Vanderbilt University's John Anthony Capra tells the New York Times' Claudia Dreifus in a Q&A that mating between humans and Neanderthals likely took place about 50,000 years ago after some modern humans migrated out of Africa. Modern Europeans and Asians, but not modern Africans, have inherited between 1 percent and 5 percent of their DNA from a Neanderthal ancestor.
Capra tells Dreifus that at that time having Neanderthal genes might've been beneficial. His lab has found that Neanderthal-origin DNA affects people's immune systems and blood clotting. The immune-related changes might've helped modern humans cope with new pathogens they encountered in their migrations while the blood-clot trait likely meant that people's wounds closed more quickly
Capra adds, though, that traits helpful then might not be now. That blood-clot trait has been linked to a greater risk of stroke and pregnancy complications, he notes. "What helped us then doesn't necessarily now," he says.
He also tells Dreifus that humans likely mated with other hominids as well. "Sometimes when we're examining genomes, we can see the genetic afterimages of hominids who haven't even been identified yet," Capra says.