Neandertal and Denisovan Y Chromosomes

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, the study of Y chromosomes of Denisovans and Neandertals has not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other much later around 370 kya. The relationship between the Y chromosomes of these hominins therefore mirrors the discordant phylogenetic relationship observed for their mitochondrial genomes, and suggests that gene flow into Neandertals from a population closely related to modern humans resulted in a replacement not only of the original Neandertal mtDNA but also the early Neandertal Y chromosomes. We show that although such replacement is unlikely under neutrality, simulations which take into account lower effective population size and, consequently, higher deleterious load in Neandertals result in the rapid increase in frequency of introgressed uniparental loci.