Neanderthal Sex Debate Highlights Benefits of Pre- Publication

by Ewen Callaway 

nature.com newsblog
August 13, 2012 

http://blogs.nature.com/news/2012/08/neanderthal-sex-debate-highlights-benefits-of-pre-publication.html/

An argument over sex that has been going on for more than a
year is finally seeing the light of day. Today, scientists at
the University of Cambridge and Harvard Medical School let the
world in on a long-running discussion over whether or not
humans and Neanderthals really interbred -- and how you go
about proving it.

I'll get to the sex. But this debate underscores a topic I
wrote about last month (see `Geneticists eye the potential of
ArXiv`) that noted that high-profile papers from population
geneticists are beginning to appear on the pre-print server,
once just the domain of theoretical physicists. That story is
relevant because a new paper entitled "The date of
interbreeding between Neandertals and modern humans" was
posted to ArXiv on Friday. Meanwhile, a second paper raising
doubts about human-Neanderthal hanky-panky appears in the
Proceedings of the National Academy of Sciences today.

Both papers were presented at conferences more than a year
ago. Their publication today raises the question of whether
this debate would have been more timely if it had occurred on
pre-print servers like ArXiv.org and not at specialist
conferences and behind the walls of peer review.

In putting a date - 37,000 to 86,000 years ago - on human-
Neanderthal relations, Harvard's David Reich attempt to
address a question created when he and his co-author Svante
Pääbo, of the Max Planck Institute of Evolutionary
Anthropology in Leipzig, Germany, published a draft sequence
of the Neanderthal genome in 2010.

Just about every science reporter (see `European and Asian
genomes have traces of Neanderthal`, for example) led with the
conclusion that Neanderthals and non- African humans had
interbred.

But Pääbo, Reich and their co-authors said there could be
another explanation for their observation that all non-
Africans surveyed (that is people with deep Asian and European
ancestry) owed about 1-4% of their genome to Neanderthals,
while African genomes contain no detectable Neanderthal DNA.
Neanderthals and humans share an ancestor that lived in Africa
about half a million years ago. It is possible that modern
non- African's Neanderthal DNA dates to the time of these
early humans - and not more recent escapades. By chance or
quirk of geography, the humans who left Africa could have been
more closely related to Neanderthals than the humans who
stayed behind.

In other words, it only looks like humans and Neanderthals
interbred when we compare their genomes, but 500,000 year-old
population structure in Africa is the real explanation. Anders
Eriksson and Andrea Manica, at Cambridge, elaborate on this
scenario in their new PNAS paper.

Not so, say Reich and Pääbo in their ArXiv paper, which
reports a nifty new method for determining when two
populations interbred. It's based on the fact that our
maternal and paternal chromosomes reshuffle after each
generation. This mixing makes the contiguous chunks smaller
with each generation. Reich and his colleague Sriram
Sankararaman take advantage of this feature to conclude that
humans and Neanderthals interbred between 37,000 to 86,000
years ago, and probably more like 47,000 to 65,000 years ago.

Reich tells Nature that the paper will soon be published in
PLoS Genetics. Meanwhile, Monty Slatkin's team at the
University of California Berkeley came to a similar conclusion
as Reich using a different method. They published their
results in April and presented them at a conference last
summer.

Fair enough, one might say, this is how science works. One
paper raises questions that are addressed by others. But Reich
believes that the discussion would have been different if it
had happened in the open. The PNAS paper questioning
Neanderthal admixture addresses issues swirling around two
years ago but not Reich and Slatkin's latest work. "It's been
an issue for several years. They were right to work on this,"
says Reich. But now "it's kind of an obsolete paper," he says.

Manica says more data is needed to reach any firm conclusion
on human-Neanderthal relations.  "I think one take home
message is that establishing the presence and strength of
hybridisation is far from trivial if you only have one
Neanderthal genome." He supports pre- publication, in theory.
"The problem is that papers are not routinely uploaded as soon
as they are ready, as it the case in physics.So, for ArXiv to
be functional, everyone needs to upload their drafts on a
regular basis."

Reich, who posted another high-profile paper on the genetic
history of southern Africans to ArXiv two weeks ago, thinks
this debate would have been different if geneticists routinely
posted to pre-print servers. The conversation could be
happening in near real-time and not with a two year lag. "We
think there's no reason not to [post to ArXiv] and it's
interesting for other people to read about that work," Reich
says. "Maybe it would have been helpful in this context as
well."

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