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The evolutionary history of Neanderthal and Denisovan Y chromosomes

Evolution of the Y chromosome in Neanderthals

The genomes of archaic hominins have been sequenced and compared to those of modern humans. However, most archaic individuals with high-quality sequences are women. Peter and others. performed targeted sequencing of the paternally inherited Y chromosomes of three Neanderthals and two denized ones (see Schierup Perspective). Comparisons with the available archaic and diverse modern human Y chromosomes show that, like maternal inherited mitochondria, human and Neanderthal Y chromosomes are more closely related than the Denisovan chromosome. This result supports the conclusion that crossbreeding between early humans and Neanderthals and selection replaced older Denisonian-like Y chromosomes and mitochondria in Neanderthals.

Science, this issue p. 1

653; see also page 1565


Ancient DNA has given new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals, as most of the samples that have been sequenced to sufficient coverage are female. Sequencing of Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans separated about 700,000 years ago from a line shared by Neanderthals and modern human Y chromosomes, which diverged from each other about 370,000 years ago. The phylogenetic linkages of archaic and modern human Y chromosomes differ from the population linkages derived from autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both mitochondrial and Y chromosomal gene pools in the late Neanderthals. This substitution is plausible if the low effective size of the Neanderthal population has led to an increased genetic load on Neanderthals compared to modern humans.

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