title: Natural selection reduced diversity on human y chromosomes.
abstract: 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.
authors.affiliation: Statistics Department, University of California-Berkeley, Berkeley, California, United States of America ; Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Wilson Sayres
authors.affiliation: Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America ; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America.
authors.forename: Kirk E
authors.initials: KE
authors.lastname: Lohmueller
authors.affiliation: Statistics Department, University of California-Berkeley, Berkeley, California, United States of America ; Integrative Biology Department, University of California-Berkeley, Berkeley, California, United States of America.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
mesh_terms: D041322:Chromosomes, Human, Y / Q000235:genetics*; D003198:Computer Simulation; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D040961:Genetic Drift; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D008297:Male; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial