title: Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys.
abstract: In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papionin monkeys (macaques, mangabeys, mandrills, drills, baboons, and geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To explore the potential genomic consequences of such sex differences, we used a reduced representation genome sequencing approach to quantifying polymorphism at sites on autosomes and sex chromosomes of the tonkean macaque (Macaca tonkeana), a species endemic to the Indonesian island of Sulawesi. The ratio of nucleotide diversity of the X chromosome to that of the autosomes was less than the value (0.75) expected with a 1:1 sex ratio and no sex differences in the variance in reproductive success. However, the significance of this difference was dependent on which outgroup was used to standardize diversity levels. Using a new model that includes the effects of varying population size, sex differences in mutation rate between the autosomes and X chromosome, and GC-biased gene conversion (gBGC) or selection on GC content, we found that the maximum-likelihood estimate of the ratio of effective population size of the X chromosome to that of the autosomes was 0.68, which did not differ significantly from 0.75. We also found evidence for 1) a higher level of purifying selection on genic than nongenic regions, 2) gBGC or natural selection favoring increased GC content, 3) a dynamic demography characterized by population growth and contraction, 4) a higher mutation rate in males than females, and 5) a very low polymorphism level on the Y chromosome. These findings shed light on the population genomic consequences of sex differences in the variance in reproductive success, which appear to be modest in the tonkean macaque; they also suggest the occurrence of hitchhiking on the Y chromosome.
authors.affiliation: Biology Department, McMaster University, Hamilton, ON, Canada evansb@mcmaster.ca.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Evans
authors.affiliation: Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Kai
authors.initials: K
authors.lastname: Zeng
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University.
authors.forename: Jacob A
authors.initials: JA
authors.lastname: Esselstyn
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Brian
authors.initials: B
authors.lastname: Charlesworth
authors.affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University.
authors.forename: Don J
authors.initials: DJ
authors.lastname: Melnick
mesh_terms: D000818:Animals; D001482:Base Composition; D033481:Chromosomes, Mammalian / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D016678:Genome; D007214:Indonesia; D016013:Likelihood Functions; D008251:Macaca / Q000145:classification / Q000235:genetics*; D008297:Male; D059645:Mutation Rate; D011110:Polymorphism, Genetic; D011156:Population Density; D012098:Reproduction; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012730:Sex Chromosomes / Q000235:genetics*; D012744:Sex Ratio
keywords: GC-biased gene conversion; X chromosome; Y chromosome; demography; male driven evolution; molecular polymorphism