Early admixture with humans led to Y chromosome replacement in late Neanderthals

In one of the first studies to comprehensively analyze Y chromosomes of humans' two closest relatives, Denisovans and Neanderthals, researchers report what prior studies have suggested: early gene flow events between archaic and modern humans led to the eventual replacement of archaic Neanderthal Y chromosomes by introgressed Homo sapiens Y chromosomes. There was no replacement of Denisovan Y chromosomes with H. sapiens Y chromosomes. "Until [this] new study ... archaeologists had only limited Y chromosome data from two Neanderthals and no information on exchanges of Y chromosomes during the early meeting," writes Mikkel Heide Schierup in a related Perspective. A growing number of ancient DNA studies on Neanderthals, Denisovans and H. sapiens suggest intertwined evolutionary and population histories, including several admixture events between early modern and archaic humans. However, ancient nuclear and mitochondrial DNA sequences (mtDNA) have revealed phylogenetic discrepancies between the three groups that are hard to explain. For example, autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans more than 550,000 years ago. However, all but the earliest Neanderthal mtDNA samples are far more similar to those of modern humans than to those from Denisovans. These studies suggest that Neanderthals originally carried a Denisovan-like mtDNA, which was later wholly replaced through early admixture with early modern humans, likely between 350,000 and 150,000 years ago. While genomic data for the paternally inherited Y chromosome would help resolve puzzling gene flows, virtually none of the male Neanderthal and Denisovan remains studied to date contain well-preserved Y chromosome DNA. To address this gap in the data, Martin Petr and colleagues used a targeted capture-based DNA sequencing approach to enrich and extract Y chromosome sequences from the less-than-well-preserved remains of three male Neanderthals and two male Denisovans. Petr et al. found that, like maternally inherited mtDNA, modern human and Neanderthal Y chromosomes were more related to each other than to the Denisovan Y, supporting the suggestion that interbreeding between early humans and Neanderthals and subsequent selection led to the total replacement of more ancient Denisovan-like genetic material in late Neanderthals.

American Association for the Advancement of Science