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Not Neandertal: Genome from fossil fingers a new, recently extinct human

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fossil human tooth from siberian cave might be from DenisovansWhat can be gleaned from a fragment of a 30,000- to 50,000-year-old finger? With highly sensitive genetic sequencing technology, researchers now claim to have spotted a new form of extinct humans that were neither Neandertals nor modern humans.


Meet the Denisovans, whose existence was deduced not from a skull or piecemeal skeleton, but mostly from DNA recovered from a solitary distal manual phalanx.


Named for the Siberian cave in which the finger bone (likely from a juvenile female) was discovered in 2008, the Denisovans seem to be closer genetically to Neandertals than to modern humans (having likely split off from the Neandertal gene pool some 640,000 years ago and from the Africa-based group that led to modern humans some 804,000 years ago; by contrast humans and Neandertals are proposed to have split 270,000 to 440,000 years ago). The findings were published in the December 23 issue of Nature (Scientific American is part of Nature Publishing Group).


"The fragments of ancient DNA illuminate our understanding of human origins and, like the shadows in Plato's proverbial cave, give us the broad outlines of ancient human migrations," Carlos Bustamante and Brenna Henn, both of the Stanford University School of Medicine's Department of Genetics, wrote in an essay published in the same issue of Nature. The researchers behind the new study have not yet proposed a formal Latin name for the Denisovans, but they suggest that the group might have been a widespread eastern analogue to Europe's Neandertals during the Late Pleistocene.


"The story now gets a bit more complicated," Richard Green, of the University of California, Santa Cruz, and coauthor of the study, said in a prepared statement. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neandertals, we now see these very intertwined story lines with more players and more interactions than we knew of before."


More clues should emerge as more samples are unearthed—and as genetic sequencing technology continues to improve. Eight years before the finger bone was found, a well-preserved, curious-looking tooth was discovered in the same cave. The researchers proposed that the tooth (likely the second or third upper left molar) also came from a Denisovan, though likely from a different individual (a young adult) than the finger bone. The molar is unusually large and more closely resembles the teeth of earlier hominins than it does dentition from Neandertals or modern humans.


Although the tooth did not retain as much endogenous genetic information as the finger bone, it still provided traces of DNA. "The tooth is just amazing," Bence Viola, of the Max Planck Institute for Evolutionary Anthropology and coauthor of the study, said in a prepared statement. "It allows us to connect the morphological and genetic information."


Genetic distinctions

A scan of the mitochondrial DNA from the finger bone (published this March) had indicated that it might have come from a third hominin group, and the new nuclear genome, sequenced to 1.9-fold coverage, provides further support for this hypothesis. "It is almost miraculous how well-preserved the DNA is," Green said. Although northern latitudes have provided some of the best genetic samples, this finger was found in the southern edge of Siberia and contained far more endogenous DNA than expected given its less-frozen location.


The timing of the find was also advantageous. "It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome," Green said.


The Neandertal genome, published in May, revealed that these early humans contributed some 1 to 4 percent of the genetic material found in most non-Africans' genomes—including those of geneticist George Church and heavy metal rocker Ozzy Osbourne.


The Denisovans, on the other hand, did not seem to mix much with the modern human Eurasian gene pool. However, genetic variants similar to those in the Denisovan genome crop up unexpectedly in the genomes of people in Papua New Guinea, suggesting some mixing with Melanesian ancestors. Denisovan genes might compose as much as 4 to 6 percent of some Melanesian's genomes, the researchers noted. Such a surprising large north-south connection might indicate that the Denisovans had a large range in the east, as modern humans are thought to have lived on those islands in Oceania for some 45,000 years.


"In combination with the Neandertal genome sequence, the Denisovan genome suggests a complex picture of genetic interactions between our ancestors and different ancient hominin groups," Svante Pääbo, of the Max Planck Institute for Evolutionary Anthropology and coauthor on this and several related papers, said in a prepared statement.


But why this whole group of humans had not previously been detected raises questions. "It could be that other samples are misclassified," Green said, noting that the finger bone had previously been thought to have come from a modern human. And the unclear origins of the small "hobbit" remains (Homo floresiensis) found on the Indonesian island of Flores and dated to about 17,000 years old suggest there might be more recently extinct human relatives yet to be found.


"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?"


Image of tooth courtesy of David Reich et al., Nature

The views expressed are those of the author and are not necessarily those of Scientific American.

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