Recent and recurrent polyploidy in Tragopogon (Asteraceae): Cytogenetic, genomic and genetic comparisons

Biological Journal of the Linnean Society

Volumn 82, Issue 4, 2004, Pages 485-501

  Soltis, Douglas E ^a   Soltis, Pamela S ^b   Pires, J Chris ^c   Kovarik, Ales ^d   Tate, Jennifer A ^b   Mavrodiev, Evgeny ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

Concerted evolution; Gene expression; Molecular cytogenetics

Indexed keywords

EVOLUTION; GENE EXPRESSION; POLYPLOIDY; POPULATION GENETICS;

ASTERACEAE; TRAGOPOGON; TRAGOPOGON DUBIUS; TRAGOPOGON MIRUS; TRAGOPOGON MISCELLUS; TRAGOPOGON PORRIFOLIUS; TRAGOPOGON PRATENSIS;

EID: 0347352354     PISSN: 00244066     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1095-8312.2004.00335.x     Document Type: Conference Paper

References (108)

1. Abbott RJ, Brochmann C. 2003. History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology 12: 299-313.
2. Abbott RJ, Forbes DG. 2002. Extinction of the Edinburgh lineage of the allopolyploid neospecies, Senecio cambrensis Rosser (Asteraceae). Heredity 88: 267-269.
3. 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.
4. Adams KL, Cronn RC, Percifield R, Wendel JF. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences, USA 100: 4649-4654.
5. Ainouche ML, Baumel A, Salmon A. 2004. Spartina anglica C. E. Hubbard: a natural model system for studying early evolutionary changes that affect allopolyploid genomes. Biological Journal of the Linnean Society 82: 475-484.
6. Álvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
7. Arnheim N. 1983. Concerted evolution of multigene families. In: Nei M, Koehn RK, eds. Evolution of genes and proteins. Sunderland, MA: Sinauer, 38-61.
8. Ashton PA, Abbott RJ. 1992. Multiple origins and genetic diversity in the newly arisen allopolyploid species, Senecio cambrensis Rosser (Compositae). Heredity 68: 25-32.
9. Bachem CWB, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF. 1996. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant Journal 9: 745-753.
10. Baumel A, Ainouche ML, Levasseur JE. 2001. Molecular investigations in populations of Spartina anglica C. E. Hubbard (Poaceae) invading coastal Brittany (France). Molecular Ecology 10: 1689-1701.
11. Bayer RJ, Purdy BG, Lebedyx DG. 1991. Niche differentiation among sexual species of Antennaria gaertner (Asteraceae: Inuleae) and A. rosea, their allopolyploid derivative. Evolutionary Trends in Plants 5: 109-123.
12. Brehm BG, Ownbey M. 1965. Variation in chromatographic patterns in the Tragopogon dubius-pratensis-porrifolius complex (Compositae). American Journal of Botany 52: 811-818.
13. Bretagnolle F, Lumaret R. 1995. Bilateral polyploidization in Dactylis glomerata L. ssp. Lusitanica: occurrence, morphological and generic characteristics of first polyploids. Euphytica 84: 197-207.
14. Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen A-C, Elven R. 2004. Polyploidy in arctic plants. Biological Journal of the Linnean Society 82: 521-536.
15. Brochmann C, Elven R. 1992. Ecological and genetic consequences of polyploidy in Arctic Draba (Brassicaceae). Evolutionary Trends in Plants 6: 111-124.
16. Brochmann C, Soltis PS, Soltis DE. 1992a. Recurrent formation and polyphyly of Nordic polyploids in Draba (Brassicaceae). American Journal of Botany 79: 673-688.
17. Brochmann C, Soltis PS, Soltis DE. 1992b. Multiple origins of the octoploid Scandinavian endemic Draba cacuminum: electrophoretic and morphological evidence. Nordic Journal of Botany 12: 257-272.
18. Brown RK, Schaak CG. 1972. Two new species of Tragopogon for Arizona. Madroño 21: 304.
19. Chen ZJ, Comai L, Pikaard CS. 1998. Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proceedings of the National Academy of Sciences, USA 95: 14891-14896.
20. Chen ZJ, Pikaard CS. 1997a. Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/ silencing of progenitor rRNA genes is developmentally regulated in Brassica. Proceedings of the National Academy of Sciences, USA 94: 3442-3447.
21. Chen ZJ, Pikaard CS. 1997b. Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes and Development 11: 2124-2136.
22. Chen ZJ, Wang J, Tian L, Lee H-S, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B, Lippman Z, Vaughn M, Pires JC, Colot V, Doerge RW, Martienssen RA, Comai L, Osborn TC. 2004. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society 82: 689-700.
23. Comai L. 2000. Genetic and epigenetic interactions in allopolyploid plants. Plant Molecular Biology 43: 387-399.
24. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B. 2000. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12: 1551-1567.
25. Cook LM, Soltis PS. 1999. Mating systems of diploid and allotetraploid populations of Tragopogon (Asteraceae). I. Natural populations. Heredity 82: 237-244.
26. Cook LM, Soltis PS, Brunsfeld SJ, Soltis DE. 1998. Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers. Molecular Ecology 7: 1293-1302.
27. Doyle JJ, Doyle JL, Brown AHD. 1999. Origins, colonization, and lineage recombination in a widespread perennial soybean polyploid complex. Proceedings of the National Academy of Sciences, USA 96: 10741-10745.
28. Doyle JJ, Doyle JL, Brown AHD, Palmer RG. 2002. Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3D sequences. Evolution 56: 1388-1402.
29. Doyle JJ, Doyle JL, Rauscher J, Brown AHD. 2004a. Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts. Biological Journal of the Linnean Society 82: 583-597.
30. Doyle JJ, Doyle JL, Rauscher JT, Brown AHD. 2004b. Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytologist in press.
31. Ehrendorfer F. 1980. Polyploidy and distribution. In: Lewis WH, ed. Polyploidy: biological relevance. New York: Plenum Press, 45-60.
32. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM. 1997. Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147: 1381-1387.
33. Franzke A, Mummenhoff K. 1999. Recent hybrid speciation in Cardamine (Brassicaceae) - conversion of nuclear ribosomal ITS sequences in statu nascendi. Theoretical and Applied Genetics 98: 831-834.
34. Gaut BS, Doebley JF. 1997. DNA sequence evidence for the segmental allotetraploid origin of maize. Proceedings of the National Academy of Sciences, USA 94: 6809-6814.
35. Grisebach RJ, Kamo KK. 1996. The effect of induced polyploidy on the flavonols of Petunia 'Mitchell'. Phytochemistry 423: 361-363.
36. Hamby R, Zimmer EA. 1992. Ribosomal RNA as a phylogenetic tool in plant systemtaics. In: Soltis PS, Soltis DE, Doyle JJ, eds. Molecular systematics of plants. New York: Chapman & Hall, 50-91.
37. Hanski I. 1998. Metapopulation dynamics. Nature 396: 41-49.
38. Heslop-Harrison JS. 2000. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12: 617-636.
39. Hubbard JCE. 1965. Spartina marshes in southern England. VI. Patterns of invasion in Poole harbour. Journal of Ecology 53: 799-813.
40. Husband BC, Barrett SCH. 1996. A metapopulation perspective in plant population biology. Journal of Ecology 84: 461-469.
41. Husband BC, Schemske DW. 1997. The effect of inbreeding in diploid and tetraploid Epilobium angustifolium (Onagraceae): implications of the genetic basis of inbreeding depression. Evolution 51: 737-746.
42. Huskins CL. 1931. The origin of Spartina townsendii. Genetica 12: 531.
43. Jiang J, Gill BS. 1996. Current status and potential of fluorescence in situ hybridization in plant genome mapping. In: Paterson AH, ed. Genome mapping in plants. Austin, TX: RG Landes Co., 127-135.
44. Kashkush K, Feldman M, Levy AA. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
45. Kenton A, Parokonny AS, Gleba YY, Bennett MD. 1993. Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Molecular and General Genetics 240: 15969.
46. Kochert G, Stocker HT, Gimenes M, Galgaro L, Lopes CR, Moore K. 1996. RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogea (Leguminosae). American Journal of Botany 83: 1282-1291.
47. Kovarik A, Matyasek R, Lim KY, Skalická K, Koukalová B, Knapp S, Chase M, Leitch AR. 2004. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 82: 615-625.
48. Kroschewsky JR, Mabry TR, Markham KR, Alston RE. 1969. Flavonoids from the genus Tragopogon (Compositae). Phytochemistry 8: 1495-1498.
49. Lee H-S, Chen ZJ. 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Academy of Sciences, USA 98: 6753-6758.
50. Leitch IJ, Bennett MD. 1997. Polyploidy in angiosperms. Trends in Plant Science 2: 470-476.
51. Levin DA. 2000. The origin, expansion, and demise of plant species. New York: Oxford University Press.
52. Lim KY, Kovarík A, Matyásek R, Bezdek M, Lichtenstein CP, Leitch AR. 2000. Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109: 161-172.
53. Lim KY, Matyasek R, Kovarik A, Leitch AR. 2004. Genome evolution in allotetraploid Nicotiana. Biological Journal of the Linnean Society 82: 599-606.
54. Little TJ, Hebert PDN. 1994. Abundant asexuality in tropical freshwater ostracods. Heredity 73: 549-555.
55. Lowe AJ, Abbott RJ. 1996. Origins of the new allopolyploid species Senecio cambrensis (Asteraceae) and its relationship to the Canary Islands endemic Senecio teneriffae. American Journal of Botany 83: 1365-1372.
56. Lynch M, Conery JS. 2000. The evolutionary fate of duplicated genes. Science 290: 1151-1154.
57. Lynch M, Force A. 2000a. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
58. Lynch M, Force A. 2000b. The origin of interspecific genomic incompatibility via gene duplication. American Naturalist 156: 590-605.
59. Madlung A, Masuelli R, Watson B, Reynolds S, Davison J, Comai L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology 129: 733-746.
60. Marchant CJ. 1967. Evolution in Spartina (Gramineae). I. The history and morphology of the genus in Britain. The Journal of the Linnean Society, Botany 60: 1-24.
61. Marchant CJ. 1968. Evolution in Spartina (Gramineae). II. Chromosomes, basic relationships and the problem of S. x townsendii. The Journal of the Linnean Society, Botany 60: 381-409.
62. Mavrodiev EV, Edwards CE, Albach DC, Gitzendanner MA, Soltis PS, Soltis DE. in press a. Phylogenetic relationships in subtribe Scorzonerinae (Asteraceae: Cichorioideae: Lactuceae) based on ITS sequence data. Taxon in press.
63. Mavrodiev EV, Tancing ME, Gitzendanner MA, Rocca J, Soltis PS, Soltis DE. in press b. Phylogenetic relationships in Tragopogon L. (Asteraceae: Scorzonerinae) based on ITS and ETS sequence data. International Journal of Plant Sciences, in press.
64. McCauley DE, Raveill J, Antonovics J. 1995. Local founding events as determinants of genetic structure in a plant metapopulation. Heredity 75: 630-636.
65. McClintock B. 1984. The significance of responses of the genome to challenge. Science 226: 792-801.
66. Mittelstein Scheid O, Jakovleva L, Afsar K, Maluszynska J, Paszkowski J. 1996. A change of ploidy can modify epigenetic silencing. Proceedings of the National Academy of Sciences, USA 93: 7114-7119.
67. Novak SJ, Soltis DE, Soltis PS. 1991. Ownbey's Tragopogons: 40 years later. American Journal of Botany 78: 1586-1600.
68. O'Neill RJW, O'Neill MJ, Graves JAM. 1998. Undermethylation associated with retroelement activation and chromosome remodeling in an interspecific mammalian hybrid. Nature 393: 68-72.
69. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19: 141-147.
70. Ownbey M. 1950. Natural hybridization and amphiploidy in the genus Tragopogon. American Journal of Botany 37: 487-499.
71. Ownbey M, McCollum GD. 1953. Cytoplasmic inheritance and reciprocal amphiploidy in Tragopogon. American Journal of Botany 40: 788-796.
72. Ownbey M, McCollum GD. 1954. The chromosomes of Tragopogon. Rhodora 56: 7-21.
73. Pikaard CS, Chen ZJ. 1998. Nucleolar dominance. In: Paule MR, ed. RNA polymerase I: Transcription of eukaryotic ribosomal RNA. Austin, TX: R. G. Landes Co., 275-293.
74. Pires JC, Lim KY, Kovarik A, Matyasek R, Boyd A, Leitch AR, Leitch IJ, Bennett MD, Soltis PS, Soltis DE. 2004. Molecular cytogenetic analysis of the recently evolved Tragopogon (Asteraceae) allopolyploids reveals a karyotype that is additive of the diploid progenitors. American Journal of Botany in press.
75. Ptacek MB, Gerhardt HC, Sage RD. 1994. Speciation by polyploidy in treefrogs: multiple origins of the tetraploid, Hyla versicolor. Evolution 48: 898-908.
76. Raybould AF, Gray AJ, Lawrence MJ, Marshall DF. 1991. The evolution of Spartina anglica C.E. Hubbard (Gramineae): origin and genetic variability. Biological Journal of the Linnean Society 43: 111-126.
77. Reeder RH. 1985. Mechanisms of nucleolar dominance in animals and plants. Journal of Cell Biology 101: 2013-2016.
78. Riven CJ, Cullis CA, Walbot V. 1986. Evaluating quantitative variation in the genome of Zea mays. Genetics 113: 1009-1019.
79. Roose ML, Gottlieb LD. 1976. Genetic and biochemical consequences of polyploidy in Tragopogon. Evolution 30: 818-830.
80. Rosser EM. 1955. A new British species of Senecio. Watsonia 3: 228-232.
81. Russo VEA, Martienssen RA, Riggs AD. 1996. Epigenetic mechanisms of gene regulation. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
82. Sang T, Crawford DJ, Steussy TF. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution. Proceedings of the National Academy of Sciences, USA 92: 6813-6817.
83. Sauber KL. 2000. Habitat differentiation between derivative tetraploid and progenitor diploid species of Tragopogon. Masters of Science thesis, Washington State University.
84. Segraves KA, Thompson JN. 1999. Plant polyploidy and pollination: floral traits and insect visits to diploid and tetraploid Heuchera grossulariifolia. Evolution 53: 1114-1127.
85. Segraves KA, Thompson JN, Soltis PS, Soltis DE. 1999. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Molecular Ecology 8: 253-262.
86. 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.
87. Soltis PS, Doyle JJ, Soltis DE. 1992. Molecular data and polyploid evolution in plants. In: Soltis PS, Doyle JJ, Soltis DE, eds. Molecular systematics of plants. New York: Chapman & Hall, 177-201.
88. Soltis PS, Plunkett GM, Novak SJ, Soltis DE. 1995. Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). American Journal of Botany 82: 1329-1341.
89. Soltis DE, Soltis PS. 1989. Allopolyploid speciation in Tragopogon: insights from chloroplast DNA. American Journal of Botany 76: 1119-1124.
90. Soltis PS, Soltis DE. 1991. Multiple origins of the allotetraploid Tragopogon mirus (Compositae): rDNA evidence. Systematic Botany 16: 407-413.
91. Soltis DE, Soltis PS. 1993. Molecular data and the dynamic nature of polyploidy. Critical Reviews in Plant Sciences 12: 243-273.
92. Soltis DE, Soltis PS. 1999. Polyploidy: recurrent formation and genome evolution. Trends in Ecology and Evolution 14: 348-352.
93. Soltis PS, Soltis DE. 2000. The role of genetic and genomic changes in the success of polyploids. Proceedings of the National Academy of Sciences, USA 97: 7051-7057.
94. Song K, Lu P, Tang K, Osborn TC. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences, USA 92: 7719-7723.
95. Stebbins GL. 1950. Variation and evolution in plants. New York: Columbia University Press.
96. Taylor JS, Van de Peer Y, Meyer A. 2001. Genome duplication, divergent resolution and speciation. Trends in Genetics 17: 299-301.
97. Turgeon J, Hebert PDN. 1995. Genetic characterization of breeding systems, ploidy levels and species boundaries in Cypricercus (Ostracoda). Heredity 75: 561-570.
98. Urbanska KM, Hurka H, Landolt E, Neuffer B, Mummenhoff K. 1997. Hybridization and evolution in Cardamine (Brassicaceae) at Urnerboden, central Switzerland: biosystematic and molecular evidence. Plant Systematics and Evolution 204: 233-256.
99. Volkov RA, Borisjuk NV, Panchuk II, Schweizer D, Hemleben V. 1999. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Molecular Biology and Evolution 16: 311-320.
100. Vrana PB, Fossella JA, Matteson P, del Rio T, O'Neill MJ, Tilghman SM. 2000. Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus. Nature Genetics 25: 120-124.
101. Wagner WH. 1970. Biosystematics and evolutionary noise. Taxon 19: 146-151.
102. Wagner WH. 1983. Reticulistics: the recognition of hybrids and their role in cladistics and classification. In: Platnick NI, Funk VA, eds. Advances in cladistics 2. New York: Columbia University Press, 63-79.
103. Warner DA, Edwards GE. 1989. Effects of polyploidy on photosynthetic rates, photosynthetic enzymes, content of DNA, chlorophyll, and sizes and numbers of photosynthetic cells in the C4 dicot Atriplex confertifolia. Plant Physiology 91: 1143-1151.
104. 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.
105. Werth CR, Windham MD. 1991. A model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. American Naturalist 137: 515-526.
106. Wolf PG, Soltis DE, Soltis PS. 1990. Chloroplast-DNA and allozymic variation in diploid and autotetraploid Heuchera grossulariifolia (Saxifragaceae). American Journal of Botany 77: 232-244.
107. Zhang L, Gaut BS, Vision TJ. 2001. Gene duplication and evolution. Science 293: 1551.
108. Zimmer EA, Martin SL, Beverley SM, Kan YW, Wilson AC. 1980. Rapid duplication and loss of genes coding for the α chains of hemoglobin. Proceedings of the National Academy of Sciences, USA 77: 2158-2162.