The MUC19 gene: An evolutionary history of recurrent introgression and natural selection

We study the gene MUC19 , for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed American individuals and at highest frequency in 23 ancient Indigenous American individuals, all pre-dating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30–base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in admixed American populations. Finally, we find that some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into modern human populations through Neanderthal introgression rather than Denisovan introgression.