humans, in this case leaving behind a genetic fingerprint in modern-day Melanesians of Papua New Guinea and Bougainville Island, nearly 10,000 kilometers from where the fossil was found.

The new genetic information, reported December 23 in Nature, underscores the fluidity of human evolution and hints that even more groups are waiting to be uncovered, says paleoanthropologist Milford Wolpoff of the University of Michigan in Ann Arbor. “We’re just scraping the outside of what’s probably a much more complex picture.”

As recently as a year ago, evidence suggested that modern humans spread throughout the world in a single migration out of Africa that wiped out any genetic traces of other early hominids. But the new study suggests that the lineage of modern humans is much more intertwined.

“This is quite exciting,” says genomicist Webb Miller of Pennsylvania State University in University Park. “A lot of people are going to hate it and a lot of people are going to love it.”

The presence of the ancient group’s genes in modern-day humans suggests that the new group, christened “Denisovans” after the Denisova Cave in southern Siberia where the finger bone was found, was once widespread throughout Asia.

“This was a place where Neandertals and modern humans were already known to be living, right in this region,” says study coauthor David Reich of the Broad Institute of MIT and Harvard in Cambridge, Mass. “Now there’s a third group that’s neither Neandertal nor modern human.” 

Earlier this year, researchers reported sequencing the mitochondrial DNA from the finger bone (SN: 4/24/10), leading them to conclude that the girl belonged to a new group that split from the line leading to modern humans about a million years ago, before the Neandertal-human split about 270,000 to 400,000 years ago. But mitochondrial DNA, a small loop of genetic material inherited only through the female line, isn’t as informative as the DNA packed into cells’ nuclei. So Reich and his colleagues decided to sequence the entire nuclear genome.

In so doing the team found that the Denisovans were much more closely related to Neandertals, who had their genomes sequenced earlier this year (SN: 6/5/10). And comparing the Denisovan DNA to that of modern-day humans turned up a big surprise: DNA samples from people living in Melanesia carried about 4 to 6 percent of the ancient Denisovan genome.

“It’s a really amazing observation,” Reich says, “and it indicates there was gene flow from Denisovans into modern humans.”

This Denisovan genetic stamp isn’t found in other modern human populations, suggesting that there was a unique interbreeding event in Melanesians’ history, which likely happened after a similar genome mingling between Neandertals and non-African modern humans.

Combing through these ancient genes that survived in modern humans could yield important information about how the genome works, Wolpoff says. These sets of genes must be beneficial in some way, or they wouldn’t have stuck around for so long, he says.

The study is one of the first examples of genetic information defining a new ancient group. “This is kind of a topsy-turvy world, where now we’re starting from the genome and going from there to learn about a new group,” Reich says.

While details about the Denisovan girl’s life are lacking, her cave may have been a busy place: Artifacts suggest that modern humans and Neandertals were in close proximity in the region. Mitochondrial DNA thought to belong to a Neandertal turned up in a site about 100 kilometers away from Denisova Cave (though some, like Wolpoff, don’t think Neandertals spread that far east).

The researchers also found a tooth in the cave that’s “like nothing we’ve ever seen before,” Reich says. Differences in the mitochondrial genome in the tooth led the team to conclude that the tooth didn’t belong to the girl, but another Denisovan. The large and unusually shaped tooth is presumed to be an upper molar from a young adult.

The importance of the tooth is controversial. Anthropologist Erik Trinkaus of Washington University in St. Louis says that it is almost identical to that of a hominid from Romania called Oase 2, which he says is “an unquestionable early modern human.” Reich contends that the tooth from Oase 2 was likely to be diseased, and therefore not useful for comparisons.

For now, details such as the Denisovan girl’s appearance and cultural habits remain a mystery. “All we have is this tooth, and this finger bone and this incredibly informative genome,” Reich says. After this new group’s debut, Reich is hoping that perhaps more Denisovan bones will turn up.