Selection by climatic regime and neutral evolutionary processes in holocentric chromosomes (Carex gr. laevigata: Cyperaceae): A microevolutionary approach

Perspectives in Plant Ecology, Evolution and Systematics

Volumn 15, Issue 2, 2013, Pages 118-129

  Escudero, Marcial ^a,b   Maguilla, Enrique ^a   Luceño, Modesto ^a  

^a UNIVERSIDAD PABLO DE OLAVIDE   (Spain)

^b MORTON ARBORETUM   (United States)

Author keywords

Carex; Cyperaceae; Generalized linear mixed models; Recombination rate optima; Suppression of recombination

Indexed keywords

CHLOROPLAST; CHROMOSOME; CLIMATE CHANGE; CLIMATE VARIATION; DATA SET; DATABASE; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENOME; MIGRATION; MONOCOTYLEDON; NUMERICAL MODEL; POPULATION DISTRIBUTION; RECOMBINATION; SPECIATION (BIOLOGY);

WESTERN EUROPE;

CAREX; CAREX LAEVIGATA; CYPERACEAE;

EID: 84875518009     PISSN: 14338319     EISSN: 16180437     Source Type: Journal    
DOI: 10.1016/j.ppees.2013.01.001     Document Type: Article

References (89)

1. Arens P., Bijlsma R., Van't Westende W., Van Os B., Smulders M.J.M., Vosman B. Genetic structure in populations of an ancient woodland sedge, Carex sylvatica Hudson, at a regional and local scale. Plant Biol. 2005, 7:387-396.
2. Baines J.F., Das A., Mousset F., Stephan W. The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics 2004, 168:1987-1998.
3. Barton N.H. A general model for the evolution of recombination. Genet. Res. 1995, 65:123-144.
4. Beerli P., Felsenstein J. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 1999, 152:763-773.
5. Bell G. The Masterpiece of Nature: The Evolution and Genetics of Sexuality 1982, University of California Press, Berkeley.
6. Burt A. The evolution of fitness. Evolution 1995, 49:1-8.
7. Burt A. Perspective: sex, recombination, and the efficacy of selection - was Weismann right?. Evolution 2000, 54:337-351.
8. Charlesworth B. Directional selection and the evolution of sex and recombination. Genet. Res. 1993, 61:205-224.
9. Burt A., Bell G. Mammalian chiasma frequencies as a test of two theories of recombination. Nature 1987, 326:803-805.
10. Butlin R.K. Recombination and speciation. Mol. Ecol. 2005, 14:2621-2635.
11. Claeskens G., Hjort N.L. Model Selection and Model Averaging 2008, Cambridge University Press, Cambridge.
12. Clement M., Posada D., Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 2000, 9:1657-1659.
13. Clerc-Blain J.L., Starr J.R., Bull R.D., Saarela J.M. A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago. Mol. Ecol. Resour. 2010, 10:69-91.
14. Coghlan A., Eichler E.E., Oliver S.G., Paterson A.H., Stein L. Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet. 2005, 21:673-682.
15. Dincǎ V., Lukhtanov V.A., Talavera G., Vila R. Unexpected layers of cryptic diversity in wood white Leptidea butterflies. Nat. Commun. 2011, 2:324.
16. Dumont B.L., Payseur B.A. Evolution of the genomic recombination rate in murid rodents. Genetics 2011, 187:643-657.
17. Dumont B.L., Payseur B.A. Evolution of the genomic rate of recombination in mammals. Evolution 2008, 62:276-294.
18. Eanes W.F. Analysis of selection on enzyme polymorphisms. Annu. Rev. Ecol. Syst. 1999, 30:301-326.
19. Escudero M., Hipp A.L., Luceño M. Karyotype stability and predictors of chromosome number variation in sedges: a study in Carex section Spirostachyae (Cyperaceae). Mol. Phylogenet. Evol. 2010, 57:353-363.
20. Escudero M., Luceño M. Systematics and evolution of Carex sects. Spirostachyae and Elatae (Cyperaceae). Plant Syst. Evol. 2009, 279:163-189.
21. Escudero M., Valcárcel V., Vargas P., Luceño M. Bipolar disjunctions in Carex: long-distance dispersal, vicariance, or parallel evolution?. Flora 2010, 205:118-127.
22. Escudero M., Vargas P., Arens P., Ouborg N.J., Luceño M. The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae). Mol. Ecol. 2010, 19:352-370.
23. Escudero M., Valcárcel V., Vargas P., Luceño M. Evolution in Carex L. sect Spirostachyae (Cyperaceae): a molecular and cytogenetic approach. Org. Div. Evol. 2008, 7:271-291.
24. Escudero M., Hipp A.L., Hansen T.F., Voge K.L., Luceño M. Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). New Phytol. 2012, 195:237-247.
25. Excoffier L., Lischer H.E.L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 2010, 10:564-567.
26. Faria R., Navarro A. Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends Ecol. Evol. 2010, 2:660-669.
27. Faulkner J.S. Chromosome studies on Carex section Acutae in north-west Europe. Bot. J. Linn. Soc. 1972, 65:271-300.
28. Felsenstein J. Phylogenies and the comparative method. Am. Nat. 1985, 125:1-15.
29. Felsenstein J. The evolution advantage of recombination. Genetics 1974, 78:737-756.
30. Felsenstein J. The effect of linkage on directional selection. Genetics 1965, 52:349-363.
31. Forni-Martins E.R., da Cruz N.D. Recombination indices in species of Erythtina L. (Leguminoseae, Papilionoideae). Bot. J. Linn. Soc. 1996, 122:163-170.
32. Friedman J., Barrett S.C.H. The consequences of monoecy and protogyny for mating in wind-pollinated Carex. New Phytol. 2009, 181:489-497.
33. Grant V.E. The regulation of recombination in plants. Cold Spring Harbor Symp. Quant. Biol. 1958, 23:337-363.
34. Hadfield J.D. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R Package. J. Stat. Softw. 2010, 33:1-22.
35. Hansen T.F. Stabilizing selection and the comparative analysis of adaptation. Evolution 1997, 51:1341-1351.
36. Hansen T.F., Pienaar J., Orzack S.H. A comparative method for studying adaptation to a randomly evolving environment. Evolution 2008, 62:1965-1977.
37. Harvey P.H., Pagel M.D. The Comparative Method in Evolutionary Biology 1991, Oxford University Press, Oxford.
38. Hadfield J.D., Nakagawa S. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J. Evol. Biol. 2010, 23:494-508.
39. Hey J. Isolation with migration models for more than two populations. Mol. Biol. Evol. 2010, 27:905-920.
40. Hijmans, R.J., van Etten, J., 2010. Raster: geographic analysis and modeling with raster data. R package version 1.0.0-1. http://cran.r-project.org/package=raster.
41. Hijamns R.J., Cameron S.E., Parra J.L., Jones P.G., Javis A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 2005, 25:1965-1978.
42. Hijmans, R.J., Phillips, S., Leathwick, J., Elith, J., 2010. Dismo: species distribution modeling. R package version 0.5-4. http://cran.r-project.org/web/packages/dismo/index.html.
43. Hipp A.L. Nonuniform processes of chromosome evolution in sedges (Carex: Cyperaceae). Evolution 2007, 61:2175-2194.
44. Hipp A.L., Rothrock P.E., Roalson E.H. The evolution of chromosome arrangements in Carex (Cyperaceae). Bot. Rev. 2009, 75:96-109.
45. Hipp A.L., Rothrock P.E., Whitkus R., Weber J.A. Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Mol. Ecol. 2010, 19:3124-3138.
46. Hipp, A.L., Chung, K.-S., Escudero, M. Holocentric chromosomes. In: Maloy, S., Hughes, K. (Eds.) Encyclopedia of Genetics, 2nd ed. Elsevier, Amsterdam, in press.
47. Hoffmann A.A., Rieseberg L.H. Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation?. Ann. Rev. Ecol. Evol. Syst. 2008, 39:21-42.
48. Ives A.R., Zhu J. Statistics for correlated data: phylogenies, space, and time. Ecol. Appl. 2006, 16:20-32.
49. Jiménez-Mejías P., Escudero M., Guerra-Cárdenas S., Lye K.A., Luceño M. Taxonomic delimitation and drivers of speciation in the Ibero-North African Carex sect Phacocystis river-shore group (Cyperaceae). Am. J. Bot. 2011, 98:1855-1867.
50. Jiménez-Mejías P., Luceño M., Lye K.A., Brochmann C., Gussarova G. Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae). J. Biogeogr. 2012, 39:2279-2291.
51. Joron M., Frezal L., Jones R.T., Chamberlain N.L., Lee S.F., Haag C.R., Whibley A., Becuwe M., Baxter S.W., Ferguson L., et al. Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature 2011, 477:203-206.
52. Kandul N.P., Lukhtanov V.A., Pierce N.E. Karyotypic diversity and speciation in Agrodiaetus butterflies. Evolution 2007, 61:546-559.
53. Kirkpatrick M. How and why chromosome inversions evolve. PLoS Biol. 2010, 8:e1000501.
54. Koella J.C. Ecological correlates of chiasma frequency and recombination index of plants. Biol. J. Linn. Soc. 1993, 48:227-238.
55. Lawrence M.E. Senecio L. (Asteraceae) in Australia: recombination systems of a polyploid series. Aust. J. Bot. 1985, 33:209-219.
56. Luceño M. Notas caricologicas III. An. Jard. Bot. Madrid 1988, 45:189-196.
57. Luceño M. Chromosome studies on Carex (L.) section Mitratae Kükenth (Cyperaceae) in the Iberian Peninsula. Cytologia (Tokyo) 1993, 58:321-330.
58. Luceño M., Castroviejo S. Cytotaxonomic studies in the sections Spirostachyae (Drejer) Bailey and Ceratocystis Dumort. of the genus Carex L. (Cyperaceae) with special reference to Iberian and North African taxa. Bot. J. Linn. Soc. 1993, 112:335-350.
59. Luceño M., Castroviejo S. Agmatoploidy in Carex laevigata (Cyperaceae). Fusion and fission of chromosomes as the mechanism of cytogenetic evolution in Iberian populations. Plant Syst. Evol. 1991, 177:149-159.
60. Lukhtanov V.A., Dinc V., Talavera G., Vila R. Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation. BMC Evol. Biol. 2011, 11:109.
61. Lukhtanov V.A., Kandul N.P., Plotkin J.B., Dantchenko A.V., Haig D., Pierce N.E. Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies. Nature 2005, 436:385-389.
62. Manly B.F.J. The Statistics of Natural Selection 1985, Chapman and Hall, London.
63. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27:209-220.
64. Mather K. Polygenic inheritance and natural selection. Biol. Rev. 1943, 18:32-64.
65. Mayrose I., Barker M.S., Otto S.P. Probabilistic models of chromosome number evolution and the inference of polyploidy. Syst. Biol. 2010, 59:132-144.
66. Médail F., Diadema K. Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J. Biogeogr. 2009, 36:1333-1345.
67. Mola L.M., Papeschi A.G. Holokinetic chromosomes at a glance. BAG 2006, 17:17-33.
68. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U. S. A. 1979, 76:5269-5273.
69. Nijalingappa B.M.H. Cytological studies in Fimbristylis (Cyperaceae). Cytologia (Tokyo) 1975, 40:177-183.
70. Nokkala S., Kuznetsova V.G., Maryanska-Nadachowska A., Nokkala C. Holocentric chromosomes in meiosis I. Restriction of the number of chiasmata in bivalents. Chrom. Res. 2004, 12:733-739.
71. Otto S.P., Barton N.H. Selection for recombination in small populations. Evolution 2001, 55:1921-1931.
72. Peakall R., Smouse P.E. GenAlEx v. 6: genetic analysis in Excel Population genetic software for teaching and research. Mol. Ecol. Notes 2006, 6:288-295.
73. Petit R.J., Pineau E., Demesure B., Bacilieri R., Ducousso A., Kremer A. Chloroplast DNA footprints of postglacial recolonization by oaks. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:996-1001.
74. R Development Core Team. R: A Language and Environment for Statistical Computing 2011, R Foundation for Statistical Computing, Vienna.
75. Rohlf F.J. A comment on phylogenetic correction. Evolution 2006, 60:1509-1515.
76. Revell L.J. Phylogenetic signal and linear regression on species data. Methods Ecol. Evol. 2010, 1:319-329.
77. Ross-Ibarra J. The evolution of recombination under domestication: a test of two hypotheses. Am. Nat. 2004, 163:105-112.
78. Shaw J., Lickey E.B., Beck J.T., Farmer S.B., Liu W., Miller J., Siripun K.C., Winder C.T., Schilling E.E., Small R.L. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005, 92:142-166.
79. Schmitt T. Molecular biogeography of Europe: pleistocene cycles and postglacial trends. Front. Zool. 2007, 4:11.
80. Schönswetter P., Elven R., Brochmann C. Trans-Atlantic dispersal and large-scale lack of genetic structure in the circumpolar, arctic-alpine sedge Carex bigelowii s.l (Cyperaceae). Am. J. Bot. 2008, 95:1006-1014.
81. Stegemann S., Keuthe M., Greiner S., Bock R. Horizontal transfer of chloroplast genomes between plant species. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:2434-2438.
82. Storz J.F. Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation. Mol. Ecol. 2002, 11:2537-2551.
83. Starr J.R., Naczi R.F.C., Chouinard B.N. Plant DNA barcodes and species resolution in sedges (Carex Cyperaceae). Mol. Ecol. Resour. 2009, 9:151-163.
84. Stebbins G.L. The inviability, weakness and sterility of interspecific hybrids. Adv. Genet. 1958, 9:147-215.
85. Stone G.N., Nee S., Felsenstein J. Controlling for non-independence in comparative analysis of patterns across populations within species. Philos. Trans. R. Soc. B: Biol. Sci. 2011, 366:1410-1424.
86. Templeton A.R., Crandall K.A., Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data III. Cladogram estimation. Genetics 1992, 132:619-633.
87. Vasemägi A. The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics 2006, 173:2411-2414.
88. Whitkus R. Experimental hybridization among chromosome races of Carex pachystachya and the related species Carex macloviana and Carex preslii (Cyperaceae). Syst. Bot. 1988, 13:146-153.
89. Wolfe K.H., Li W.-H., Sharp P.M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:9054-9058.