Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: Multiple origins of Veronica cymbalaria (Plantaginaceae)

New Phytologist

Volumn 176, Issue 2, 2007, Pages 481-498

  Albach, Dirk C ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

Amplified fragment length polymorphism (AFLP); Bayesian inference; Distance analysis; Parsimony; Phylogenetic analysis; Polyploidy; Veronica cymbalaria

Indexed keywords

ANGIOSPERM; BAYESIAN ANALYSIS; DNA FINGERPRINTING; PARSIMONY ANALYSIS; PHYLOGENETICS; POLYMERASE CHAIN REACTION; POLYMORPHISM; POLYPLOIDY; TAXONOMY;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; PHYLOGENY; PLANTAGO; POLYMERASE CHAIN REACTION; POLYPLOIDY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; GENETIC MARKERS; PHYLOGENY; PLANTAGO; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POLYPLOIDY; SEQUENCE ANALYSIS, DNA;

PLANTAGINACEAE; VERONICA; VERONICA CYMBALARIA;

EID: 34748924257     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2007.02172.x     Document Type: Article

References (97)

1. Abbott RJ, Lowe AJ. 2004. Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles. Biological Journal of the Linnean Society 82 : 467 474.
2. Abdallah AR, Reddy OUK, El-Zik KM, Pepper AE. 2001. Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theoretical and Applied Genetics 102 : 222 229.
3. Adams RP, Rieseberg LH. 1998. The effects of non-homology in RAPD bands on similarity and multivariate statistical ordination in Brassica and Helianthus. Theoretical and Applied Genetics 97 : 323 326.
4. Adams RP, Wendel JF. 2005. Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8 : 135 141.
5. Albach DC, Chase MW. 2004. Incongruence in Veroniceae (Plantaginaceae): Evidence from two plastid and a nuclear region. Molecular Phylogenetics and Evolution 32 : 183 197.
6. Albach DC, Greilhuber J. 2004. Genome size variation and evolution in Veronica. Annals of Botany 94 : 897 911.
7. Albach DC, Martínez-Ortega MM, Chase MW. 2004a. Veronica: Parallel morphological evolution and phylogeography in the Mediterranean. Plant Systematics and Evolution 246 : 177 194.
8. Albach DC, Martínez-Ortega MM, Fischer MA, Chase MW. 2004b. Evolution of Veroniceae: a phylogenetic perspective. Annals of the Missouri Botanical Garden 91 : 275 302.
9. Albert VA, Mishler BD, Chase MW. 1992. Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. In : Soltis DE, Soltis PS, Doyle JF, eds. Molecular systematics of plants. New York, NY, USA : Chapman & Hall, 369 403.
10. Alice LA, Eriksson T, Eriksen B, Campbell CS. 2001. Hybridization and gene flow between distantly related species of Rubus (Rosaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer region sequences. Systematic Botany 26 : 769 778.
11. Axelrod DI. 1973. History of the Mediterranean ecosystem in California. In : Di Castri F, Mooney HA, eds. Mediterranean type ecosystems - origin and structure. Berlin, Germany : Springer Verlag, 225 277.
12. Beismann H, Barker JHA, Karp A, Speck T. 1997. AFLP analysis sheds light on distribution of two Salix species and their hybrid along a natural gradient. Molecular Ecology 6 : 989 993.
13. Benham JJ. 1998. Genographer, version 1.1. Bozeman, MT, USA : Montana State University.
14. Brandt JP. 1961. Cytotaxomomie et cytogéographie de Veronica prostrata L. Bulletin de la Sociète Neuchâteloise des Sciences Naturelles 84 : 35 88.
15. Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen AC, Elven R. 2004. Polyploidy in arctic plants. Biological Journal of the Linnean Society 82 : 521 536.
16. Brochmann C, Soltis DE, Soltis PS. 1992. Electrophoretic relationships and phylogeny of Nordic polyploids in Draba (Brassicaceae). Plant Systematics and Evolution 182 : 35 70.
17. Brouat C, McKey D, Douzery EJP. 2004. Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers. Molecular Ecology 13 : 1157 1171.
18. Campbell CS, Wojciechowski MF, Baldwin BG, Alice LA, Donoghue MJ. 1997. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Molecular Biology and Evolution 14 : 81 90.
19. Casgrain P, Legendre P. 2001. The R package for multivariate and spatial analysis, version 4.0 d5. Montreal, Canada : Départment de Sciences Biologiques, Université de Montreal.
20. Comes HP, Abbott RJ. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55 : 1943 1962.
21. Després L, Gielly L, Redoutet B, Taberlet P. 2003. Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. Molecular Phylogenetics and Evolution 27 : 185 196.
22. Dice LR. 1945. Measures of the amount of ecologic association between species. Ecology 26 : 297 302.
23. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19 : 1 15.
24. Ehrendorfer F. 1980. Polyploidy and distribution. In : Lewis WH, ed. Polyploidy: biological relevance. New York, NY, USA : Plenum Publishing Corp, 45 60.
25. Ellstrand NC, Schierenbeck KA. 2000. Hybridization as a stimulus for the evolution of invasiveness in plants? In : Ayala FJ, Fitch WM, Clegg MT, eds. Variation and evolution in plants and microorganisms: toward a new synthesis 50 years after Stebbins. Washington, DC, USA : National Academy Press, 289 309.
26. El-Rabey HA, Badr A, Schäfer-Pregl R, Martin W, Salamini F. 2002. Speciation and species separation in Hordeum L. (Poaceae) resolved by discontinuous molecular markers. Plant Biology 4 : 67 575.
27. Felsenstein J. 1993. phylip (phylogeny inference package), version 3 5c. Seattle, WA, USA : Department of Genetics, University of Washington (distributed by the author).
28. Felsenstein J. 2004. Inferring phylogenies. Sunderland, MA, USA : Sinauer Associates.
29. Fischer MA. 1967. Beiträge zur Cytotaxonomie der Veronica hederifolia-Gruppe (Scrophulariaceae). Österreichische Botanische Zeitschrift 114 : 189 233.
30. Fischer MA. 1975. Untersuchungen über den Polyploidkomplex Veronica cymbalaria agg. (Scrophulariaceae). Plant Systematics and Evolution 123 : 97 105.
31. Fischer MA. 1978. Veronica L. In : Davis PH, ed. Flora of Turkey and the East Aegean Islands. Edinburgh, UK : Edinburgh University Press, 689 753.
32. Fischer M, Greuter W. 1976. Über zwei diploide, in Südwest-Anatolien endemische Arten aus dem Komplex der Veronica cymbalaria (Scrophulariaceae). Plant Systematics and Evolution 125 : 245 252.
33. Ganter PF, de Barros Lopes M. 2000. The use of anonymous DNA markers in assessing worldwide relatedness in the yeast species Pichia kluyveri Bedford and Kudrjavzev. Canadian Journal of Microbiology 46 : 967 980.
34. Gobert V, Moja S, Colson M, Taberlet P. 2002. Hybridization in the section Mentha (Lamiaceae) inferred from AFLP markers. American Journal of Botany 89 : 2017 2023.
35. Goldman DH, Jansen RK, van den Berg C, Leitch IJ, Fay M, Chase MW. 2004. Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): Circumscription, phylogeny, polyploidy, and possible hybrid speciation. American Journal of Botany 91 : 707 723.
36. Grant V. 1981. Plant speciation. New York, NY, USA : Columbia University Press.
37. Guo Y-P, Saukel J, Mittermayr R, Ehrendorfer F. 2005. AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidizatioin in the evolution of Achillea (Asteraceae-Anthemideae). New Phytologist 166 : 273 290.
38. Hagen A, Giese H, Brochmann C. 2001. Trans-atlantic dispersal and phylogeography of Cerastium arcticum (Caryophyllaceae) inferred from RAPD and SCAR markers. American Journal of Botany 88 : 103 112.
39. Hedrén M, Fay MF, Chase MW. 2001. Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidaceae). American Journal of Botany 88 : 1868 1880.
40. Hetherington AM, Woodward IF. 2003. The role of stomata in sensing and driving environmental change. Nature 424 : 901 908.
41. Hillis DM, Huelsenbeck JP, Cunningham CW. 1994. Application and accuracy of molecular phylogenies. Science 264 : 671 677.
42. Hodkinson TR, Chase MW, Takahashi T, Leitch IJ, Bennett MD, Renvoize SA. 2002. The use of DNA sequencing (ITS and trnL-F), AFLP, and fluorescent in situ hybridization to study allopolyploid Miscanthus (Poaceae). American Journal of Botany 89 : 279 286.
43. Hofelich A. 1935. Die Sektion Alsinebe Griseb. der Gattung Veronica in ihren chromosomalen Grundlagen. Jahrbücher wissenschaftlicher Botanik 81 : 541 572.
44. Huelsenbeck JP. 1995. Performance of phylogenetic methods in simulation. Systematic Biology 44 : 17 48.
45. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17 : 754 755.
46. Jaccard P. 1908. Nouvelles recherches sur la distribution florale. Bulletin de la Sociète Vaudense des Sciences Naturelles 44 : 223 270.
47. Kadereit JW, Uribe-Convers S, Westberg E, Comes HP. 2005. 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 169 : 431 441.
48. Keiper FJ, McConchie R. 2000. An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (StJohn)] using amplified fragment length polymorphism (AFLP) markers. Molecular Ecology 9 : 571 581.
49. Koch M, Bernhardt K-G. 2004. Comparative biogeography of the cytotypes of annual Microthlaspi perfoliatum (Brassicaceae) in Europe using isozymes and cpDNA data: Refugia, diversity centers, and postglacial colonization. American Journal of Botany 91 : 115 124.
50. Koopman WJM. 2005. Phylogenetic signal in AFLP data sets. Systematic Biology 54 : 197 217.
51. Koopman WJM, Zevenbergen MJ, van den Berg RG. 2001. Species relationships in Lactuca s.1. (Lactuceae, Asteraceae) inferred from AFLP fingerprints. American Journal of Botany 88 : 1881 1887.
52. Kosman E, Leonard KJ. 2005. Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Molecular Ecology 14 : 415 424.
53. Kuhner MK, Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11 : 459 468.
54. Lehmann E, Schmitz-Lohner M. 1954. Entwicklung und Polyploidie in der Veronica-Gruppe Agrestis. Zeitschrift für induktive Abstammungs- und Vererbungslehre 86 : 1 34.
55. Levin DA. 2004. Ecological speciation: the role of disturbance. Systematic Botany 29 : 225 233.
56. Link W, Dixkens C, Singh M, Schwall M, Melchinger AE. 1995. Genetic diversity in European and Mediterranean faba bean germ plasm revealed by RAPD markers. Theoretical and Applied Genetics 90 : 27 32.
57. McDade LA. 1992. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. Evolution 46 : 1329 1346.
58. Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA 76 : 5269 5273.
59. Nybom H, Bartish IV. 2000. Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspectives in Plant Ecology, Evolution and Systematics 3 : 93 114.
60. Otto SP, Whitton J. 2000. Polyploid incidence and evolution. Annual Reviews in Genetics 34 : 401 437.
61. Özkan H, Brandolini A, Schäfer-Pregl R, Salamini F. 2002. AFLP analysis of a collection of tetraploid wheat indicates the origin of emmer and hard wheat domestication in southeast Turkey. Molecular Biology and Evolution 19 : 1797 1801.
62. TM plant mapping protocol. Foster City, CA, USA : PE Applied Biosystems.
63. Pelser PB, Gravendeel B, van der Meijden R. 2003. Phylogeny reconstruction in the gap between too little and too much divergence: the closest relatives of Senecio jacobaea (Asteraceae) according to DNA sequences and AFLPs. Molecular Ecology 29 : 613 628.
64. Ramsey J, Schemske DW. 1998. Pathways, mechanisms, and rates of polyploid formation in flowering plant. Annual Review in Ecology and Systematics 29 : 467 501.
65. Richardson JE, Fay MF, Cronk QCB, Chase MW. 2003. Species delimitation and the origin of populations in island representatives of Phylica (Rhamnaceae). Evolution 57 : 816 827.
66. Robinson JP, Harris SA. 1999. Amplified fragment length polymorphisms and microsatellites: A phylogenetic perspective. In : Gillet EM, ed. Which DNA marker for which purpose? Final compendium of the research project 'Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees' in the European Union DGXII Biotechnology FW IV research programme 'Molecular tools for biodiversity'. http://webdoc.sub.gwdg.de/ebook/y/ 1999/whichmarker/index.htm
67. Rokas A, Atkinson RJ, Webster L, Csóka G, Stone GN. 2003. Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum-Mediterranean oak gallwasp Andricus quercustozae. Molecular Ecology 12 : 2153 2174.
68. Ronquist F, Huelsenbeck JP. 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574.
69. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 : 406.
70. Sewell MM, Qiu Y-L, Parks CR, Chase MW. 1993. Genetic evidence for trace paternal transmission of plastids in Liriodendron and Magnolia (Magnoliaceae). American Journal of Botany 80 : 854 858.
71. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13 : 1749 1759.
72. Soltis DE, Johnson LA, Looney C. 1996. Discordance between ITS and chloroplast topologies in the Boykinia group (Saxifragaceae). Systematic Botany 21 : 169 186.
73. Soltis DE, Kuzoff RK. 1995. Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49 : 727 742.
74. Soltis DE, Soltis PS. 1989. Allopolyploid speciation in Tragopogon: insights from chloroplast DNA. American Journal of Botany 76 : 1119 1124.
75. Soltis DE, Soltis PS. 1993. Molecular data and the dynamic nature of polyploidy. Critical Review in Plant Sciences 12 : 243 273.
76. Soltis DE, Soltis PS. 1999. Polyploidy: recurrent formation and genome evolution. Trends in Ecology and Evolution 14 : 348 352.
77. Soltis DE, Soltis PS, Tate JA. 2003. Advances in the study of polyploidy since plant speciation. New Phytologist 161 : 173 191.
78. Soltis PS, Soltis DE. 1991. Multiple origins of the allotetraploid Tragopogon mirus (Compositae): rDNA Evidence. Systematic Botany 16 : 407 413.
79. Song K, Lu P, Tang K, Osborn TC. 1995. Rapid genome change in synthetic polyploids of Brassica and its implication for polyploid evolution. Proceedings of the National Academy of Sciences, USA 92 : 7719 7723.
80. Stebbins GL. 1971. Chromosomal evolution in higher plants. London, UK : Edward Arnold.
81. Sullivan JP, Lavoué S, Arnegard ME, Hopkins CD. 2004. AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei). Evolution 58 : 825 841.
82. Sun Y, Skinner DZ, Liang GH, Hulbert SH. 1994. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics 89 : 26 32.
83. Swofford DL. 2002. paup*: phylogenetic analysis using parsimony (*and other methods), version 4. Sunderland, MA, USA : Sinauer Associates.
84. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In : Hillis DM, Moritz C, Mable BK, eds. Molecular systematics. Sunderland, MA, USA : Sinauer Associates, 407 514.
85. Taberlet P, Gielly L, Pautou G, Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17 : 1105 1109.
86. Thiede J. 1978. A glacial Mediterranean. Nature 276 : 680 683.
87. Travnicek B, Vinter V. 1999. Studium der Beziehung der Ploidie zur Pollengrösse und Stomatalänge bei der Art Pseudolysimachion maritimum (Veronica longifolia auct., Scrophulariaceae). Acta Universitatis Palackianae Olomucensia, Facultas Rerum Naturalium 37 : 35 45.
88. Tremetsberger K, Stuessy TF, Samuel RM, Baeza CM, Fay MF. 2003. Genetics of colonization in Hypochaeris tenuifolia (Asteraceae, Lactuceae) on Volcan Longiquimay, Chile. Molecular Ecology 12 : 2649 2659.
89. Van de Peer Y, De Wachter R. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computer Applications in the Biosciences 10 : 569 570.
90. Veith M, Schmidtler JF, Kosuch J, Baran I, Seitz A. 2003. Palaeoclimatic changes explain Anatolian mountain frog evolution: a test for alternating vicariance and dispersal events. Molecular Ecology 12 : 185 199.
91. Vincze T, Posfai J, Roberts RJ. 2003. NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Research 31 : 3688 3691.
92. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23 : 4407 4414.
93. Wendel JF, Schnabel A, Seelanan T. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences, USA 92 : 280 284.
94. White TJ, Bruns T, Lee S, Taylor J. 1991. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In : Innis MA, Gelfand DH, Sninsky J, White T, eds. PCR protocols: a guide to methods and applications. San Diego, CA, USA : Academic Press, 315 322.
95. Whittall J, Hellquist CB, Schneider EL, Hodges SA. 2004. Cryptic species in an endangered pondweed community (Potamogeton, Potamogetonaceae) revealed by AFLP markers. American Journal of Botany 91 : 2022 2029.
96. Whittall J, Liston A, Gisler S, Meinke RJ. 2000. Detecting nucleotide additivity from direct sequences is a SNAP: An example from Sidalcea (Malvaceae). Plant Biology 2 : 211 217.
97. Zhang L, Comes HP, Kadereit JW. 2001. Phylogeny and quaternary history of the European montane/alpin endemic Soldanella (Primulaceae) based on ITS and AFLP variation. American Journal of Botany 88 : 2331 2345.