Analyzing the expression levels of genes associated with the 126 loci, the team found that 13 of the sites varied the expression of 34 genes across different tissue types. One locus resulted in significantly increased expression of a Toll-like receptor (TLR) gene cluster involved in innate immunity in lymphoblast cell lines, and lower expression in primary B cells and fibroblasts. The team tested whether this differential expression was a result of different levels of innate immune system activation. Using whole blood samples from healthy volunteers, they showed that those individuals with Neanderthal-derived TLR alleles could be specifically activated with a TLR4 agonist within immune cells. “We showed that this effect is specific to activated immune cells, which highlights the challenges in interpreting the effect of sequence variation. If you look in the wrong cell type or time point you would never see the effects,” Akey told The Scientist.

“It’s interesting to see that, like alleles that arise by other evolutionary mechanisms, adaptive introgression appears to commonly influence gene expression,” said Capra.

The results provide new clues about one particular route of human evolution. “Instead of waiting for a new beneficial mutation, we can just pick one up by hybridizing with a population that was already adapted to this new environment,” said Akey. “Finding advantageous genes inherited from archaic humans also shows that hybridization was not just some side note to human history, but had important consequences that we can still see in present day individuals.”