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Fossil finger bone yields genome of a previously unknown human relative
http://esciencenews.com/articles ... nown.human.relative
A 30,000-year-old finger bone found in a cave in southern Siberia came from
a young girl who was neither an early modern human nor a Neanderthal, but
belonged to a previously unknown group of human relatives who may have lived
throughout much of Asia during the late Pleistocene epoch. Although the
fossil evidence consists of just a bone fragment and one tooth, DNA
extracted from the bone has yielded a draft genome sequence, enabling
scientists to reach some startling conclusions about this extinct branch of
the human family tree, called "Denisovans" after the cave where the fossils
were found. The findings are reported in the December 23 issue of Nature by
an international team of scientists, including many of the same researchers
who earlier this year published the Neanderthal genome. Coauthor Richard
Green of the University of California, Santa Cruz, played a lead role in the
analysis of the genome sequence data, for which a special portal was
designed on the UCSC Genome Browser. The team was led by Svante Pää
;bo of the Max Planck Institute for Evolutionary Anthropology in Leipzig,
Germany.
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 surprising 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 Green, an assistant
professor of biomolecular engineering in the Baskin School of Engineering at
UC Santa Cruz. "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. Pääbo, 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, 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 a
completely 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?"
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