Natural selection reduced diversity on human y chromosomes.

Bibliographic Collection: 
Publication Type: Journal Article
Authors: Wilson Sayres, Melissa A; Lohmueller, Kirk E; Nielsen, Rasmus
Year of Publication: 2014
Journal: PLoS Genet
Volume: 10
Issue: 1
Pagination: e1004064
Date Published: 2014 Jan
Publication Language: eng
ISSN: 1553-7404
Keywords: Chromosomes, Human, Y, Computer Simulation, DNA, Mitochondrial, Evolution, Molecular, Female, Genetic Drift, Genetic Variation, Genetics, Population, Genome, Human, Humans, Male, Mutation, Open Reading Frames, Selection, Genetic

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

DOI: 10.1371/journal.pgen.1004064
Alternate Journal: PLoS Genet.