NYT: "The Little Bit of Neanderthal in All of Us" -- Who you calling "us," white man?

Carl Zimmer writes in the NYT:

The Little Bit of Neanderthal in All of Us 

Ever since the discovery in 2010 that Neanderthals interbred with the ancestors of [some] living humans, scientists have been trying to determine how their DNA affects people today. Now two new studies have traced the history of Neanderthal DNA, and have pinpointed a number of genes that may have medical importance today. 

Among the findings, the studies have found clues to the evolution of skin and fertility, as well as susceptibility to diseases like diabetes. More broadly, they show how the legacy of Neanderthals has endured 30,000 years after their [quasi-] extinction. ...

Neanderthals, who became extinct about 30,000 years ago, were among the closest relatives of modern humans. They shared a common ancestor with us that lived about 600,000 years ago.

In the 1990s, researchers began finding fragments of Neanderthal DNA in fossils. By 2010 they had reconstructed most of the Neanderthal genome. When they compared it with the genomes of five living humans, they found similarities to small portions of the DNA in the Europeans and Asians.

But not sub-Saharan Africans.

But recently, researchers sequenced a far more accurate genome from a Neanderthal toe bone. 

Scientists at Harvard Medical School and the Max Planck Institute for Evolutionary Anthropology in Germany compared this high-quality Neanderthal genome to the genomes of 1,004 living people. They were able to identify specific segments of Neanderthal DNA from each person’s genome. 

“It’s a personal map of Neanderthal ancestry,” said David Reich of Harvard Medical School, who led the research team. He and his colleagues published their results in the journal Nature. 

Living humans do not have a lot of Neanderthal DNA, Dr. Reich and his colleagues found, but some Neanderthal genes have become very common. That’s because, with natural selection, useful genes survive as species evolve. “What this proves is that these genes were helpful for non-Africans in adapting to the environment,” said Dr. Reich.

This was predicted by Harpending and Cochran before the confirmatory discoveries.

In a separate study published in Science, Benjamin Vernot and Joshua M. Akey of the University of Washington came to a similar conclusion, using a different method. 

Mr. Vernot and Dr. Akey looked for unusual mutations in the genomes of 379 Europeans and 286 Asians. The segments of DNA that contained these mutations turned out to be from Neanderthals. 

Both studies suggest that Neanderthal genes involved in skin and hair were favored by natural selection in humans. Today, they’re very common in living non-Asians. 

Oops! See below.

The fact that two independent studies pinpointed these genes lends support to their importance, said Sriram Sankararaman of Harvard Medical School, a co-author on the Nature paper. “The two methods seem to be converging on the same results.” 

It’s possible, Dr. Akey speculated, that the genes developed to help Neanderthal skin adapt to the cold climate of Europe and Asia.

Cochran's view, which I think he first told me in 1999 or 2000, was that Neanderthals had longer periods to evolve adaptations to cold climates, so it's likely that Out-of-Africa modern humans would have occasionally bred with them and picked up more highly evolved gene variants for living in Europe.

Both teams of scientists also found long stretches of the living human genomes where Neanderthal DNA was glaringly absent. This pattern could be produced if modern humans with certain Neanderthal genes couldn’t have as many children on average as people without them. For example, living humans have very few genes from Neanderthals involved in making sperm. That suggests that male human-Neanderthal hybrids might have had lower fertility or were even sterile. 

Overall, said Dr. Reich, “most of the Neanderthal genetic material was more bad than good.” 

The Neanderthal Anti-Defamation League would like to have a word with you, Dr. Reich, about your insensitive choice of adjectives.

Some of the Neanderthal genes that have endured until today may be influencing people’s health. Dr. Reich and his colleagues identified nine Neanderthal genes in living humans that are known to raise or reduce the risk of various diseases, including diabetes and lupus. 

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

How about IQ tests?

“This experiment of nature has been done,” said Dr. Reich, “and we can study it.”

Correction: January 29, 2014 An earlier version of this article misstated the living groups in which Neanderthal genes involved in skin and hair are very common. They are very common in non-Africans, not non-Asians. 

Oops.