1 Kashimada, K. & Koopman, P. Sry: the master switch in mammalian sex determination. Development 137, 3921–3930 (2010)

2 Wilson, M. A. & Makova, K. D. Genomic analyses of sex chromosome evolution. Annu. Rev. Genomics Hum. Genet. 10, 333–354 (2009)

3 Potrzebowski, L. et al. Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol. 6, e80 (2008)

4 Veyrunes, F. et al. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. 18, 965–973 (2008)

5 Grützner, F. et al. In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature 432, 913–917 (2004)

6 Charlesworth, B. & Charlesworth, D. The degeneration of Y chromosomes. Phil. Trans. R. Soc. Lond. B 355, 1563–1572 (2000)

7 Bachtrog, D. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nature Rev. Genet. 14, 113–124 (2013)

8 Julien, P. et al. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 10, e1001328 (2012)

9 Hughes, J. F. et al. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463, 536–539 (2010)

10 Hughes, J. F. et al. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 483, 82–86 (2012)

11 Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003)

12 Li, G. et al. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution. Genome Res. 23, 1486–1495 (2013)

13 Marais, G. A., Campos, P. R. & Gordo, I. Can intra-Y gene conversion oppose the degeneration of the human Y chromosome? A simulation study. Genome Biol. Evol. 2, 347–357 (2010)

14 Murphy, W. J., Pevzner, P. A. & O’Brien, S. J. Mammalian phylogenomics comes of age. Trends Genet. 20, 631–639 (2004)

15 Ayers, K. L. et al. RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome. Genome Biol. 14, R26 (2013)

16 Moghadam, H. K., Pointer, M. A., Wright, A. E., Berlin, S. & Mank, J. E. W chromosome expression responds to female-specific selection. Proc. Natl Acad. Sci. USA 109, 8207–8211 (2012)

17 Ross, M. T. et al. The DNA sequence of the human X chromosome. Nature 434, 325–337 (2005)

18 Murtagh, V. J. et al. Evolutionary history of novel genes on the tammar wallaby Y chromosome: implications for sex chromosome evolution. Genome Res. 22, 498–507 (2012)

19 Lahn, B. T. & Page, D. C. Four evolutionary strata on the human X chromosome. Science 286, 964–967 (1999)

20 Wilson Sayres, M. A. & Makova, K. D. Genome analyses substantiate male mutation bias in many species. Bioessays 33, 938–945 (2011)

21 Pearks Wilkerson, A. J. et al. Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics 92, 329–338 (2008)

22 Chang, T. C., Yang, Y., Retzel, E. F. & Liu, W. S. Male-specific region of the bovine Y chromosome is gene rich with a high transcriptomic activity in testis development. Proc. Natl Acad. Sci. USA 110, 12373–12378 (2013)

23 Weller, P. A., Critcher, R., Goodfellow, P. N., German, J. & Ellis, N. A. The human Y chromosome homologue of XG: transcription of a naturally truncated gene. Hum. Mol. Genet. 4, 859–868 (1995)

24 Rodríguez-Delgado, C. L., Waters, P. D., Gilbert, C., Robinson, T. J. & Graves, J. A. Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years. Chromosome Res. 17, 917–926 (2009)

25 Rens, W. et al. The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z. Genome Biol. 8, R243 (2007)

26 Warren, W. C. et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175–183 (2008)

27 Cutting, A., Chue, J. & Smith, C. A. Just how conserved is vertebrate sex determination? Dev. Dyn. 242, 380–387 (2013)

28 Western, P. S., Harry, J. L., Graves, J. A. & Sinclair, A. H. Temperature-dependent sex determination in the American alligator: AMH precedes SOX9 expression. Dev. Dyn. 216, 411–419 (1999)

29 Hattori, R. S. et al. A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination. Proc. Natl Acad. Sci. USA 109, 2955–2959 (2012)

30 Tsend-Ayush, E. et al. Identification of mediator complex 26 (Crsp7) gametologs on platypus X1 and Y5 sex chromosomes: a candidate testis-determining gene in monotremes? Chromosome Res. 20, 127–138 (2012)

31 Dalloul, R. A. et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 8, e1000475 (2010)

32 Warren, W. C. et al. The genome of a songbird. Nature 464, 757–762 (2010)

33 Adolfsson, S. & Ellegren, H. Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches. Mol. Biol. Evol. 30, 806–810 (2013)

34 Nam, K. & Ellegren, H. The chicken (Gallus gallus) Z chromosome contains at least three nonlinear evolutionary strata. Genetics 180, 1131–1136 (2008)

35 Matunis, M. J., Michael, W. M. & Dreyfuss, G. Characterization and primary structure of the poly(C)-binding heterogeneous nuclear ribonucleoprotein complex K protein. Mol. Cell. Biol. 12, 164–171 (1992)

36 Wu, Z. et al. Targeted ubiquitination and degradation of G-protein-coupled receptor kinase 5 by the DDB1–CUL4 ubiquitin ligase complex. PLoS ONE 7, e43997 (2012)

37 Smith, C. A. et al. The avian Z-linked gene DMRT1 is required for male sex determination in the chicken. Nature 461, 267–271 (2009)

38 Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25, 25–29 (2000)

39 Zhou, Q. & Bachtrog, D. Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science 337, 341–345 (2012)

40 Kondrashov, F. A. & Koonin, E. V. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20, 287–290 (2004)

41 Soumillon, M. et al. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell Rep. 3, 2179–2190 (2013)

42 Cocquet, J. et al. The multicopy gene Sly represses the sex chromosomes in the male mouse germline after meiosis. PLoS Biol. 7, e1000244 (2009)

43 Wilson, M. A. & Makova, K. D. Evolution and survival on eutherian sex chromosomes. PLoS Genet. 5, e1000568 (2009)

44 Berlin, S. & Ellegren, H. Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds. J. Mol. Evol. 62, 66–72 (2006)

45 Hughes, J. F., Skaletsky, H. & Page, D. C. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes. Bioessays 34, 1035–1044 (2012)

46 Charlesworth, B. Model for evolution of Y chromosomes and dosage compensation. Proc. Natl Acad. Sci. USA 75, 5618–5622 (1978)

47 Sutton, E. et al. Identification of SOX3 as an XX male sex reversal gene in mice and humans. J. Clin. Invest. 121, 328–341 (2011)

48 Park, C., Carrel, L. & Makova, K. D. Strong purifying selection at genes escaping X chromosome inactivation. Mol. Biol. Evol. 27, 2446–2450 (2010)

49 Necsulea, A. et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505, 635–640 (2014)

50 Brawand, D. et al. The evolution of gene expression levels in mammalian organs. Nature 478, 343–348 (2011)

51 Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012)

52 Kircher, M., Stenzel, U. & Kelso, J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol. 10, R83 (2009)

53 Chen, N., Bellott, D. W., Page, D. C. & Clark, A. G. Identification of avian W-linked contigs by short-read sequencing. BMC Genomics 13, 183 (2012)

54 Carvalho, A. B., Dobo, B. A., Vibranovski, M. D. & Clark, A. G. Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 98, 13225–13230 (2001)

55 Carvalho, A. B. & Clark, A. G. Efficient identification of Y chromosome sequences in the human and Drosophila genomes. Genome Res. 23, 1894–1907 (2013)

56 Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009)

57 Flicek, P. et al. Ensembl 2012. Nucleic Acids Res. 40, D84–D90 (2012)

58 Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012)

59 Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (2008)

60 Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol. 29, 644–652 (2011)

61 Kent, W. J. BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

62 Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

63 Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004)

64 Huang, X. & Madan, A. CAP3: A DNA sequence assembly program. Genome Res. 9, 868–877 (1999)

65 Church, D. M. et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol. 7, e1000112 (2009)

66 Untergasser, A. et al. Primer3–new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012)

67 Löytynoja, A. & Goldman, N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl Acad. Sci. USA 102, 10557–10562 (2005)

68 Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010)

69 Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010)

70 Katsura, Y. & Satta, Y. No evidence for a second evolutionary stratum during the early evolution of mammalian sex chromosomes. PLoS ONE 7, e45488 (2012)

71 Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997)

72 Yang, Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568–573 (1998)

73 Chamary, J. V., Parmley, J. L. & Hurst, L. D. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nature Rev. Genet. 7, 98–108 (2006)

74 Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511–515 (2010)

75 Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

76 Schriml, L. M. et al. Tyramide signal amplification (TSA)-FISH applied to mapping PCR-labeled probes less than 1 kb in size. Biotechniques 27, 608–613 (1999)

77 Kortschak, R. D., Tsend-Ayush, E. & Grutzner, F. Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus. Reprod. Fertil. Dev. 21, 964–975 (2009)

78 Goto, H., Peng, L. & Makova, K. D. Evolution of X-degenerate Y chromosome genes in greater apes: conservation of gene content in human and gorilla, but not chimpanzee. J Mol Evol. 68, 134–144 (2009)

79 Kim, H. S. & Takenaka, O. Evolution of the X-linked zinc finger gene and the Y-linked zinc finger gene in primates. Mol. Cells 10, 512–518 (2000)

80 Whitfield, L. S., Lovell-Badge, R. & Goodfellow, P. N. Rapid sequence evolution of the mammalian sex-determining gene SRY. Nature 364, 713–715 (1993)

81 Moreira, M. A. SRY evolution in Cebidae (Platyrrhini: Primates). J. Mol. Evol. 55, 92–103 (2002)

82 Gubbay, J. et al. A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature 346, 245–250 (1990)

83 Ma, K. et al. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. Cell 75, 1287–1295 (1993)

84 Agulnik, A. I. et al. A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens. Hum. Mol. Genet. 3, 873–878 (1994)

85 Mitchell, M. J. et al. Homology of a candidate spermatogenic gene from the mouse Y chromosome to the ubiquitin-activating enzyme E1. Nature 354, 483–486 (1991)

86 Ehrmann, I. E. et al. Characterization of genes encoding translation initiation factor from X-inactivation and evolution. Hum. Mol. Genet. 7, 1725–1737 (1998)

87 Strausberg, R. L. et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl Acad. Sci. USA 99, 16899–16903 (2002)

88 Hall, N. M. et al. Usp9y (ubiquitin-specific protease 9 gene on the Y) is associated with a functional promoter and encodes an intact open reading frame homologous to Usp9x that is under selective constraint. Mamm. Genome 14, 437–447 (2003)

89 Mazeyrat, S. et al. The mouse Y chromosome interval necessary for spermatogonial proliferation is gene dense with syntenic homology to the human AZFa region. Hum. Mol. Genet. 7, 1713–1724 (1998)

90 Mardon, G. & Page, D. C. The sex-determining region of the mouse Y chromosome encodes a protein with a highly acidic domain and 13 zinc fingers. Cell 56, 765–770 (1989)

91 Touré, A. et al. Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm. Genome Biol. 6, R102 (2005)