Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

• Published in: Nature (London) Vol. 483; no. 7387; pp. 82 - 86
• Main Authors: Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Graves, Tina, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Buhay, Christian J., Kremitzki, Colin, Wang, Qiaoyan, Shen, Hua, Holder, Michael, Villasana, Donna, Nazareth, Lynne V., Cree, Andrew, Courtney, Laura, Veizer, Joelle, Kotkiewicz, Holland, Cho, Ting-Jan, Koutseva, Natalia, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., Page, David C.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.03.2012; Nature Publishing Group
• Subjects: 631/181/2474; 631/337/103; Animals; Artificial chromosomes; Biological and medical sciences; Chimpanzees; Chromosome mapping; Chromosomes; Chromosomes, Human, Y - genetics; Classical genetics, quantitative genetics, hybrids; Cloning; Confidence intervals; Conserved Sequence - genetics; Crossing Over, Genetic - genetics; Evolution, Molecular; Evolutionary genetics; Fundamental and applied biological sciences. Psychology; Gene Amplification - genetics; Gene Deletion; Genes; Genetic aspects; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Haplotypes; Human; Human chromosomes; Human genetics; Humanities and Social Sciences; Humans; Hybridization; In Situ Hybridization, Fluorescence; letter; Macaca mulatta - genetics; Male; Methods; Models, Genetic; Molecular Sequence Data; multidisciplinary; Pan troglodytes - genetics; Properties; Radiation Hybrid Mapping; Regression analysis; Rhesus monkey; Science; Science (multidisciplinary); Selection, Genetic - genetics; Stratigraphy; Time Factors; Y chromosome; Y Chromosome - genetics; United States; Human; Molecular evolution; Vertebrata; Mammalia; Sex chromosome; Primates; Simioidea; Macaca mulatta; X-Chromosome; Y-Chromosome; Comparative study
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature10843

The male-specific region of rhesus macaque and human Y chromosome (MSY) are sequenced and compared to the human MSY, showing that during the last 25 million years MSY gene loss in the rhesus and human lineages was limited to the youngest stratum (stratum 5), whereas gene loss in the older strata ceased more than 25 million years ago. The fate of the Y chromosome The mammal sex-determining X and Y chromosomes evolved from a pair of autosomes ('normal' non-sex chromosomes), but as a result of genetic decay, the male-specific region of the human Y chromosome retains only 3% of the ancestral autosomal genes. Here, the authors have sequenced the corresponding region of the rhesus macaque Y, and reconstructed the trajectory of its evolution through an analysis of the rhesus, human and chimpanzee Y chromosomes. The results show that initial rapid loss of genes is followed by strict conservation through purifying selection. This runs counter to the view that the human Y chromosome is destined inevitably for extinction. The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200–300 million years 1 , 2 , 3 . The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes’ genes owing to genetic decay 4 , 5 . This evolutionary decay was driven by a series of five ‘stratification’ events. Each event suppressed X–Y crossing over within a chromosome segment or ‘stratum’, incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over 2 , 6 . The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome 7 , 8 , 9 , 10 , remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1–4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.