Inference of human pigmentation from ancient DNA by genotype likelihoods

Abstract

Inference from ancient DNA may be flawed when informative sites are typed at low coverage, i.e., when they are read only once or a few times. We empirically show that a widely used protocol for pigmentation inference, HIrisPlex-S, often yields incorrect results if the coverage level is <8×, but accuracy is improved by an approach based on the calculation of genotype likelihoods from raw sequencing data. We used that approach to describe changes in eye, hair, and skin color in prehistoric Eurasia. We showed that the Neolithic diffusion of early farmers introduced lighter phenotypes, but for millennia, pigmentation diversity remained extensive, so that many Europeans kept the dark skins of their African ancestors well within the Bronze and Iron ages. Keywords: ancient DNA, human evolution, phenotype inference, pigmentation, genotype likelihood