Multicopy gene family evolution on primate Y chromosomes

Abstract

Unlike the autosomes, the Y chromosome in humans and other primates has few protein coding genes, with only a few dozen single-copy genes and several tandem duplicated gene families, called the "ampliconic" genes. The interaction of many biological and evolutionary factors is responsible for this structural heterogeneity among different parts of the genome. We sequenced and assayed the copy numbers of Y-linked, single-copy genes and ampliconic genes in a group of closely related macaque monkeys, then fit models of gene family evolution to this data along with whole genome data from human, chimpanzee, and rhesus macaque. Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys, (ii) indicate that ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome, and that (iii) Y-linked singleton and autosomal gene families evolved faster in great apes than they do in other Old World higher Primates. These findings highlight the evolutionary eccentricity of duplicated genes on the Y chromosome and suggest an important role for natural selection and gene conversion in the evolution of Y-linked gene duplicates.