The utility of nuclear gapCp in resolving polyploid fern origins

Systematic Botany

Volumn 33, Issue 4, 2008, Pages 621-629

  Schuettpelz, Eric ^a   Grusz, Amanda L ^a   Windham, Michael D ^a   Pryer, Kathleen M ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Allopolyploidy; Autopolyploidy; Ferns; gapCp; GAPDH; Molecular systematics; Nuclear marker

Indexed keywords

FILICOPHYTA;

EID: 57149104180     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364408786500127     Document Type: Article

References (79)

1. Abraham, A. and C. A. Ninan. 1954. Chromosomes of Ophioglossum reticulaturn L. Current Science (Bangalore) 23: 213-214.
2. Álvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
3. Bradley, R. D. and D. M. Hillis. 1997. Recombinant DNA sequences generated by PCR amplification. Molecular Biology and Evolution 14: 592-593.
4. Breathnach, R., C. Benoist, K. O'Hare, F. Gannon, and P. Chambon. 1978. Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries. Proceedings of the National Academy of Sciences USA 75: 4853-4857.
5. Brinkmann, H., R. Cerff, M. Salomon, and J. Soll. 1989. Cloning and sequence analysis of cDNAs encoding the cytosolic precursors of subunits GapA and GapB of chloroplast glyceraldehyde-3-phosphate dehydrogenase from pea and spinach. Plant Molecular Biology 13: 81-94.
6. Brinkmann, H., P. Martinez, F. Quigley, W. Martin, and R. Cerff. 1987. Endosymbiotic origin and codon bias of the nuclear gene for chloroplast glyceraldehyde-3-phosphate dehydrogenase from maize. Journal of Molecular Evolution 26: 320-328.
7. Bult, C., M. Källersjö, and Y. Suh. 1992. Amplification and sequencing of 16/18S rDNA from gel-purified total plant DNA. Plant Molecular Biology Reporter 10: 273-284.
8. Cronn, R., M. Cedroni, T. Haselkorn, C. Grover, and J. F. Wendel. 2002. PCR-mediated recombination in amplification products derived from polyploid cotton. Theoretical and Applied Genetics 104: 482-489.
9. Ebihara, A., H. Ishikawa, S. Matsumoto, S.-J. Lin, K. Iwatsuki, M. Takamiya, Y. Watano, and M. Ito. 2005. Nuclear DNA, chloroplast DNA, and ploidy analysis clarified biological complexity of the Vandenboschia radicans complex (Hymenophyllaceae) in Japan and adjacent areas. American Journal of Botany 92: 1535-1547.
10. Frohlich, M. W. and E. M. Meyerowitz. 1997. The search for flower homeotic gene homologs in basal angiosperms and Gnetales: a potential new source of data on the evolutionary origin of flowers. International Journal of Plant Sciences 158: S131-S142.
11. Gastony, G. J. and D. R. Rollo. 1998. Cheilanthoid ferns (Pteridaceae: Cheilanthoideae) in the southwestern United States and adjacent Mexico: a molecular phylogenetic reassessment of generic lines. Aliso 17: 131-144.
12. Gastony, G. J. and M. D. Windham. 1989. Species concepts in pteridophytes: the treatment and definition of agamosporous species. American Fern Journal 79: 65-77.
13. Gastony, G. J. and G. Yatskievych. 1992. Maternal inheritance of the chloroplast and mitochondrial genomes in cheilanthoid ferns. American Journal of Botany 79: 716-722.
14. Ge, S., T. Sang, B.-R. Lu, and D.-Y. Hong. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proceedings of the National Academy of Sciences USA 96: 14400-14405.
15. Grant, V. 1981. Plant speciation. New York: Columbia University Press.
16. Gregory, T. R. and B. K. Mable. 2005. Polyploidy in animals. Pp. 428-501 in The Evolution of the Genome, ed. T. R. Gregory. San Diego: Elsevier Academic Press.
17. Haufler, C. H. 1987. Electrophoresis is modifying our concepts of evolution in homosporous pteridophytes. American Journal of Botany 74: 953-966.
18. Haufler, C. H., M. D. Windham, and E. W. Rabe. 1995. Reticulate evolution in the Polypodium vulgare complex. Systematic Botany 20: 89-109.
19. Hoot, S. B. and W. C. Taylor. 2001. The utility of nuclear ITS, a LEAFY homolog intron, and chloroplast atpB-rbcL spacer region data in phylogenetic analyses and species delimitation in Isoëtes. American Fern Journal 91: 166-177.
20. Huelsenbeck, J. P. and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 17: 754-755.
21. Ishikawa, H., Y. Watano, K. Kano, M. Ito, and S. Kurita. 2002. Development of primer sets for PCR amplification of the pgiC gene in ferns. Journal of Plant Research 115: 65-70.
22. Jackson, R. C. 1982. Polyploidy and diploidy: new perspectives on chromosome pairing and its evolutionary implications. American Journal of Botany 69: 1512-1523.
23. Klekowski, E. J. 1972. Genetical features of ferns as contrasted to seed plants. Annals of the Missouri Botanical Garden 59: 138-151.
24. Klekowski, E. J. and H. G. Baker. 1966. Evolutionary significance of polyploidy in the Pteridophyta. Science 153: 305-307.
25. Kovarik, A., R. Matyasek, K. Y. Lim, K. Skalická, B. Koukalová, S. Knapp, M. Chase, and A. R. Leitch. 2004. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 82: 615-625.
26. Kovarik, A., J. C. Pires, A. R. Leitch, K. Y. Lim, A. M. Sherwood, R. Matyasek, J. Rocca, D. E. Soltis, and P. S. Soltis. 2005. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169: 931-944.
27. Levin, D. A. 1983. Polyploidy and novelty in flowering plants. American Naturalist 122: 1-25.
28. Lihová, J., K. K. Shimizu, and K. Marhold. 2006. Allopolyploid origin of Cardamine asarifolia (Brassicaceae): incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene. Molecular Phylogenetics and Evolution 39: 759-786.
29. Lim, K. Y., R. Matyasek, A. Kovarik, and A. Leitch. 2007. Parental origin and genome evolution in the allopolyploid Iris versicolor. Annals of Botany 100: 219-224.
30. Löve, Á., D. Löve, and R. E. G. Pichi Sermolli. 1977. Cytotaxonomical atlas of the Pteridophyta. Vaduz: Cramer.
31. Ma, X.-F. and J. P. Gustafson. 2005. Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenetic and Genome Research 109: 236-249.
32. Maddison, D. R. and W. P. Maddison. 2005. MacClade: Analysis of Phylogeny and Character Evolution, version 4.08. Sunderland: Sinauer Associates.
33. Manton, I. and G. Vida. 1968. Cytology of the fern flora of Tristan da Cunha. Proceedings of the Royal Society of London. Series B. Biological Sciences 170: 361-379.
34. Martin, W. and R. Cerff. 1986. Prokaryotic features of a nucleus-encoded enzyme. cDNA sequences for chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases from mustard (Sinapis alba). European Journal of Biochemistry 159: 323-331.
35. Martin, W. and C. Schnarrenberger. 1997. The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis. Current Genetics 32: 1-18.
36. Mason-Gamer, R. J., C. F. Weil, and E. A. Kellogg. 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Molecular Biology and Evolution 15: 1658-1673.
37. +-dependent glyceraldehyde-3-phosphate dehydrogenase from Pinus sylvestris chloroplasts. Gene 209: 167-174.
38. +- dependent glyceraldehyde-3-phosphate dehydrogenase in plastids of the gymnosperm Pinus sylvestris L. Plant Molecular Biology 26: 1155-1166.
39. Osborn, T. C., J. C. Pires, J. A. Birchler, D. L. Auger, Z. J. Chen, H.-S. Lee, L. Comai, A. Madlung, R. W. Doerge, V. Colot, and R. A. Martienssen. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19: 141-147.
40. Otto, S. P. and J. Whitton. 2000. Polyploid incidence and evolution. Annual Review of Genetics 34: 401-437.
41. Petersen, J., H. Brinkmann, and R. Cerff. 2003. Origin, evolution, and metabolic role of a novel glycolytic GAPDH enzyme recruited by land plant plastids. Journal of Molecular Evolution 57: 16-26.
42. Petersen, J., R. Teich, B. Becker, R. Cerff, and H. Brinkmann. 2006. The gapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants). Molecular Biology and Evolution 23: 1109-1118.
43. Popp, M. and B. Oxelman. 2001. Inferring the history of the polyploid Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences. Molecular Phylogenetics and Evolution 20: 474-481.
44. Popp, M. and B. Oxelman. 2007. Origin and evolution of North American polyploid Silene (Caryophyllaceae). American Journal of Botany 94: 330-349.
45. Pryer, K. M., E. Schuettpelz, P. G. Wolf, H. Schneider, A. R. Smith, and R. Cranfill. 2004. Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. American Journal of Botany 91: 1582-1598.
46. Rambaut, A. and A. Drummond. 2007. Tracer, version 1.4. Edinburgh: University of Edinburgh (http://tree.bio.ed.ac.uk/software/tracer/). Downloaded October, 2007.
47. Ramsey, J. and D. W. Schemske. 2002. Neopolyploidy in flowering plants. Annual Review of Ecology and Systematics 33: 589-639.
48. Reeves, T. 1979. A monograph of the fern genus Cheilanthes subgenus Physapteris (Adiantaceae). Ph.D dissertation, Arizona State University.
49. Reid, J. D., G. M. Plunkett, and G. A. Peters. 2006. Phylogenetic relationships in the heterosporous fern genus Azolla (Azollaceae) based on DNA sequence data from three noncoding regions. International Journal of Plant Sciences 167: 529-538.
50. Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England) 19: 1572-1574.
51. Sang, T. and D. Zhang. 1999. Reconstructing hybrid speciation using sequences of low copy nuclear genes: hybrid origins of five Paeonia species based on Adh gene phylogenies. Systematic Botany 24: 148-163.
52. Schuettpelz, E. and K. M. Pryer. 2007. Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes. Taxon 56: 1037-1050.
53. Schuettpelz, E., P. Korall, and K. M. Pryer. 2006. Plastid atpA data provide improved support for deep relationships among ferns. Taxon 55: 897-906.
54. Schuettpelz, E., H. Schneider, L. Huiet, M. D. Windham, and K. M. Pryer. 2007. A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera. Molecular Phylogenetics and Evolution 44: 1172-1185.
55. Sears, B. B. 1980. Elimination of plastids during spermatogenesis and fertilization in the plant kingdom. Plasmid 4: 233-255.
56. Small, R. L., R. C. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17: 145-170.
57. Small, R. L., E. B. Lickey, J. Shaw, and W. D. Hauk. 2005. Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae. Molecular Phylogenetics and Evolution 36: 509-522.
58. Small, R. L., J. A. Ryburn, R. C. Cronn, T. Seelanan, and J. F. Wendel. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
59. Smith, A. R., K. M. Pryer, E. Schuettpelz, P. Korall, H. Schneider, and P. G. Wolf. 2006. A classification for extant ferns. Taxon 55: 705-731.
60. Soltis, D. E. and L. H. Rieseberg. 1986. Autopolyploidy in Tolmiea menziesii (Saxifragaceae): genetic insights from enzyme electrophoresis. American Journal of Botany 73: 310-318.
61. Soltis, D. E. and P. S. Soltis. 1987. Polyploidy and breeding systems in homosporous Pteridophyta: a reevaluation. American Naturalist 130: 219-232.
62. Soltis, D. E., P. S. Soltis, D. W. Schemske, J. F. Hancock, J. N. Thompson, B. C. Husband, and W. S. Judd. 2007. Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56: 13-30.
63. Soltis, P. S. and D. E. Soltis. 2000. The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences USA 97: 7051-7057.
64. Tate, J. A., D. E. Soltis, and P. S. Soltis. 2005. Polyploidy in plants. Pp. 371-426 in The Evolution of the Genome, ed. T. R. Gregory. San Diego: Elsevier Academic Press.
65. Thompson, J. D. and R. Lumaret. 1992. The evolutionary dynamics of polyploid plants: origins, establishment and persistence. Trends in Ecology & Evolution 9: 302-307.
66. Van den heede, C. J., R. L. L. Viane, and M. W. Chase. 2003. Phylogenetic analysis of Asplenium subgenus Ceterach (Pteridophyta: Aspleniaceae) based on plastid and nuclear ribosomal ITS DNA sequences. American Journal of Botany 90: 481-495.
67. Vida, G. 1976. The role of polyploidy in evolution. Pp. 267-294 in Evolutionary Biology, eds. V. J. A. Novák and B. Pacltová. Prague: Czechoslovak Academy of Science.
68. Volkov, R. A., N. Y. Komarova, and V. Hemleben. 2007. Ribosomal DNA in plant hybrids: inheritance, rearrangement, expression. Systematics and Biodiversity 5: 261-276.
69. Walker, T. G. 1966. A cytotaxonomic survey of the Pteridophytes of Jamaica. Transactions of the Royal Society of Edinburgh 66: 169-237.
70. Walker, T. G. 1984. Chromosomes and evolution in pteridophytes. Pp. 101-141 in Chromosomes in Evolution of Eukaryotic Groups Volume 2, eds. A. K. Sharma and A. Sharma. Boca Raton: CRC Press.
71. Wall, D. P. 2002. Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae). Molecular Phylogenetics and Evolution 25: 10-26.
72. Wendel, J. F. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.
73. Wendel, J. F., A. Schnabel, and T. Seelanan. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences USA 92: 280-284.
74. Werth, C. R. and M. D. Windham. 1991. A model for divergent allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression. American Naturalist 137: 515-526.
75. Werth, C. R., S. I. Guttman, and W. H. Eshbaugh. 1985. Electrophoretic evidence of reticulate evolution in the Appalachian Asplenium complex. Systematic Botany 10: 184-192.
76. Windham, M. D. and E. W. Rabe. 1993. Cheilanthes. Pp. 152-169 in Flora of North America North of Mexico, Volume 2, ed. Flora of North America Editorial Committee. New York: Oxford University Press.
77. Windham, M. D. and G. Yatskievych. 2003. Chromosome studies of cheilanthoid ferns (Pteridaceae: Cheilanthoideae) from the western United States and Mexico. American Journal of Botany 90: 1788-1800.
78. Wolf, P. G. 1995. Phylogenetic analyses of rbcL and nuclear ribosomal RNA gene sequences in Dennstaedtiaceae. American Fern Journal 85: 306-327.
79. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.