Testing for the footprint of sexually antagonistic polymorphisms in the pseudoautosomal region of a plant sex chromosome pair

Genetics

Volumn 194, Issue 3, 2013, Pages 663-672

  Qiu, Suo ^a   Bergero, Roberta ^a   Charlesworth, Deborah ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ALLELE; ARTICLE; BALANCING SELECTION; DNA POLYMORPHISM; GENE FREQUENCY; GENE IDENTIFICATION; GENE MAPPING; HAPLOTYPE; NATURAL POPULATION; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOAUTOSOMAL REGION; SEX CHROMOSOME; SILENE; SILENE LATIFOLIA; X CHROMOSOME; Y CHROMOSOME;

SILENE LATIFOLIA;

EID: 84879767860     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.152397     Document Type: Article

References (76)

1. Baird, N., P. Etter, T. Atwood, M. Currey, A. Shiver et al., 2008 Rapid SNP discovery and genetic mapping using se-quenced RAD markers. PLoS ONE 3: e3376.
2. Bergero, R., and D. Charlesworth, 2011 Preservation of the Y transcriptome in a 10MY old plant sex chromosome system. Curr. Biol. 21: 1470-1474.
3. Bergero, R., A. Forrest, E. Kamau, and D. Charlesworth, 2007 Evolutionary strata on the X chromosomes of the dioe-cious plant Silene latifolia: evidence from new sex-linked genes. Genetics 175: 1945-1954.
4. Bergero, R., A. Forrest, and D. Charlesworth, 2008 Active miniature transposons from a plant genome and its nonrecombining Y chro-mosome. Genetics 178: 1085-1092.
5. Bergero, R., S. Qiu, A. Forrest, H. Borthwick, and D. Charlesworth, 2013 Expansion of the pseudoautosomal region and ongoing recombination suppression in the Silene latifolia sex chromo-somes. Genetics 194: 673-686.
6. Blavet, N., H. Blavet, R. Cegan, N. Zemp, J. Zdanska et al., 2012 Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S. vulgaris au-tosome. BMC Genomics 13: 226.
7. Bonduriansky, R., and S. F. Chenoweth, 2009 Intralocus sexual conflict. Trends Ecol. Evol. 25: 280-288.
8. Bussell, J. J., N. M. Pearson, R. Kanda, D. A. Filatov, and B. T. Lahn, 2006 Human polymorphism and human-chimpanzee diver-gence in pseudoautosomal region correlate with local recombi-nation rate. Gene 368: 94-100.
9. Calafell, F., F. Roubinet, A. Ramírez-Soriano, N. Saitou, J. Bertran-petit et al., 2008 Evolutionary dynamics of the human ABO gene. Hum. Genet. 124: 123-135.
10. Cermak, T., Z. Kubat, R. Hobza, A. Koblizkova, A. Widmer et al., 2008 Survey of repetitive sequences in Silene latifolia with re-spect to their distribution on sex chromosomes. Chromosome Res. 16: 961-976.
11. Charlesworth, B., I. Mori, and D. Charlesworth, 1985 Genetic varia-tion in recombination in Drosophila. 3.3. Regional effects on cross-ing over and effects on non-disjunction. Heredity 55: 209-221.
12. Charlesworth, B., M. Nordborg, and D. Charlesworth, 1997 The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided inbreeding and outcrossing populations. Genet. Res. 70: 155-174.
13. Charlesworth, D., and B. Charlesworth, 1980 Sex differences in fitness and selection for centric fusions between sex-chromo-somes and autosomes. Genet. Res. 35: 205-214.
14. Chibalina, M., and D. Filatov, 2011 Plant Y chromosome degen-eration is retarded by haploid purifying selection. Curr. Biol. 21: 1475-1479.
15. Comeron, J., R. Ratnappan, and S. Bailin, 2012 The many land-scapes of recombination in Drosophila melanogaster. PLoS Genet. 8: e1002905.
16. Cooke, H., W. Brown, and G. Rappold, 1985 Hypervariable telo-meric sequences from the human sex chromosomes are pseu-doautosomal. Nature 317: 687-692.
17. Corbett-Detig, R. B., and D. L. Hartl, 2012 Population genomics of inversion polymorphisms in Drosophila melanogaster. PLoS Genet. 8: e1003056.
18. Delcourt, M., M. W. Blows, and H. D. Rundle, 2009 Sexually antagonistic genetic variance for fitness in an ancestral and a novel environment. Proc. Biol. Sci. 276: 2009-2014.
19. Delph, L., A. Arntz, C. Scotti-Saintagne, and I. Scotti, 2010 The genomic architecture of sexual dimorphism in the dioecious plant Silene latifolia. Evolution 64: 2873-2886.
20. Delph, L. F., and C. R. Herlihy, 2012 Sexual, fecundity, and via-bility selection on flower size and number in a sexually dimor-phic plant. Evolution 66: 1154-1166.
21. DePaulis, F., and M. Veuille, 1998 Neutrality tests based on the distribution of haplotypes under an infinite sites model. Mol. Biol. Evol. 15: 1788-1790.
22. Dooner, H., and L. He, 2008 Maize genome structure variation: interplay between retrotransposon polymorphisms and genic re-combination. Plant Cell 20: 249-258.
23. Dooner, H. K., and I. M. Martinez-Férez, 1997 Recombination occurs uniformly in the bronze gene, a recombination hotspot in the maize genome. Plant Cell 9: 1633-1646.
24. Ebinuma, H., 1987 Selective recombination system in Bombyx mori. 1. chromosome specificity of the modification effect. Ge-netics 117: 521-531.
25. Ellegren, H., 2011 Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nat. Rev. Genet. 12: 157-166.
26. Eronen, L., F. Geerts, and H. Toivonen, 2006 HaploRec: efficient and accurate large-scale reconstruction of haplotypes. BMC Bio-informatics 7: 542.
27. Filatov, D. A., F. Monéger, I. Negrutiu, and D. Charlesworth, 2000 Evolution of a plant Y-chromosome: variability in a Y-linked gene of Silene latifolia. Nature 404: 388-390.
28. Filatov, D. A., V. Laporte, C. Vitte, and D. Charlesworth, 2001 DNA diversity in sex linked and autosomal genes of the plant species Silene latifolia and S. dioica. Mol. Biol. Evol. 18: 1442-1454.
29. Fu, H., Z. Zheng, and H. K. Dooner, 2002 Recombination rates be-tween adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99: 1082-1087.
30. Gordon, S. P., A. López-Sepulcre, and D. N. Reznick, 2012 Predation-associated differences in sex-linkage of wild guppy coloration. Evo-lution 66: 912-918.
31. Graur, D., and W.-H. Li, 2000 Fundamentals of Molecular Evolu-tion. Sinauer Associates, Sunderland, Massachusetts.
32. Grover, C., J. Hawkins, and J. Wendel, 2008 Phylogenetic insights into the pace and pattern of plant genome size evolution, pp. 57-68 in Plant Genomes, edited by J.-N. Volff Karger, Basel, Switzerland.
33. Hudson, R. R., and N. L. Kaplan, 1988 The coalescent process in models with selection and recombination. Genetics 120: 831-840.
34. Hudson, R. R., D. D. Boos, and N. L. Kaplan, 1992 A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.
35. Iwase, M., Y. Satta, Y. Hirai, and N. Takahata, 2010 Frequent gene conversion events between the X and Y homologous chro-mosomal regions in primates. BMC Evol. Biol. 10: 225.
36. Jordan, C., and D. Charlesworth, 2012 The potential for sexually antagonistic polymorphism in different genome regions. Evolu-tion 66: 505-516.
37. Kelly, J. K., 1997 A test of neutrality based on interlocus associa-tions. Genetics 146: 1197-1206.
38. Kirkpatrick, M., R. Guerrero, and S. Scarpino, 2010 Patterns of neutral genetic variation on recombining sex chromosomes. Ge-netics 184: 1141-1152.
39. Kitano, J., J. A. Ross, S. Mori, M. Kume, F. C. Jones et al., 2009 A role for a neo-sex chromosome in stickleback speciation. Nature 461: 1079-1083.
40. Lahn, B. T., and D. C. Page, 1999 Four evolutionary strata on the human X chromosome. Science 286: 964-967.
41. Laporte, V., D. A. Filatov, E. Kamau, and D. Charlesworth, 2005 Indirect evidence from DNA sequence diversity for ge-netic degeneration of Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs. J. Evol. Biol. 18: 337-347.
42. Lawson-Handley, L. J., H. Ceplitis, and H. Ellegren, 2004 Evolutionary strata on the chicken Z chromosome: implications for sex chro-mosome evolution. Genetics 167: 367-376.
43. Lemaitre, C., M. D. V. Braga, C. Gautier, M.-F. Sagot, E. Tannier et al., 2009 Footprints of inversions at present and past pseu-doautosomal boundaries in human sex chromosomes. Genome Biol. Evol. 1: 56-66.
44. Librador, P., and J. Rozas, 2009 DnaSP v5: a software for com-prehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
45. Lindholm, A., and F. Breden, 2002 Sex chromosomes and sexual selection in Poeciliid fishes. Am. Nat. 160: S214-S224.
46. Liu, Z., P. H. Moore, H. Ma, C. M. Ackerman, M. Ragiba et al., 2004 A primitive Y chromosome in Papaya marks the begin-ning of sex chromosome evolution. Nature 427: 348-352.
47. Macas, J., E. Kejnovsky, P. Neumann, P. Nova, A. Koblizkova et al., 2008 Next generation sequencing-based analysis of repetitive DNA in the model dioecious plant Silene latifolia. PLoS ONE 6: e27335.
48. Mank, J. E., and H. Ellegren, 2009 Sex-linkage of sexually antag-onistic genes is predicted by female, but not male, effects in birds. Evolution 63: 1464-1472.
49. Mank, J. E., L. Hultin-Rosenberg, M. Zwahlen, and H. Ellegren, 2008 Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. Am. Nat. 171: 35-43.
50. Matsubara, K., H. Tarui, M. Toriba, K. Yamada, C. Nishida-Umehara et al., 2006 Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes. Proc. Natl. Acad. Sci. USA 103: 18190-18195.
51. Matsunaga, S., E. Isono, E. Kejnovsky, B. Vyskot, S. Kawano et al., 2003 Duplicative transfer of a MADS box gene to a plant Y chromosome. Mol. Biol. Evol. 20: 1062-1069.
52. McDaniel, S.F., J.H. Willis, and A.J. Shaw, 2007 Alinkagemapreveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus. Genetics 176: 2489-2500.
53. McVean, G. A. T., P. Awadalla, and P. Fearnhead, 2002 A coales-cent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
54. Muir, G., C. J. Dixon, A. L. Harper, and D. A. Filatov, 2011 Dynamics of drift, gene flow and selection during speciation in Silene. Evo-lution 66: 1447-1458.
55. Nam, K., and H. Ellegren, 2008 Scrambled eggs: the chicken (Gal-lus gallus) Z chromsome contains at least three non-linear evo-lutionary strata. Genetics 180: 1131-1136.
56. Nishida-Umehara, C., Y. Tsuda, J. Ishijima, J. Ando, A. Fujiwara et al., 2007 The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res. 15: 721-734.
57. Nordborg, M., B. Charlesworth, and D. Charlesworth, 1996 Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc. Biol. Sci. 163: 1033-1039.
58. Otto, S. P., J. R. Pannell, C. L. Peichel, T. Ashman, D. Charlesworth et al., 2011 About PAR: the distinct evolutionary dynamics of the pseudoautosomal region. Trends Genet. 27: 358-367.
59. Patten, M. M., D. Haig, and F. Úbeda, 2010 Fitness variation due to sexual antagonism and linkage disequilibrium. Evolution 64: 3638-3642.
60. Perkins, D. D., and M. Bojko, 1992 The basis of decreased recombina-tion in certain outcrosses of Neurospora crassa. Genome 35: 503-509.
61. Qiu, S., R. Bergero, A. Forrest, V. B. Kaiser, and D. Charlesworth, 2010 Nucleotide diversity in Silene latifolia autosomal and sex-linked genes. Proc. Biol. Sci. 277: 3283-3290.
62. Rice, W. R., 1987 The accumulation of sexually antagonistic genes as a selective agent promoting the evolution of reduced recombination between primitive sex-chromosomes. Evolution 41: 911-914.
63. Roberts, R. B., J. R. Ser, and T. D. Kocher, 2009 Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes. Science 326: 998-1001.
64. Rosser, Z. H., P. Balaresque, and M. A. Jobling, 2009 Gene con-version between the X chromosome and the male-specific region of the Y chromosome at a translocation hotspot. Am. J. Hum. Genet. 851: 130-134.
65. Salome, P., K. Bomblies, J. Fitz, R. Laitinen, N. Warthmann et al., 2012 The recombination landscape in Arabidopsis thaliana F2 populations. Heredity 108: 447-455.
66. Ségurel, L., E. E. Thompson, T. Flutre, J. Lovstad, A. Venkat et al., 2012 The ABO blood group is a trans-species polymorphism in primates. Proc. Natl. Acad. Sci. USA 109: 18493-18498.
67. Skaletsky, H., T. Kuroda-Kawaguchi, P. J. Minx, H. S. Cordum, L. Hillier et al., 2003 The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837.
68. Slattery, J. P., L. Sanner-Wachter, and S. J. O'Brien, 2000 Novel gene conversion between X-Y homologues located in the non-recombining region of the Y chromosome in Felidae (Mamma-lia). Proc. Natl. Acad. Sci. USA 97: 5307-5312.
69. Spigler, R., K. Lewers, D. Main, and T.-L. Ashman, 2008 Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity 101: 507-517.
70. Stulp, G., B. Kuijper, A. P. Buunk, T. V. Pollet, and S. Verhulst, 2012 Intralocus sexual conflict over human height. Biol. Lett. 8: 976-978.
71. Tajima, F., 1989 Statistical method for testing the neutral muta-tion hypothesis. Genetics 123: 585-595.
72. Trombetta, B., F. Cruciani, P. Underhill, D. Sellitto, and R. Scozzari, 2010 Footprints of X-to-Y gene conversion in recent human evolution. Mol. Biol. Evol. 27: 714-725.
73. Úbeda, F., D. Haig, and M. M. Patten, 2011 Stable linkage dis-equilibrium owing to sexual antagonism. Proc. Biol. Sci. 278: 855-862.
74. Wang, J., J. Na, Q. Yu, A. R. Gschwend, J. Han et al., 2012 Sequencing papaya Xand Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc. Natl. Acad. Sci. USA 109: 13710-13715.
75. Wright, S. I., and B. Charlesworth, 2004 The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model. Genetics 168: 1071-1076.
76. Yi, S., and W.-H. Li, 2005 Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in Hominoids. Mol. Biol. Evol. 22: 1223-1230.