Fossil Genome Reveals Ancestral Link

A Distant Cousin Raises Questions About Human Origins.

Ewen Callaway
Published online 22 December 2010 |
http://www.nature.com/news/2010/101222/full/4681012a.html
Nature 468, 1012 (2010) |
doi:10.1038/4681012a

The ice-age world is starting to look cosmopolitan.
While Neanderthals held sway in Europe and modern
humans were beginning to populate the globe, another
ancient human relative lived in Asia, according to a
genome sequence recovered from a finger bone in a cave
in southern Siberia. A comparative analysis of the
genome with those of modern humans suggests that a
trace of this poorly understood strand of hominin
lineage survives today, but only in the genes of some
Papuans and Pacific islanders.

Named after the cave that yielded the 30,000-50,000-
year-old bone, the Denisova nuclear genome follows
publication of the same individual's mitochondrial
genome in March[1]. From that sequence, Svante Pääbo of
the Max Planck Institute for Evolutionary Anthropology
in Leipzig, Germany, and his colleagues could tell
little, except that the individual, now known to be
female, was part of a population long diverged from
humans and Neanderthals.

Her approximately 3-billion-letter nuclear genome,
reported in this issue of Nature[2], now provides a
more telling glimpse into this mysterious group. It
also raises previously unimagined questions about its
history and relationship to Neanderthals and humans.
"The whole story is incredible. It's like a surprising
Christmas present," says Carles Lalueza Fox, a
palaeogeneticist at Pompeu Fabra University in
Barcelona, Spain, who was not involved in the research.

When the ancient genome was compared to a spectrum of
modern human populations, a striking relationship
emerged. Unlike most groups, Melanesians -- inhabitants
of Papua New Guinea and islands northeast of Australia
-- seem to have inherited as much as one-twentieth of
their DNA from Denisovan roots. This suggests that
after the ancestors of today's Papuans split from other
human populations and migrated east, they interbred
with Denisovans, but precisely when, where and to what
extent is unclear.

More answers could come from a closer look at
Denisovan, human and even Neanderthal DNA. So far,
conclusions about interbreeding have been drawn from a
relatively small number of human genomes using
conservative DNA-analysis methods, says David Reich, a
geneticist at Harvard Medical School in Boston,
Massachusetts, who led the Denisova analysis. "There
may have been many more interactions," he says. Pääbo
says it may be possible to determine roughly when
humans interbred with Denisovans by examining the
length of DNA segments lurking in various human
genomes, with shorter segments corresponding to more
shuffling of genes and a longer elapsed time.

A molar discovered in the same cave also yielded
mitochondrial DNA resembling that of the finger bone.
But the Denisovans were probably more widespread, says
Pääbo. Some fossils from China, for example, resemble
neither Neanderthals nor modern humans -- nor Homo
erectus, an earlier human ancestor. Pääbo wonders
whether they could be more closely related to
Denisovans. His Russian collaborators plan to search
for more complete Denisovan fossils that could be
matched to others from China.

Chris Stringer, a palaeoanthropologist at London's
Natural History Museum, agrees that Asian fossils, such
as the 200,000-year-old Dali skull from central China,
could have links to the Denisovans. But he says that
firm conclusions about such relationships will have to
await the discovery of more complete Denisovan fossils.

Preserved DNA from other Asian fossils would also
provide a clearer picture of the Denisovans, which
Pääbo, to sidestep controversy, has opted not to call a
new species or subspecies of hominin. The challenge
will be to make sense of such discoveries and put them
in the context of ancient human history, says Lalueza
Fox. Palaeoanthropologists are just beginning to
scrutinize the Neanderthal genome published earlier
this year[3] for clues to ancient human history. With
the Denisova genome, "they will need to deal with
another surprise", he says.

See also News & Views, p.1044

References

1 Krause, J. et al. Nature 464, 894-897 (2010).
2 Reich, D. et al. Nature 468, 1053-1060 (2010).
3 Green, R. E. et al. Science 328, 710-722 (2010).

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