The evolutionary history of Neanderthal and Denisovan Y chromosomes

The genomes of archaic hominins have been sequenced and compared with that of modern humans. However, most archaic individuals with high-quality sequences available have been female. Petr et al. performed targeted sequencing of the paternally inherited Y chromosomes from three Neanderthals and two Denisovans (see the Perspective by Schierup). Comparisons with available archaic and diverse modern human Y chromosomes indicated that, similar to the maternally inherited mitochondria, the human and Neanderthal Y chromosomes were more closely related to each other compared with the Denisovan Y chromosome. This result supports the conclusion that interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals.Science, this issue p. 1653; see also p. 1565Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.