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Tony Capra of Vanderbilt University in Nashville hypothesized last week at the annual meeting of The American Society of Human Genetics that genes we have considered to variant of Neanderthals and inherited to modern humans outside of Africa are not particularly Neanderthal genes, but rather, represent ancestral humans. In other words, we can thank Neanderthals for giving back thousands of ancient African gene variants that were lost to Eurasians as their ancestors swept out of Africa in small bands, perhaps 60,000 to 80,000 years ago.

He and his team came about this finding by identifying African variants as they scoured the genomes of more than 20,000 people in the 1000 Genomes Project and Vanderbilt’s BioVU data bank of electronic health records. Curiously they found vast stretches of chromosomes inherited from Neanderthals also carried ancient alleles, or mutations, found in all the Africans such as the Yoruba, Esan, and Mende peoples. In fact, there’s about 47,261 of these SNPs across the genomes of Europeans and 56,497 SNPs in Asians. In Eurasians people, these alleles are only found next to Neanderthal genes, suggesting all this DNA was acquired at the same time, when the ancestors of today’s Eurasians mated with Neanderthals roughly 50,000 years ago.

Applying the concepts of population genetics, the most parsimonious explanation is that these alleles represent the ancestral human condition, inherited by both Neanderthals and modern humans in Africa from their common ancestor. As ancient people migrated out of Africa, their small numbers resulted in a bottleneck, in which they lost many alleles that remained in larger populations in Africa. Later, the Neandertals reintroduced these alleles—along with distinct Neandertal genes—to the ancestors of Eurasians.

Just as interesting as finding these areas of genetic convergence, there are genetic deserts. These are areas where living humans have inherited no DNA from Neanderthals or other archaic humans. One of these regions includes the site of the FOXP2, the ‘language gene,’  Vanderbilt graduate student Laura Colbran found that Neandertal versions of FOXP2 would have pumped out much less of its protein than is expressed in modern brains. But I thought we had the same FOXP2? Anyways, we know that rare mutation that causes members of a family to produce half the usual amount of FOXP2 protein also triggered severe speech defects. The absence of archaic DNA suggests that in our ancestors, natural selection flushed out the Neanderthal version of this gene.