title: Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.
abstract: The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay. 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. 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, 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.
authors.affiliation: Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA. jhughes@wi.mit.edu
authors.forename: Jennifer F
authors.initials: JF
authors.lastname: Hughes
authors.forename: Helen
authors.initials: H
authors.lastname: Skaletsky
authors.forename: Laura G
authors.initials: LG
authors.lastname: Brown
authors.forename: Tatyana
authors.initials: T
authors.lastname: Pyntikova
authors.forename: Tina
authors.initials: T
authors.lastname: Graves
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.forename: Shannon
authors.initials: S
authors.lastname: Dugan
authors.forename: Yan
authors.initials: Y
authors.lastname: Ding
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Buhay
authors.forename: Colin
authors.initials: C
authors.lastname: Kremitzki
authors.forename: Qiaoyan
authors.initials: Q
authors.lastname: Wang
authors.forename: Hua
authors.initials: H
authors.lastname: Shen
authors.forename: Michael
authors.initials: M
authors.lastname: Holder
authors.forename: Donna
authors.initials: D
authors.lastname: Villasana
authors.forename: Lynne V
authors.initials: LV
authors.lastname: Nazareth
authors.forename: Andrew
authors.initials: A
authors.lastname: Cree
authors.forename: Laura
authors.initials: L
authors.lastname: Courtney
authors.forename: Joelle
authors.initials: J
authors.lastname: Veizer
authors.forename: Holland
authors.initials: H
authors.lastname: Kotkiewicz
authors.forename: Ting-Jan
authors.initials: TJ
authors.lastname: Cho
authors.forename: Natalia
authors.initials: N
authors.lastname: Koutseva
authors.forename: Steve
authors.initials: S
authors.lastname: Rozen
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: David C
authors.initials: DC
authors.lastname: Page
mesh_terms: D000818:Animals; D041322:Chromosomes, Human, Y / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics*; D003434:Crossing Over, Genetic / Q000235:genetics; D019143:Evolution, Molecular; D005784:Gene Amplification / Q000235:genetics; D017353:Gene Deletion; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008253:Macaca mulatta / Q000235:genetics*; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000235:genetics; D021101:Radiation Hybrid Mapping; D012641:Selection, Genetic / Q000235:genetics; D013997:Time Factors; D014998:Y Chromosome / Q000235:genetics*