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Back in the 2000s I used to write a lot about “adaptive introgression.” This was partly due to conversations with, and influence from, people like John Hawks and Greg Cochran. The theoretical framework can be found in papers such as A genetic legacy from archaic Homo. And planet geneticists, such as Loren Rieseberg, have been studying gene flow between structured populations for decades.
That was why I was a bit surprised when the authors of A Draft Sequence of the Neandertal Genome kept emphasizing there was no selection detected in their work. This is true in the strict sense, but it seems reasonable that the expectation was that this will change.
Nearly ten years after John Hawks et al. began talking about introgression and adaptation in humans, their views are now commonplace, and perhaps even orthodox. A case in point, Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments:
Here, we describe a comprehensive set of analyses that identified 126 high-frequency archaic haplotypes as putative targets of adaptive introgression in geographically diverse populations. These loci are enriched for immune-related genes (such as OAS1/2/3, TLR1/6/10, and TNFAIP3) and also encompass genes (including OCA2 and BNC2) that influence skin pigmentation phenotypes. Furthermore, we leveraged existing and novel large-scale gene expression datasets to show many positively selected archaic haplotypes act as expression quantitative trait loci (eQTLs), suggesting that modulation of transcript abundance was a common mechanism facilitating adaptive introgression. Our results demonstrate that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments.
The more we learn, the more we comprehend that the patterns of selection and phylogenetic relationships in hominins was quite complex.