Mammalian Sex Chromosome Evolution


Although they are highly dissimilar in sequence content in extant organisms, the mammalian sex chromosomes (i.e. the X and Y) evolved from a pair of autosomes. Differentiation of the sex chromosomes during evolution was initiated by the suppression of X–Y recombination, likely through changes in genomic structure. This was followed by the degeneration of genes on the Y chromosome, with specific instances of gene specialisation on the nonrecombining portion of the Y. Findings of evolutionary ‘strata’ on the sex chromosomes of mammals suggest that multiple events have given rise to the current arrangement of genes on the X and Y chromosomes of mammals. However, new studies utilising more divergent genomic data are challenging conclusions regarding the number and frequency of events that led to the current arrangement of mammalian sex chromosomes, and future studies with complete genomic sequences of marsupials will continue to further our understanding of the evolution of these critical chromosomes.

Key Concepts:

  • Mammalian sex chromosomes arose from a pair of autosomes.

  • Genomic rearrangements repressed recombination in a stepwise fashion on these chromosomes.

  • Genes on these chromosomes diverged due to a combination of forces, including sexual antagonism and removal of deleterious mutations.

  • Chromosomal studies outside placental mammals continue to contribute to our understanding of mammalian sex chromosome evolution.

  • Groups of genes on sex chromosomes with similar evolutionary origins are called gene ‘strata’ and exist on both the X and Y chromosomes in the nonrecombining regions.

Keywords: X chromosome; Y chromosome; mammalian sex chromosomes; Y degeneration; pseudoautosomal region; nonrecombining Y

Figure 1.

The evolutionary strata on the human X chromosome (after Lahn and Page, ). Blue tick marks symbolise representative genes within a stratum, and red tick marks show stratum boundaries. The arrows show the decreasing age of the strata (red arrow) and increasing synonymous mutation rate (Ks) for the genes on the strata used to estimate the age of inversions (blue arrow).



Crow J (1993) How much do we know about spontaneous human mutation rates? Environmental and Molecular Mutagenesis 21: 122–129.

Deakin JE, Graves JA and Rens W (2012) The evolution of marsupial and monotreme chromosomes. Cytogenetic and Genome Research 137(2–4): 113–129.

Foster JW and Graves JA (1994) An SRY‐related sequence on the marsupial X chromosome: implications for the evolution of the mammalian testis‐determining gene. Proceedings of the National Academy of Sciences of the USA 91: 1927–1931.

Gavrilov LA, Gavrilova NS, Kroutko VN et al. (1997) Mutation load and human longevity. Mutation Research 377: 61–62.

Graves JM, Wakefield MJ and Toder R (1998) The origin and evolution of the pseudoautosomal regions of human sex chromosomes. Molecular Genetics 7: 1991–1996.

Grossen C, Neuenschwander S and Perrin N (2012) The evolution of XY recombination: sexually antagonistic selection versus deleterious mutation load. Evolution 66(10): 3155–3166.

Handley LJ, Ceplitis H and Ellegren H (2004) Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics 167(1): 367–376.

Hughes JF, Skaletsky H and Pyntikova T (2005) Conservation of Y‐linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437(7055): 100–103.

Johnson NA and Lachance J (2012) The genetics of sex chromosomes: evolution and implications for hybrid incompatibility. Annals of the New York Academy of Sciences 1256: E1–22.

Katsura Y and Satta Y (2012) No evidence for a second evolutionary stratum during the early evolution of mammalian sex chromosomes. PLoS One 7(10): e45488.

Katsura Y, Iwase M and Satta Y (2012) Evolution of genomic structures on mammalian sex chromosomes. Current Genomics 13(2): 115–123.

Lahn BT and Page DC (1997) Functional coherence of the human Y chromosome. Science 278: 675–680.

Lahn BT and Page DC (1999a) Four evolutionary strata on the human X chromosome. Science 286: 964–967.

Lahn BT and Page DC (1999b) Retroposition of autosomal mRNA yielded testis‐specific gene family on human Y chromosome. Nature Genetics 21: 429–433.

Mácha J, Teichmanová R, Sater AK et al. (2012) Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis. BMC Genomics 13: 315.

Malcom CM, Wyckoff GJ and Lahn BT (2003) Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X‐versus‐autosome disparity. Molecular Biology and Evolution 20: 1633–1641.

Muller HJ (1964) The relation of recombination to mutational advance. Mutation Research 1: 2–9.

Pamilo P and Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Molecular Biology and Evolution 10: 271–281.

Rappold GA (1993) The pseudoautosomal regions of the human sex chromosomes. Human Genetics 92: 315–324.

Rens W, O'Brien PC, Grutzner F et al. (2007) The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biology 8(11): R243.

Rice WR (1987) Genetic hitchhiking and the evolution of reduced genetic activity of the Y sex chromosome. Genetics 116: 161–167.

Saxena R, Brown LG, Hawkins T et al. (1996) The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nature Genetics 14: 292–299.

Shen P, Wang F, Underhill P et al. (2000) Population genetic implications from sequence variation in four Y chromosome genes. Proceedings of the National Academy of Sciences of the USA 97: 7354–7359.

Shimmin LC, Chang BH, Hewett‐Emmett D and Li WH (1993) Potential problems in estimating the male‐to‐female mutation rate ratio from DNA sequence data. Journal of Molecular Evolution 37: 160–166.

Skaletsky H, Kuroda‐Kawaguchi T, Minx PJ et al. (2003) The male‐specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825–837.

Stevanovic M, Lovell‐Badge R, Collignon J and Goodfellow PN (1993) SOX3 is an X‐linked gene related to SRY. Human Molecular Genetics 2: 2013–2018.

Vallender EJ and Lahn BT (2004) How mammalian sex chromosomes acquired their peculiar gene content. BioEssays 26: 159–169.

Wyckoff GJ, Li J and Wu CI (2002) Molecular evolution of functional genes on the mammalian Y chromosome. Molecular Biology and Evolution 19: 1633–1636.

Yoshida K and Sugano S (1999) Identification of a novel protocadherin gene (PCDH11) on the human XY homology region in Xq21.3. Genomics 62: 540–543.

Further Reading

Charlesworth B (1991) The evolution of sex chromosomes. Science 251: 1030–1033.

Graves JA (1995) The origin and function of the mammalian Y chromosome and Y‐borne genes – an evolving understanding. BioEssays 17: 311–320.

Graves JA (2006) Sex chromosome specialization and degeneration in mammals. Cell 124: 901–914.

Gvozdev VA, Kogan GL and Usakin LA (2005) The Y chromosome as a target for acquired and amplified genetic material in evolution. BioEssays 27(12): 1256–1262.

Jegalian K and Page DC (1998) A proposed path by which genes common to mammalian X and Y chromosomes evolve to become X inactivated. Nature 394: 776–780.

Kohn M, Kehrer‐Sawatzki H, Vogel W, Graves JA and Hameister H (2004) Wide genome comparisons reveal the origins of the human X chromosome. Trends in Genetics 20: 598–603.

Lahn BT, Pearson NM and Jegalian K (2001) The human Y chromosome, in the light of evolution. Nature Reviews Genetics 2: 207–216.

Page DC, Hughes JF, Bellott DW et al. (2010) Reconstructing sex chromosome evolution. Genome Biology 11(Suppl. 1): I21

Rice WR (1994) Degeneration of a nonrecombining chromosome. Science 263: 230–232.

Vicoso B and Charlesworth B (2006) Evolution of the X chromosome: unusual patterns and processes. Nature Reviews Genetics 7: 645–653.

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Wyckoff, Gerald J, and Malcom, Christine M(Sep 2013) Mammalian Sex Chromosome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005792.pub3]