The story of how Neanderthal DNA made its way into the human genome may be a bit complex. As Carl Zimmer writes at the New York Times, two recent papers indicate that there were varying numbers of interbreeding events between Neanderthals and the ancestors of different modern human populations.
In the American Journal of Human Genetics, the University of Washington's Benjamin Vernot and Joshua Akey report on their examination of the effects of purifying selection on the amount of Neanderthal DNA in East Asians and Europeans. They found that two models could explain what they observed: Either there were two instances of gene flow into the ancestors of East Asians from Neanderthals or there was admixture between European ancestors and another unknown population that then diluted Neanderthal DNA in Europeans.
Bernard Kim and Kirk Lohmueller at the University of California, Los Angeles, similarly report in a separate AJHG paper that their population simulations support a complex admixture scenario. Lohmueller tells GenomeWeb that a likely possibility is that there was a second pulse of Neanderthal DNA introduced into the ancestors of East Asians, though other scenarios could be possible.
Akey tells Zimmer that it's gratifying that the two studies come to the same conclusion from different perspectives.
Still, Zimmer notes that this two-pulse theory poses puzzles of its own — Neanderthals went extinct some 40,000 years ago, possibly before the Europeans and Asian populations split. "How could there have been Neanderthals left to interbreed with Asians a second time?" he says, adding that there are a few theories to now be tested.