A phenotypic takeaway from the ancient European DNA preprint has been that the hunter-gatherer from Luxembourg was light eyed and darker skinned (and dark haired), while the early farmer from Germany was lighter skinned and darker eyed (and dark haired). In yesterday’s post a reader pointed out that I misinterpreted the genotypes of these two individuals at a very important pigmentation locus: I thought that it was homozygous for the lighter skin conferring allele which is at very high frequency in modern Europeans. I was wrong. A SNP at this locus, SLC45A2, correlated with darker complexion and eyes, is present at ~3% in Europeans (as opposed to ~100% in East Asia and Sub-Saharan Africa). In a European American sample the genotypes are as follows:
Both the hunter-gather and the farmer are CC. Combined with the hunter-gatherer being GG (which is nearly absent in modern Europeans) at SLC24A5 it does seem that as the authors of the preprint were right, the hunter-gatherer had darker skin. The twist is that the region of the genome, OCA2/HERC2, that seems to explain most of the blue vs. non-blue eye color difference in Europe, is homozygous for the blue variant in the hunter-gatherer. I would say that if I had just the pigmentation loci I would think that the hunter-gatherer in this study was from a population mixed between Europeans and non-Europeans. For example, inhabitants of Cape Verde.
The hunter-gatherer individual sequenced from Loschbour rock shelter may be an anomaly. But you wouldn’t find this sort of individual among modern Europeans without recent non-European ancestry, even as an anomaly. So there’s something to explain.