Species-level phylogenetics of large genera: Prospects of studying coevolution and polyploidy

Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa

Volumn , Issue , 2006, Pages 129-147

  Ronsted N ^a   Yektaei Karin, E ^a   Turk, K ^a   Clarkson, J J ^a   Chase, M W ^a  

^a JODRELL LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84889751929     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420009538     Document Type: Chapter

References (105)

1. Frodin, D.G., History and concepts of big plant genera, Taxon, 53, 753, 2004.
2. Bronstein, J.L. and McKey, D., The fig-pollinator mutualism: a model system for comparative biology, Experientia, 45, 601, 1989.
3. Perret, M. et al., Systematics and evolution of tribe Sinningieae (Gesneriaceae): evidence from phylogenetic analyses of six plastid DNA regions and nuclear ncpGS, Amer. J. Bot., 90, 445, 2003.
4. Albach, D.C., Martinez-Ortega, M.M., and Chase, M.W., Veronica: parallel morphological evolution and phylogeography in the Mediterranean, Pl. Syst. Evol., 246, 177, 2004.
5. Pennington, R.T., Cronk, Q.C.B. and Richardson, J.A., Introduction and synthesis: plant phylogeny and the origin of major biomes, Phil. Trans. R. Soc. Lond. B, 359, 1455, 2004.
6. Rutschmann, F. et al., Did Crypteroniaceae really disperse out of India? Molecular dating evidence from rbcL, ndhF, and rpl16 intron sequences, Int. J. Plant Sci., 165, S69, 2004.
7. Davies, T.J. et al., Darwińs abominable mystery: insights from a supertree of the angiosperms, Proc. Natl. Acad. Sci. USA, 101, 1904, 2004.
8. Davies, T.J. et al., Environmental causes for plant biodiversity gradients, Phil. Trans. R. Soc. Lond. B, 359, 1645, 2004.
9. Davies, T.J. et al., Environmental energy and evolutionary rates in flowering plants, Phil. Trans. R. Soc. Lond. B., 271, 2195, 2004.
10. Linder, H.P., Hardy, C.R., and Rutschmann, F., Taxon sampling effects in molecular clock dating: an example from the African Restionaceae, Mol. Phyl. Evol., 35, 569, 2005.
11. Bremer, K., Ancestral areas: a cladistic reinterpretation of the center of origin concept, Syst. Biol., 41, 436, 1992.
12. Chase, M.W. et al., When in doubt, put it in Flacourtiaceae: a molecular phylogenetic analysis based on plastid rbcL DNA sequences, Kew Bull., 57, 141, 2002.
13. Rønsted et al., Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria, Mol. Phyl. Evol., 35, 509, 2005.
14. Weiblen, G.D., Phylogenetic relationships of functionally dioecious Ficus (Moraceae) based on ribosomal DNA sequences and morphology, Amer. J. Bot., 87, 1342, 2000.
15. Cook, J.M. and Rasplus, J.-Y., Mutualists with attitude: coevolving fig wasps and figs, Trends Ecol. Evol., 18, 241, 2003.
16. Machado, C.A. et al., Phylogenetic relationships, historical biogeography and character evolution of fig-pollinating wasps, Proc. R. Soc. Lond. B, 268, 685, 2001.
17. Datwyler, S.L. and Weiblen, G.D., On the origin of the fig: phylogenetic relationships of Moraceae from ndhF sequences, Amer. J. Bot., 91, 767, 2004.
18. Rønsted, N. et al., 60 million years of co-divergence in the fig-wasp symbiosis, Proc. R. Soc. Lond. B, 272, 2593, 2005.
19. Zerega, N.J.C. et al., Biogeography and divergence times in the mulberry family (Moraceae), Mol. Phyl. Evol., 37, 402, 2005.
20. Page, R.D.M., Introduction, in Tangled Trees: Phylogeny, Cospeciation and Coevolution, Page, R.D.M., Ed., The University of Chicago Press, Chicago, 2003, 1.
21. Pellmyr, O., Yuccas, yucca moths, and coevolution: a review, Ann. Missouri Bot. Gard., 90, 35, 2003.
22. Henderson, A., A review of pollination studies in the Palmae, Bot. Rev., 52, 221, 1986.
23. Meekijjaroenroj, A. and Anstett, M.C., A weevil pollinating the Canary Islands date palm: between parasitism and mutualism, Naturwissenschaften, 90, 452, 2003.
24. Kato, M., Takimura, A., and Kawakita, A., An obligate pollination mutualism and reciprocal diversification in the tree genus Glochidion (Euphorbiaceae), Proc. Natl. Acad. Sci. USA, 100, 5264, 2003.
25. Bronstein, J.L., The costs of mutualism, Amer. Zool., 41, 825, 2001.
26. Page, R.D.M., Clayton, D.H., and Patterson, A.M., Lice and cospeciation: a response to Barker, Int. J. Parasit., 26, 213, 1996.
27. Herre, E.A. et al., Molecular phylogenies of figs and their pollinator wasps, J. Biogeogr., 23, 521, 1996.
28. Jousselin, E., Rasplus, J.-Y., and Kjellberg, F., Convergence and coevolution in a mutualism: evidence from a molecular phylogeny of Ficus, Evolution, 57, 1255, 2003.
29. Weiblen, G.D., Correlated evolution in fig pollination, Syst. Biol., 53, 1, 2004.
30. Shaw, J. et al., The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analyses, Amer. J. Bot., 92, 142, 2005.
31. Swofford, D.L., PAUP*: Phylogenetic Methods Using Parsimony (*and Other Methods), version 4, Sinauer, Sunderland, MA, 2002.
32. Rønsted, N. et al., unpublished data, 2005.
33. Chase, M.W., Fay, M.F., and Savolainen, V., Higher-level classification in the angiosperms: new insights from the perspective of DNA sequence data, Taxon, 49, 685, 2000.
34. Asmussen, C.B. and Chase, M.W., Coding and noncoding plastid DNA in palm systematics, Amer. J. Bot., 88, 1103, 2001.
35. Chase, M.W. et al., Multi-gene analyses of monocot relationships: a summary, in Monocots: Comparative Biology and Evolution, Columbus, J.T. et al., Eds., Rancho Santa Ana Botanic Garden, Claremont, CA, USA, in press.
36. Reeves, G. et al., Molecular systematics of Iridaceae: evidence from four plastid DNA regions, Amer. J. Bot., 88, 2074, 2001.
37. Goldblatt, P. et al., Radiation in the Cape flora and the phylogeny of peacock irises Moraea (Iridaceae) based on four plastid DNA regions, Mol. Phyl. Evol., 25, 341, 2002.
38. Baldwin, B.G. et al., The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny, Ann. Missouri Bot. Gard., 82, 247, 1995.
39. Rønsted, N. et al., Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data, Bot. J. Linn. Soc., 139, 323, 2002.
40. Park, S.J. and Kim, K.J., Molecular phylogeny of the genus Hypericum (Hypericaceae) from Korea and Japan: evidence from nuclear rDNA ITS sequence data, J. Plant Biol., 47, 366, 2004.
41. Huang, J.L., Giannasi, D.E., and Huang, J., Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences, Mol. Phyl. Evol., 35, 48, 2005.
42. Buckler, E.S., Ippolito, A., and Holtsford, T.P., The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications, Genetics, 145, 821, 1997.
43. Campbell, C.S. et al., Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae), Mol. Biol. Evol., 14, 81, 1997.
44. Denduangboripant, J. and Cronk, Q.C.B., High intraindividual variation in internal transcibed spacer sequences in Aeschynanthus (Gesneriaceae): implications for phylogenetics, Proc. R. Soc. Lond. B, 267, 1407, 2000.
45. Kita, Y. and Ito, M., Nuclear ribosomal ITS sequences and phylogeny in East Asian Aconitum subgenus Aconitum (Ranunculaceae), with special reference to extensive polymorphism in individual plants, Pl. Syst. Evol., 225, 1, 2000.
46. Rapini, A., Chase, M.W., and Konno, T.U.P., Phylogenetics of the South American Asclepiadoideae (Apocynaceae), Taxon, 55, 119, 2006.
47. Baldwin, B.G. and Markos, S., Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae), Mol. Phyl. Evol., 10, 449, 1998.
48. Béna, G. et al., Ribosomal external and internal transcribed spacers: combined use in the phylogenetic analyses of Medicago (Leguminosae), J. Mol. Evol., 46, 299, 1998.
49. Roalson, E.H. and Friar, E.A., Phylogenetic analysis of the nuclear alcohol dehydrogenase (Adh) gene family in Carex section Acrocystis (Cyperaceae) and combined analyses of Adh and nuclear ribosomal ITS and ETS sequences for inferring species relationships, Mol. Phyl. Evol., 33, 671, 2004.
50. Oh, S.-H. and Potter, D., Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rDNA and LEAFY, Amer. J. Bot., 92, 179, 2005.
51. Sytsma, K.J., et al., Urticalean rosids: circumscription, rosid ancestry, and phylogenetics based on rbcL, trnL-F and ndhF sequences, Amer. J. Bot., 89, 1531, 2002.
52. Soltis, D.E. and Soltis, P.S., Choosing an approach and an appropriate gene for phylogenetic analysis, in Molecular Systematics of Plants II: DNA Sequencing, Soltis, D.E., Soltis, P.S., and Doyle, J.J., Eds., Kluwer Academic, Dordrecht, 1998, 1.
53. Clegg, M.T., Cummings, M.P., and Durbin, M.L., The evolution of plant nuclear genes, Proc. Natl. Acad. Sci. USA, 94, 7791, 1997.
54. Mason-Gamer, R.J. and Kellogg, E.A., Potential utility of the nuclear gene waxy for plant phylogenetic analyses, Amer. J. Bot. (suppl.), 83, 178, 1996.
55. Mason-Gamer, R.J., Weil, C.F., and Kellogg, E.A., Granule-bound starch synthase: structure, function, and phylogenetic utility, Mol. Biol. Evol., 15, 1658, 1998.
56. Bailey, C.D. and Doyle, J.J., Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae, Mol. Phyl. Evol., 13, 20, 1999.
57. Wang, C.N., Moller, M., and Cronk, Q.C.B., Phylogenetic position of Titanotrichum oldhamii (Gesneriaceae) inferred from four different gene regions, Syst. Bot., 29, 407, 2004.
58. Grob, G.B.J., Gravendeel, B., and Eurlings, M.C.M., Potential phylogenetic utility of the nuclear FLORICAULA/LEAFY second intron: comparison with three chloroplast DNA regions in Amorphophallus (Araceae), Mol. Phyl. Evol., 30, 13, 2004.
59. Mathews, S., Lavin, M., and Sharrock, R.A., Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms, Ann. Missouri Bot. Gard., 82, 296, 1995.
60. Davis, C.C. et al., Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae, Proc. Natl. Acad. Sci. USA, 99, 6833, 2002.
61. Samuel, R. et al., Molecular phylogenetics of Phyllanthaceae: evidence from plastid matK and nuclear PHYC sequences, Amer. J. Bot., 92, 132, 2005.
62. Emshwiller, E. and Doyle, J.J., Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae), Mol. Phyl. Evol., 12, 310, 1999.
63. Morton, B.R., Gaut, B., and Clegg, M.T., Evolution of alcohol dehydrogenase gene in the palm and grass families, Proc. Natl. Acad. Sci. USA, 93, 11735, 1996.
64. Small, R.L. et al., The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group, Amer. J. Bot., 85, 1301, 1998.
65. Lewis, C.E. and Doyle, J.J., Phylogenetic utility of the nuclear gene malate synthase in the palm family (Arecaceae), Mol. Phyl. Evol., 19, 409, 2001.
66. Denton, A.L., Hall, B.D., and McConaughy, B.L., RPB2, a nuclear gene for tracing angiosperm phylogeny, Amer. J. Bot., 83 (suppl.), 150, 1996.
67. Oxelman, B. et al., RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids, Mol. Phyl. Evol., 32, 462, 2004.
68. Pfeil, B.E. et al., Paralogy and orthology in the Malvaceae RPB2 gene family: investigation of gene duplication in Hibiscus, Mol. Biol. Evol., 21, 1428, 2004.
69. Archambault, A. and Bruneau, A., Phylogenetic utility of the LEAFY/FLORICAULA gene in the Caesalpinioideae (Leguminosae): gene duplication and a novel insertion, Syst. Bot., 29, 609, 2004.
70. Vos, P. et al., AFLP: a new technique for DNA fingerprinting, Nucleic Acids Res., 23, 4407, 1995.
71. Li, G. and Quiros, C.F., Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica, Theor. Appl. Genet., 103, 455, 2001.
72. Koopman, W.J.M., Zevenbergen, M.J., and van den Berg, R.G., Species relationships in Lactuca s.l. (Lactuceae, Asteraceae) inferred from AFLP fingerprints, Amer. J. Bot., 88, 1881, 2001.
73. Hodkinson, T.R. et al., A comparison of ITS nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae), J. Pl. Res., 113, 259, 2000.
74. Hodkinson, T.R. et al., Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers, J. Pl. Res., 115, 381, 2002.
75. Hedrén, M., Fay, M.F., and Chase, M.W., Amplified fragment length polymorphisms (AFLP) reveal details of polyploid evolution in Dactylorhiza (Orchidaceae), Amer. J. Bot., 88, 1868, 2001.
76. Richardson, J.E. et al., Species delimitation and the origin of populations in island representatives of Phylica (Rhamnaceae), Evolution, 57, 816, 2003.
77. Lara-Cabrera, S.I. and Spooner, D.M., Taxonomy of North and Central American diploid wild potato (Solanum sect. Petota) species: AFLP data, Pl. Syst. Evol., 248, 129, 2004.
78. Parrish, T., Krakatau: genetic consequences of island colonization, Ph.D. thesis, University of Utrecht, Utrecht, 2002.
79. Parrish, T., personal communication, 2002.
80. Percy, D.M., Page, R.D.M., and Cronk, Q.C.B., Plant-insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations, Syst. Biol., 53, 120, 2004.
81. Weiblen, G.D. and Bush, G.L., Speciation in fig pollinators and parasites, Mol. Ecol., 11, 1573, 2002.
82. Hulsenbeck, J.P. and Ronquist, F., Mr Bayes: Bayesian inference of phylogeny, Bioinformatics, 17, 754, 2001.
83. Collinson, M.E., The fossil history of the Moraceae, Urticaceae (including Cecropiaceae), and Cannabaceae, in Evolution, Systematics, and Fossil History of the Hamamelidae Vol. 2: Higher Hamamelidae, Crane, P. and Blackmore, S., Eds., Clarendon Press, Oxford, The Systematics Association, 1989, 319.
84. Sanderson, M.J., A nonparametric approach to estimating divergence times in the absence of rate constancy, Mol. Biol. Evol., 14, 1218, 1997.
85. Sanderson, M.J., Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach, Mol. Biol. Evol., 19, 101, 2002.
86. Clarkson, J. et al., Phylogenetic relationships in Nicotiana based on multiple plastid loci, Mol. Phyl. Evol., 33, 75, 2004.
87. Doyle, J.J., Doyle, J.L., and Brown, A.H.D., Incongruence in the diploid B-genome species complex of Glycine (Leguminosae) revisited: histome H3-D alleles vs. chloroplast haplotypes, Mol. Biol. Evol., 16, 354, 1999.
88. Wendel, J.F., New world tetraploid cottons contain old world cytoplasms, Proc. Natl. Acad. Sci. USA, 86, 4132, 1989.
89. Chase, M.W. et al., Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae), Ann. Bot., 92, 107, 2003.
90. Clarkson, J. et al., Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae), New Phytol, 168, 241, 2005.
91. Clarkson, J. et al., unpublished data, 2005.
92. Goodspeed, T.H., The genus Nicotiana, Chronica Botanica Company, MA, USA, 1954.
93. Aoki, S, and Ito, M., Molecular phylogeny of Nicotiana (Solanaceae) based on the nucleotide sequence of the matK gene, Pl. Biol., 2, 316, 2000.
94. Pillon, Y. et al., Insights into the evolution and biogeography of western European species complexes in Dactylorhiza (Orchidaceae), Taxon, in press.
95. Barrier, M. et al., Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications, Mol. Biol. Evol., 16, 1105, 1999.
96. Cronn, R.C., Small, R.L., and Wendel, J.F., Duplicated genes evolve independently after polyploid formation in cotton, Proc. Natl. Acad. Sci. USA, 96, 14406, 1999.
97. Adams, K.L. et al., Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing, Proc. Natl. Acad. Sci. USA, 100, 4649, 2003.
98. Wendel, J.F., Genome evolution in polyploids, Pl. Mol. Biol., 42, 225, 2000.
99. Durbin, M.L. et al., Evolution of the chalcone synthetase gene family in the genus Ipomoea, Proc. Natl. Acad. Sci. USA, 92, 3338, 1995.
100. Huttley, G.A. et al., Nucleotide polmorphism in the chalcone synthase: a locus and evolution of the chalcone synthase multigene family of common morning glory, Ipomoea purpurea, Mol. Ecol., 6, 549, 1997.
101. Sperisen, C., Ryals, J., and Meins, F., Comparison of cloned genes provides evidence for intergenomic exchange of DNA in the evolution of a tobacco glucan endo-1,3-glucosidase gene family, Proc. Natl. Acad. Sci. USA, 88, 1820, 1991.
102. Linder, C.R. and Rieseberg, L.H., Reconstructing patterns of reticulate evolution in plants, Amer. J. Bot. 91, 1700, 2004.
103. Müntzing, A., Outlines to a genetic monograph of the genus Galeopsis, Hereditas, 13, 185, 1930.
104. Timberlake, J., unpublished data, 2005.
105. Barkman, T.J. and Simpson, B.B., Hybrid origin and parentage of Dendrochilum acuiferum (Orchidaceae) inferred in a phylogenetic context using nuclear and plastid DNA sequence data, Syst. Bot., 27, 209, 2002.