Cochran says (on GNXP):
"The major point is that Neanderthals and modern humans were probably interfertile and most likely interbred - and that we would then have picked up most favorable Neanderthal alleles. Which may have something to do with the cultural ' big bang' that happened not long after."
Dynamics of Adaptive Introgression from Archaic to Modern Humans
Recent evidence from the genomic variation of living people documents genetic contributions from archaic [e.g., Neanderthal] to later modern humans. This evidence of introgression contrasts with earlier findings from single loci that appeared to exclude archaic human genetic survival. The present evidence indicates that many “archaic” alleles may represent relicts of African archaics, and that some “archaic” variants both inside and outside of Africa have attained relatively high frequencies. Both observations may be surprising under the hypothesis that modern humans originated first in Africa and displaced archaic populations through expansion and drift. Here, we outline how natural selection may have enabled the uptake of introgressive alleles from archaic humans. Even if admixture or gene flow were minimal, the introgression of selected variants would have been highly probable. In contrast to neutral alleles, adaptive alleles may attain high frequencies after minimal genetic introgression. Adaptive introgression can therefore explain why some loci show evidence for some archaic human contribution even as others apparently exclude it. The dynamics of introgression also may explain the distribution of certain deep haplotype branches in Africa. Open questions remain, including the likelihood that archaic alleles retained their adaptive value on the genetic background of modern humans and the scope of functions influenced by adaptive introgression.
John Hawks Department of Anthropology, University of Wisconsin–Madison
Gregory Cochran Department of Anthropology, University of Utah