Neanderthal mark in the human genome

Reports of Human-Neanderthal Mating Left Its Mark in the Human Genome
Neandertal genome yields evidence of interbreeding with humans
in Discover Magazine and Science News. Carl Zimmer raises some questions in
Skull Caps and Genomes:
"Today, the people of Europe and Asia have genomes that are 1 to 4 percent Neanderthal.That interbreeding doesn’t seem to have meant much to us, in any biological sense. None of the segments our species picked up from Neanderthals was favored by natural selection. (Microcephalin D turns out to have been nothing special.)

While working on this post, I contacted two experts who have been critical of some earlier studies on hominin interbreeding, Laurence Excoffier of the University of Bern and Nick Barton of the University of Edinburgh. Both scientist gave the Neanderthal genome paper high marks and agree in particular that the interbreeding hypothesis is a good one. But they do think some alternative hypotheses have to be tested. For example, interbreeding is not the only way that some living humans might have ended up with Neanderthal-like pieces of DNA. Cast your mind back 500,000 years, before the populations of humans and Neanderthals had diverged. Imagine that those ancestral Africans were not trading genes freely. Instead imagine that some kind of barrier emerged to keep some gene variants in one part of Africa and other variants in another part.

Now imagine that the ancestors of Neanderthals leave Africa, and then much later the ancestors of Europeans and Asians leave Africa. It’s possible that both sets of immigrants came from the same part of Africa. They might have both taken some gene variants with them did not exist in other parts of Africa. Today, some living Africans still lack those variants. This scenario could lead to Europeans and Asians with Neanderthal-like pieces of DNA without a single hybrid baby ever being born.

If humans and Neanderthals did indeed interbreed, Excoffier thinks there’s huge puzzle to be solved. The new paper suggests that genes flowed from Neanderthals to humans only at some point between 50,000 and 80,000 years ago–before Europeans and Asians diverged. Yet we know that humans and Neanderthals coexisted for another 20,000 years in Europe, and probably about as long in Asia. If humans and Neanderthals interbred during that later period, Excoffier argues, the evidence should be sitting in the genomes of Europeans or Asians. The fact that the evidence is not there means that somehow humans really did find the self-restraint not to mate with Neanderthals."