Fast-Breaking Caveman News
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Here's the NYT's Nicholas Wade's article on the new finding by Svante Paabo that I hinted about on Sunday. Greg Cochran and Henry Harpending have been predicting this for quite a few years, most recently in The 10,000 Year Explosion. (By the way, although the NYT spells his name "Svante Paabo," Wikipedia spells it "Svante Pääbo," with double umlauts, giving him maximum heavy metal cred.)
Neanderthals mated with some modern humans after all and left their imprint in the human genome, a team of biologists has reported in the first detailed analysis of the Neanderthal genetic sequence.
The biologists, led by Svante Paabo of the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have been slowly reconstructing the genome of Neanderthals, the stocky hunters that dominated Europe until 30,000 years ago, by extracting the fragments of DNA that still exist in their fossil bones. Just last year, when biologists first announced they had decoded the Neanderthal genome, they reported no significant evidence of interbreeding.
Scientists say they have recovered 60 percent of the genome so far and hope to complete it. By comparing that genome with those of various present day humans, the team concluded that about 1 percent to 4 percent of the genome of non-Africans today is derived from Neanderthals. But the Neanderthal DNA does not seem to have played a great role in human evolution, they said.
Experts believe the Neanderthal genome sequence will be of extraordinary importance in understanding human evolutionary history since the two species split apart some 600,000 years ago.

So far, the team has identified only about 100 genes – surprisingly few – that modern humans have evolved since the split. The nature of the genes in humans that differ from those of Neanderthals is of particular interest since they bear on what it means to be human, or at least not Neanderthal. Some of the genes seem to be involved in cognitive function and others in bone structure.

”Seven years ago I really thought that it would remain impossible in my lifetime to sequence the whole Neanderthal genome,” Dr. Paabo said in a news conference. But the Leipzig team’s second conclusion, that there was probably interbreeding between Neanderthals and modern humans before Europeans and Asians split, is being greeted with reserve by some archaeologists.

A degree of interbreeding between modern humans and Neanderthals in Europe would not be greatly surprising given that the two species overlapped there for some 15,000 years, from 44,000 years ago when modern humans first entered Europe to 30,000 years ago when the last Neanderthals fell extinct. Archaeologists have been debating for years whether the fossil record shows evidence of individuals with mixed features.

But the new analysis, which is based solely on genetics and elaborate statistical calculations, is more difficult to match with the archaeological record. The Leipzig team asserts the interbreeding they detect did not occur in Europe but in the Middle East and at a much earlier period, some 100,000 to 60,000 years ago, before the modern human populations of Europe and East Asia had split apart. There is much less archaeological evidence for an overlap between modern humans and Neanderthals at this time and place.  ...

Dr. Paabo said that episode of human-Neanderthal breeding implied by Dr. Reich’s statistics most plausibly occurred ”in the Middle East where the first modern humans appear before 100,000 years ago and there were Neanderthals until 60,000 years ago.” According to Dr. Klein, people in Africa expanded their range and reached just Israel during a warm period some 120,000 years ago. They retreated during a cold period some 80,000 years ago and were replaced by Neanderthals. It is not clear whether or not they overlapped with Neanderthals, Dr. Klein said.

These humans, in any case, were not fully modern and they did not expand from Africa, an episode that occurred some 30,000 years later. If there was any interbreeding, the flow of genes should have been both ways, Dr. Klein said, but Dr. Paabo’s group sees evidence only for gene flow from Neanderthals to modern humans.

The Leipzig group’s interbreeding theory would undercut the present belief that all human populations today draw from the same gene pool that existed a mere 50,000 years ago. ”What we falsify here is the strong Out-of-Africa hypothesis that everyone comes from the same population,” Dr. Paabo said.

Keep in mind that only the "strong" (absolutist) version of the Out-of-Africa hypothesis that is in trouble. The weak version (that most of our genes are descended from people whose ancestors were in Africa 100,000 or so years ago) looks pretty reliable.
In his and Dr. Reich’s view, Neanderthals interbred only with non-Africans, the people who left Africa, which would mean that non-Africans drew from a second gene pool not available to Africans. Dr. Reich said that the known percentage difference in DNA units between African and non-African genomes was not changed by his proposal that some of the non-African DNA is from Neanderthals.

Steve Hsu has links to the papers.

Assuming that these Neanderthal introgressions in non-African modern humans exist (the technical problems Paabo has had to deal with — in particular, avoiding contamination by modern human DNA — and the analytical problems are daunting), they probably aren't neutral or junk genes, which would tend to disappear over the last 1,000 or so generations. They are probably useful genes that give some Darwinian advantage or advantages in some environments.

But, what do they do? I don't know. (I haven't read the papers, so I don't know if anybody knows yet.) If they haven't spread back into Africa, that might suggest they aren't that useful in Africa. For example, they might be cold weather adaptations. For instance, one reason slavery faded out quietly in Northern states after the American Revolution was that slaves weren't all that profitable because their immune systems weren't attuned to cold weather diseases. As I wrote in VDARE in 2003:

Indeed, as Brandeis historian David Hackett Fischer pointed out in his famous Albion's Seed, these racial differences had an enormous impact on the history of America. He notes that the cold climate of colonial Massachusett:
"proved to be exceptionally dangerous to immigrants from tropical Africa, who suffered severely from pulmonary infections in New England winters. Black death rates in colonial Massachusetts were twice as high as whites' - a pattern very different from Virginia where mortality rates for the two races were not so far apart, and still more different from South Carolina where white death rates were higher than those of blacks. So high was mortality among African immigrants in New England that race slavery was not viable on a large scale, despite many attempts to introduce it. Slavery was not impossible in this region, but the human and material costs were higher than many wished to pay. A labor system which was fundamentally hostile to the Puritan ethos of New England was kept at bay partly by the climate."
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