From Carl Zimmer in the NYT on a new gene study:

Joshua M. Akey, a geneticist at the University of Washington, and his colleagues analyzed a database of 1,488 genomes from people around the world. The scientists added 35 genomes from people in New Britain and other Melanesian islands in an effort to learn more about Denisovans in particular. The researchers found that all the non-Africans in their study had Neanderthal DNA, while the Africans had very little or none. That finding supported previous studies. But when Dr. Akey and his colleagues compared DNA from modern Europeans, East Asians and Melanesians, they found that each population carried its own distinctive mix of Neanderthal genes. The best explanation for these patterns, the scientists concluded, was that the ancestors of modern humans acquired Neanderthal DNA on three occasions. The first encounter happened when the common ancestor of all non-Africans interbred with Neanderthals. The second occurred among the ancestors of East Asians and Europeans, after the ancestors of Melanesians split off. Later, the ancestors of East Asians — but not Europeans — interbred a third time with Neanderthals. … The Melanesians took a different course. After a single interbreeding with Neanderthals, Dr. Akey found, their ancestors went on to interbreed just once with Denisovans, as well. … Dr. Akey and his colleagues also identified some regions of Neanderthal and Denisovan DNA that became more common in modern humans as the generations passed, suggesting that they provided some kind of a survival advantage.

Back around 2000, Greg Cochran was telling me that he figured anatomically modern humans had picked up useful genes from Neanderthals.

Many of the regions contain immune system genes, Dr. Akey noted.

“As modern humans are spreading out across the world, they’re encountering pathogens they haven’t experienced before,” he said. Neanderthals and Denisovans may have had genes that were adapted to fight those enemies. “Maybe they really helped us survive and thrive in these new environments,” he said.

Cold weather climates are hard on the health of people from Africa — that’s one reason slavery died out in the northern United States: black slaves tended to die of respiratory tract infections in expensive numbers in places like Boston. So, maybe Out of Africa humans picked up useful genes related to fighting cold weather germs from Neanderthals, who had been evolving in Europe for hundreds of thousands of years before the latest surge out of Africa arrived.

Dr. Akey and his colleagues found that Neanderthal and Denisovan DNA was glaringly absent from four regions of the modern human genome. That absence may signal that these stretches of the genome are instrumental in making modern humans unique. Intriguingly, one of those regions includes a gene called FOXP2, which is involved in speech. Scientists suspect that Neanderthals and Denisovans were not the only extinct races our ancestors interbred with. PingHsun Hsieh, a biologist at the University of Arizona, and his colleagues reported last month that the genomes of African pygmies contain pieces of DNA that came from an unknown source within the last 30,000 years.

In the lumper v. splitter debate, splitters might in the future want to classify pygmies as a slightly separate species.

Update: John Rivers asks: “How key was interbreeding with other hominids in creating the continental scale races?”

Good question.

It might turn out that Neanderthals or Denisovans contributed some important functional genes beyond the immune system, but let’s just assume the big contribution from Neanderthals to Europeans and Asians was for immune system genes that fight cold climate diseases. That in itself, trivial as it sounds, could have had a major effect on the development of modern races.

If Out of Africa anatomically modern humans in Europe or the Middle East or Eurasia picked up Neanderthal genes optimized for surviving cold weather, that might have helped bring the long Out of Africa process to an end.

Over a long time, there appear to have been numerous Out of Africa events in which new African forms of hominins move north into Eurasia. But after the last one in, say, 50,000 BC, there haven’t been many successful ones (which has therefore provided enough time for fairly distinct modern races to appear.

Why no more Out of Africa events? Perhaps because hominins such as the Neanderthals in Europe slowly became optimized for their winters. When anatomically modern humans arrived from Out of Africa and via mating picked up their alleles for surviving winter, our direct ancestors then had the genes to both win the struggle for survival with the Neanderthals and to block or outlast any subsequent Out of Africa movements north during the Ice Ages.

It’s kind of like how South Carolina is 28% black but Massachusetts is only 8% black. It’s not because white people in Massachusetts were abolitionists in the 17th Century. They were happy to partake in the Atlantic slave trade, which was universally agreed to be worse than mere slave owning. But black slaves didn’t pay well in Massachusetts — they’d get sick and die too often — while in South Carolina whites had a hard time making it through the summer without dying of warm weather fevers, so more resistant black slaves were more profitable. (And before modern medicine and public health measures, inland West Africa was a deathtrap of diseases for whites.)

David Hackett Fischer wrote in Albion’s Seed that the cold climate of colonial Massachusetts:

“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.”

So, it’s possible that immune system optimization, which seems to have been facilitated by breeding with other species in Eurasia helped set in motion the big racial divide between sub-Saharan Africa and the rest of the world. That would suggest it wasn’t just the vast Sahara Desert that divided the races (keep in mind that sometimes the Sahara was a grassland rather than a sand waste), but sheer latitude itself and the different kinds of germs that thrive at different latitudes.