title: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution.
abstract: Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here, we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multiordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 17 MSY genes, most being constrained by negative selection for nearly 100 million years. The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved noncoding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.
authors.affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.forename: Brian W
authors.initials: BW
authors.lastname: Davis
authors.forename: Terje
authors.initials: T
authors.lastname: Raudsepp
authors.forename: Alison J
authors.initials: AJ
authors.lastname: Pearks Wilkerson
authors.forename: Victor C
authors.initials: VC
authors.lastname: Mason
authors.forename: Malcolm
authors.initials: M
authors.lastname: Ferguson-Smith
authors.forename: Patricia C
authors.initials: PC
authors.lastname: O'Brien
authors.forename: Paul D
authors.initials: PD
authors.lastname: Waters
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
mesh_terms: D000818:Animals; D002415:Cats / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics*; D004285:Dogs / Q000235:genetics*; D019143:Evolution, Molecular; D056426:Genetic Loci; D008297:Male; D010802:Phylogeny; D012641:Selection, Genetic; D014998:Y Chromosome / Q000235:genetics*