If these alleles weren't under selection, why would they be so much more common amongst contemporary East compared to West Eurasians? It's been pretty well established, I think, that there was only a single Neanderthal pulse into the common pan-Eurasian ancestral population, as opposed to the multiple different Denisovan populations which were introgressed into East Eurasians. East and West Eurasians both have the same Neanderthal ancestors, but something in the East Eurasian context drove these alleles under at least a moderate selection, it seems.
I also see the paper references another super interesting growth hormone receptor allele, GHRd3, a deletion in one of the GHR exons which has had some literature around it over the years. The deletion is associated with low-birth rate but otherwise accelerated post-natal growth. It was fixed in archaic humans, remains most common in Africans, but less common in Eurasians, with East Eurasians having the lowest occurrence. So we have here multiple different GHR alleles, this deletion being strongly negatively selected in EEs but these two new reported alleles maybe being mildly selected for - maybe as compensation for negative selection on GHRd3?
The question about selection is a good one. In the initially small and rapidly growing population that mixed with Neanderthals, there was substantial opportunity for drift to increase the frequency of some genes. It's hard to rule out when looking at a single linked haplotype. Nonetheless I agree that selection seems likely in this case, and might be tested with better time-series data from ancient DNA.
The idea of compensating mutations seems likely to me as a general principle. It's one of the key advantages of introgression from diverse populations that they may have different compensatory mutations that may generalize beyond their particular genetic circumstances and be valuable in other groups.
If these alleles weren't under selection, why would they be so much more common amongst contemporary East compared to West Eurasians? It's been pretty well established, I think, that there was only a single Neanderthal pulse into the common pan-Eurasian ancestral population, as opposed to the multiple different Denisovan populations which were introgressed into East Eurasians. East and West Eurasians both have the same Neanderthal ancestors, but something in the East Eurasian context drove these alleles under at least a moderate selection, it seems.
I also see the paper references another super interesting growth hormone receptor allele, GHRd3, a deletion in one of the GHR exons which has had some literature around it over the years. The deletion is associated with low-birth rate but otherwise accelerated post-natal growth. It was fixed in archaic humans, remains most common in Africans, but less common in Eurasians, with East Eurasians having the lowest occurrence. So we have here multiple different GHR alleles, this deletion being strongly negatively selected in EEs but these two new reported alleles maybe being mildly selected for - maybe as compensation for negative selection on GHRd3?
The question about selection is a good one. In the initially small and rapidly growing population that mixed with Neanderthals, there was substantial opportunity for drift to increase the frequency of some genes. It's hard to rule out when looking at a single linked haplotype. Nonetheless I agree that selection seems likely in this case, and might be tested with better time-series data from ancient DNA.
The idea of compensating mutations seems likely to me as a general principle. It's one of the key advantages of introgression from diverse populations that they may have different compensatory mutations that may generalize beyond their particular genetic circumstances and be valuable in other groups.