Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae)

New Phytologist

Volumn 187, Issue 2, 2010, Pages 542-551

  Balao, Francisco ^a   Valente, Luis M ^b   Vargas, Pablo ^b   Herrera, Javier ^a   Talavera, Salvador ^a  

^a UNIVERSITY OF SEVILLE   (Spain)

^b CSIC   (Spain)

Author keywords

Amplified fragment length polymorphism (AFLP); CpDNA; Dianthus broteri; Internal transcribed spacer (ITS); Mediterranean; Polyploidy; Radiation; Speciation

Indexed keywords

ADAPTIVE RADIATION; CHLOROPLAST; DICOTYLEDON; EVOLUTIONARY THEORY; GENE FLOW; GENOME; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; POLYPLOIDY; RADIATIVE TRANSFER; SPECIATION (BIOLOGY);

CARYOPHYLLACEAE; DIANTHUS; DIANTHUS CARYOPHYLLUS;

CHLOROPLAST DNA; SPACER DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BAYES THEOREM; CARYOPHYLLACEAE; EVOLUTION; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; POLYPLOIDY; POPULATION GENETICS; PORTUGAL; PRINCIPAL COMPONENT ANALYSIS; SPAIN;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; BAYES THEOREM; CARYOPHYLLACEAE; DNA, CHLOROPLAST; DNA, INTERGENIC; EVOLUTION; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; POLYPLOIDY; PORTUGAL; PRINCIPAL COMPONENT ANALYSIS; SPAIN;

EID: 77954157179     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03280.x     Document Type: Article

References (69)

1. Balao F, Casimiro-Soriguer R, Talavera M, Herrera J, Talavera S. Distribution and diversity of cytotypes in Dianthus broteri as evidenced by genome size variations. Annals of Botany 2009, 104:965-973.
2. Barrier M, Baldwin B, Robichaux R, Purugganan M. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Molecular Biology and Evolution 1999, 16:1105-1113.
3. Blöch C, Weiss-Schneeweiss H, Schneeweiss GM, Barfuss MHJ, Rebernig CA, Villaseñor JL, Stuessy TF. Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae). Molecular Phylogenetics and Evolution 2009, 53:220-233.
4. Bruvo R, Michiels NK, D'Souza TG, Schulenburg H. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Molecular Ecology 2004, 13:2101-2106.
5. Carolin RC. Cytological and hybridization studies in the genus Dianthus. New Phytologist 1957, 56:81-97.
6. Cavalli-Sforza LL, Edwards AWF. Phylogenetic analysis: models and estimation procedures. Evolution 1967, 21:550-570.
7. Clement M, Posada D, Crandall KA. TCS: a computer program to estimate gene genealogies. Molecular Ecology 2000, 9:1657-1659.
8. Corander J, Marttinen P. Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology 2006, 15:2833-2843.
9. Coyne JA, Orr H. Polyploidy and hybrid speciation. Speciation 2004, 321-351. Coyne J, Orr H. eds, Sunderland, MA, USA, Sinauer Associates
10. De Silva HN, Hall AJ, Rikkerink E, McNeilage MA, Fraser LG. Estimation of allele frequencies in polyploids under certain patterns of inheritance. Heredity 2005, 95:327-334.
11. Demesure B, Sodzi N, Petit R. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 1995, 4:129-131.
12. Dixon CJ. A means of estimating the completeness of haplotype sampling using the Stirling probability distribution. Molecular Ecology Notes 2006, 6:650-652.
13. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin 1987, 19:11-15.
14. Drummond A, Ashton B, Cheung M, Heled J, Kearse M, Moir R, Stones-Havas S, Thierer T, Wilson A. Geneious v4.7 2009, http://www.geneious.com/, Available from
15. Efron B, Tibshirani R. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Statistical Science 1986, 1:54-75.
16. Ehrich D. AFLPDAT: a collection of R functions for convenient handling of AFLP data. Molecular Ecology Notes 2006, 6:603-604.
17. Escudero M, Vargas P, Valcarcel V, Luceño M. Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation. American Journal of Botany 2008, 95:745-755.
18. Excoffier L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Molecular Ecology 2004, 13:853-864.
19. Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 2005, 1:47-50.
20. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 2005, Seattle, WA, USA, Department of Genome Sciences, University of Washington
21. Gallego MJ. Una nueva especie de Dianthus del litoral del SW de España. Lagascalia 1986, 14:71-72.
22. Gaudeul M. Disjunct distribution of Hypericumn nummularium L. (Hypericaceae): molecular data suggest bidirectional colonization from a single refugium rather than survival in distinct refugia. Biological Journal of the Linnean Society 2006, 87:437-447.
23. Gaudeul M, Taberlet P, Till-Bottraud I. Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers. Molecular Ecology 2000, 9:1625-1637.
24. Gómez A, Lunt D. Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. Phylogeography in southern European refugia: evolutionary perspectives on the origins and conservation of European biodiversity 2006, 155-182. Weiss S, Ferrand N. eds, Dordrecht, the Netherlands, Springer
25. Guo Y-P, Saukel J, Mittermayr R, Ehrendorfer F. AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidization in the evolution of Achillea (Asteraceae-Anthemideae). New Phytologist 2005, 166:273-290.
26. Halverson K, Heard SB, Nason JD, Stireman JO. Origins, distribution, and local co-occurrence of polyploid cytotypes in Solidago altissima (Asteraceae). American Journal of Botany 2008, 95:50-58.
27. Hudson RR. A new statistic for detecting genetic differentiation. Genetics 2000, 155:2011-2014.
28. Johnson L, Soltis D. matK DNA sequences and phylogenetic reconstruction in Saxifragaceae s. str. Systematic Botany 1994, 19:143-156.
29. Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 2008, 24:1403-1405.
30. Jordon-Thaden I, Koch M. Species richness and polyploid patterns in the genus Draba (Brassicaceae): a first global perspective. Plant Ecology & Diversity 2008, 1:255-263.
31. Kadereit JW, Uribe-Convers S, Westberg E, Comes HP. Reciprocal hybridization at different times between Senecio flavus and Senecio glaucus gave rise to two polyploid species in north Africa and south-west Asia. New Phytologist 2006, 169:431-441.
32. Kalinowski ST. Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conservation Genetics 2004, 5:539-543.
33. Kalinowski ST. HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes 2005, 5:187-189.
34. Koch MA, Kiefer C, Ehrich D, Vogel J, Brochmann C, Mummenhoff K. Three times out of Asia Minor: the phylogeography of Arabis alpina L. (Brassicaceae). Molecular Ecology 2006, 15:825-839.
35. Lammerts W. Interspecific hybridization in Nicotiana. XII. The amphidiploid rustica-paniculata hybrid; its origin and cytogenetic behavior. Genetics 1931, 16:191.
36. Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants. Science 2008, 320:481-483.
37. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
38. Linder HP. Plant species radiations: where, when, why? Philosophical Transactions of the Royal Society B: Biological Sciences 2008, 363:3097-3105.
39. Liston A, Robinson W, Oliphant J, Alvarez-Buylla E. Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Systematic Botany 1996, 21:109-120.
40. Marhold K, Lihová J. Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae. Plant Systematics and Evolution 2006, 259:143-174.
41. Médail F, Diadema K. Glacial refugia influence plant diversity patterns in the Mediterranean Basin. Journal of Biogeography 2009, 36:1333-1345.
42. Obbard DJ, Harris SA, Pannell JR. Simple allelic-phenotype diversity and differentiation statistics for allopolyploids. Heredity 2006, 97:296-303.
43. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RG, Simpson GL, Solymos P, Henry M, Stevens H, Wagner H. vegan: community ecology package. 2010, http://CRAN.R-project.org/package=vegan/, R package version 1.17-2, Available from
44. Ortiz MA, Tremetsberger K, Talavera S, Stuessy T, Garcia-Castano JL. Population structure of Hypochaeris salzmanniana DC. (Asteraceae), an endemic species to the Atlantic coast on both sides of the Strait of Gibraltar, in relation to Quaternary sea level changes. Molecular Ecology 2007, 16:541-552.
45. Otto SP. The evolutionary consequences of polyploidy. Cell 2007, 131:452-462.
46. Parisod C, Holderegger R, Brochmann C. Evolutionary consequences of autopolyploidy. New Phytologist 2010, 186:5-17.
47. Paun O, Forest F, Fay MF, Chase MW. Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytologist 2009, 182:507-518.
48. Paun O, Schönswetter P, Winkler M, Tribsch A. Historical divergence vs. contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians. Molecular Ecology 2008, 17:4263-4275.
49. Paun O, Stuessy TF, Horandl E. The role of hybridization, polyploidization and glaciation in the origin and evolution of the apomictic Ranunculus cassubicus complex. New Phytologist 2006, 171:223-236.
50. Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl UM, van DamB, Deans JD. Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Forest Ecology and Management 2002, 156:49-74.
51. R: a language and environment for statistical computing 2008, Vienna, Austria, R Foundation for Statistical Computing
52. Ramsey J, Robertson A, Husband B. Rapid adaptive divergence in new world Achillea, an autopolyploid complex of ecological races. Evolution 2008, 62:639-653.
53. Ramsey J, Schemske DW. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annual Reviews in Ecology and Systematics 1998, 29:467-501.
54. Ramsey J, Schemske DW. Neopolyploidy in flowering plants. Annual Review of Ecology and Systematics 2002, 33:589-639.
55. Ray N, Currat M, Excoffier L. Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution 2003, 20:76-86.
56. Rogers A, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 1992, 9:552-569.
57. Salvador L, Alía R, Agúndez D, Gil L. Genetic variation and migration pathways of maritime pine (Pinus pinaster Ait) in the Iberian Peninsula. Theoretical and Applied Genetics 2000, 100:89-95.
58. Schönswetter P, Tribsch A. Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon 2005, 54:725-732.
59. Segraves KA, Thompson JN, Soltis PS, Soltis DE. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Molecular Ecology 1999, 8:253-262.
60. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. American Journal of Botany 2009, 96:336-348.
61. Soltis DE, Soltis PS. Polyploidy: recurrent formation and genome evolution. Trends in Ecology & Evolution 1999, 14:348-352.
62. Soltis PS, Soltis DE. The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences, USA 2000, 97:7051-7057.
63. Soltis PS, Soltis DE. The role of hybridization in plant speciation. Annual Review of Plant Biology 2009, 60:561-588.
64. Valente LM, Savolainen V, Vargas P. Unparalleled rates of species diversification in Europe. Proceedings of the Royal Society B: Biological Sciences 2010, 277:1489-1497.
65. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology 2002, 11:139-151.
66. Verheyen E, Salzburger W, Snoeks J, Meyer A. Origin of the superflock of cichlid fishes from Lake Victoria, East Africa. Science 2003, 300:325-329.
67. Weiss H, Dobes C, Schneeweiss GM, Greimler J. Occurrence of tetraploid and hexaploid cytotypes between and within populations in Dianthus sect. Plumaria (Caryophyllaceae). New Phytologist 2002, 156:85-94.
68. White T, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications 1990, 315-322. Innis M, Gelfand D, Sninsky J, White T. eds, San Diego, CA, USA, Academic Press
69. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences, USA 2009, 106:13875-13879.