A duplication of gcyc predates divergence within tribe Coronanthereae (Gesneriaceae): Phylogenetic analysis and evolution

Plant Systematics and Evolution

Volumn 261, Issue 1-4, 2006, Pages 245-256

  Smith, J F ^a   Funke, M M ^a   Woo, V L ^b  

^a BOISE STATE UNIVERSITY   (United States)

^b VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

Author keywords

Coronanthereae; Floral symmetry; gcyc; Gesneriaceae; Paralogs; Phylogeny; Polyploidy

Indexed keywords

CORONANTHEREAE; GESNERIACEAE; GESNERIOIDEAE; SARMIENTA;

EID: 33750568005     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-006-0445-6     Document Type: Article

References (69)

1. S. Ahn S. D. Tanksley 1993 Comparative linkage maps of the rice and maize genomes Proc. Natl. Acad. Sci. USA 90 7980 7984
2. J. Almeida M. Rocheta L. Galego 1997 Genetic control of flower shape in Antirrhinum majus Development 124 1387 1392
3. The Angiosperm Phylogeny Group II. (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141: 399-436.
4. G. S. Bailey T. M. Poulter P. A. Stockwell 1978 Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci Proc. Natl. Acad. Sci. USA 75 5575 5579
5. D. A. Baum 1998 The evolution of plant development Curr. Opin. Pl. Biol. 1 79 86
6. D. A. Baum K. J. Sytsma P. C. Hoch 1994 A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences Syst. Bot. 19 363 388
7. J. P. Bielawski Z. Yang 2001 Positive and negative selection in the DAZ gene family Molec Biol. Evol. 18 523 529
8. B. L. Burtt 1963 Studies in the Gesneriaceae of the Old World. XXIV. Tentative keys to the tribes and genera Notes Roy. Bot. Gard. Edinb. 24 205 220
9. B. L. Burtt 1998 Climatic accomodations and phytogeography of the Gesneriaceae of the Old World P. Mathew M. Sivadasan Diversity and taxonomy of tropical flowering plants Mentor Books Calicut
10. B. L. Burtt 1999 Old World Gesneriaceae VI. Six miscellaneous notes Edinb. J. Bot. 56 371 379
11. B. L. Burtt H. Wiehler 1995 Classification of the family Gesneriaceae Gesneriana 1 1 4
12. H. L. Citerne M. Möller Q. C. B. Cronk 2000 Diversity of cycloidea-like genes in Gesneriaceae in relation to floral symmetry Ann. Bot. 86 167 176
13. E. S. Coen 1996 Floral symmetry EMBO Journal 15 6777 6788
14. Coen E. S., Nugent J. M. (1994) Evolution of flowers and inflorescences. Development Supplement: 107-116.
15. E. S. Coen J. M. Nugent D. Luo D. Bradley P. Cubas M. Chadwick L. Copsey R. Carpenter 1995 Evolution of floral symmetry Phil. Trans. Roy. Soc. London B 350 35 38
16. Q. C. B. Cronk 2002 Perspectives and paradigms in plant evo-devo Q. C. B. Cronk R. M. Bateman J. A. Hawkins Developmental genetics and plant evolution Taylor and Francis New York 1 14
17. Q. C. B. Cronk M. Möller 1997 Genetics of floral symmetry revealed Trends Ecol. Evol. 12 85 86
18. P. Cubas 2002 Role of TCP genes in the evolution of morphological characters in angiosperms Q. C. B. Cronk R. M. Bateman J. A. Hawkins Developmental genetics and plant evolution Taylor and Francis New York 247 266
19. P. Cubas E. Coen J. M. M. Zapater 2001 Ancient asymmetries in the evolution of flowers Curr. Biol. 11 1050 1052
20. P. Cubas C. Vincent E. Coen 1999 An epigenetic mutation responsible for natural variation in floral symmetry Nature 401 157 161
21. M. J. Donoghue R. H. Ree D. A. Baum 1998 Phylogeny and the evolution of flower symmetry in the Asteridae Trends Pl. Sci. 3 311 317
22. E. Emshwiller J. J. Doyle 1999 Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae) Molec Phylogenet Evol. 12 310 319
23. P. K. Endress 1997 Evolutionary biology of flowers: prospects for the next century K. Iwatuski P. H. Raven Evolution and diversification Springer Tokyo 99 119
24. J. Felsenstein 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach J. Molec. Evol. 17 368 376
25. J. Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791
26. A. C. M. Gillies P. Cubas E. S. Coen R. J. Abbott 2002 Q. C. B. Cronk R. M. Bateman J. A. Hawkins Developmental genetics and plant evolution Taylor and Francis New York 233 246
27. N. Goldman 1993 Statistical tests of models of DNA substitution J. Molec. Evol. 36 182 198
28. N. Goldman Z. Yang 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences Molec. Biol. Evol. 11 725 736
29. M. Hasegawa H. Kishino T. Yano 1985 Dating of the human-ape splitting by a molecular clock J. Molec. Evol. 22 160 174
30. T. Helentjaris D. Weber S. Wright 1988 Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms Genetics 118 353 363
31. L. C. Hileman D. A. Baum 2003 Why do paralogs persist? Molecular evolution of CYCLOIDEA and related floral symmetry genes in Antirrhineae (Veronicaceae) Molec. Biol. Evol. 20 591 600
32. L. C. Hileman E. M. Kramer D. A. Baum 2003 Differential regulation of symmetry genes and the evolution of novel floral morphologies Proc. Natl. Acad. Sci., USA 100 12814 12819
33. J. P. Huelsenbeck B. Rannala 1997 Phylogenetic methods come of age: testing hypotheses in an evolutionary context Science 276 227 232
34. J. P. Huelsenbeck F. Ronquist 2001 MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 754 755
35. D. Luo R. Carpenter C. Vincent L. Copsey E. Coen 1996 Origin of floral asymmetry in Antirrhinum Nature 383 794 799
36. D. Luo R. Carpenter L. Copsey C. Vincent J. Clark E. Coen 1999 Control of organ asymmetry in flowers of Antirrhinum Cell 99 367 376
37. D. R. Maddison W. P. Maddison 2000 MacClade 4.0: Analysis of phylogeny and character evolution. Version 4.0 Sinauer Associates Sunderland, Massachusetts
38. V. Mayer M. Möller M. Perret A. Weber 2003 Phylogenetic position and generic differentiation of Epithematae (Gesneriaceae) inferred from plastid DNA sequence data Amer. J. Bot. 90 321 329
39. M. Möller Q. C. B. Cronk 1997 Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences Amer. J. Bot. 84 956 965
40. M. Möller M. Clokie P. Cubas Q. C. B. Cronk 1999 Integrating molecular phylogenies and developmental genetics: a Gesneriaceae case study P. M. Hollingsworth R. M. Bateman R. J. Gornall Molecular systematics and plant evolution Taylor and Francis London 375 402
41. M. Nei A. K. Roychoudhury 1973 Probability of fixation of nonfunctional genes at duplicate loci Amer. Naturalist 107 362 372
42. S. Ohno 1970 Evolution by gene duplication Springer Heidelberg
43. T. Ohta 1988 Evolution by gene duplication and compensatory advantageous mutations Genetics 120 841 847
44. R. G. Olmstead J. D. Palmer 1994 Chloroplast DNA systematics: a review of methods and data analysis Amer. J. Bot. 81 1205 1224
45. M. Perret A. Chautems R. Spichiger G. Kite V. Savolainen 2003 Systematics and evolution of tribe Sinningieae (Gesneriaceae): evidence from phylogenetic analyses of six plastid DNA regions and nuclear ncpGS Amer. J. Bot. 90 445 460
46. D. Posada K. A. Crandall 1998 Modeltest: testing the model of DNA substitution Bioinformatics 14 817 818
47. P. A. Reeves R. G. Olmstead 1998 Evolution of novel morphological and reproductive traits in a clade containing Antirrhinum majus (Scrophulariaceae) Amer. J. Bot. 85 1047 1056
48. M. P. Running 1997 Making asymmetric flowers Curr. Biol. 7 R89 R91
49. M. P. Simmons H. Ochoterena 2000 Gaps as characters in sequence-based phylogenetic analyses Syst. Biol. 49 369 381
50. L. E. Skog 1984 A review of chromosome numbers in the Gesneriaceae Selbyana 7 252 273
51. J. F. Smith 1996 Tribal relationships within the Gesneriaceae: a cladistic analysis of morphological data Syst. Bot. 21 497 514
52. J. F. Smith 2000 An assessment of three data sets in phylogenetic analysis: Tribal relationships within the Gesneriaceae as a model Pl. Syst. Evol. 221 179 198
53. Smith J. F., Funke M. M. (2005) A molecular phylogenetic analysis of Coronantheroideae (Gesneriaceae). p. 166. XVII International Botanical Congress.
54. Smith J. F., Hileman L. C., Powell M., Baum D. A. (2004a) Evolution of gcyc, a Gesneriaceae homolog of CYCLOIDEA, within subfamily Gesnerioideae (Gesneriaceae). Molec. Phylogenet. Evol. 31: 765-779.
55. Smith J. F., Draper S. B., Hileman L. C., Baum D. A. (2004b) A phylogenetic analysis within tribes Gloxinieae and Gesnerieae (Gesnerioideae: Gesneriaceae). Syst. Bot. 29: 947-958.
56. J. F. Smith K. J. Sytsma J. S. Shoemaker R. L. Smith 1992 A qualitative comparison of total cellular DNA extraction protocols Phytochem. Bull. 23 2 9
57. J. F. Smith J. C. Wolfram K. D. Brown C. L. Carroll D. S. Denton 1997 Tribal relationships in the Gesneriaceae: Evidence from DNA sequences of the chloroplast gene ndhF Ann. Missouri Bot. Gard. 84 50 66
58. D. L. Swofford 2000 PAUP*Phylogenetic Analysis Using Parsimony (*and other methods). Vers. 10 Sinauer Associates Sunderland, Massachusetts
59. G. Theißen 2000 Evolutionary developmental genetics of floral symmetry: the revealing power of Linnaeus' monstrous flower BioEssays 22 209 213
60. J. B. Walsh 1995 How often do duplicated genes evolve new functions? Genetics 139 421 428
61. C.-N. Wang M. Möller Q. C. B. Cronk 2004 Phylogenetic position of Titanotrichum oldhamii (Gesneriaceae) inferred from four different gene regions Syst. Bot. 29 407 418
62. A. Weber 2004 Gesneriaceae K. Kubitzki The families and genera of vascular plants. Vol 7. Dicotyledons. Lamiales Springer Berlin
63. H. Wiehler 1983 A synopsis of the neotropical Gesneriaceae Selbyana 6 1 249
64. Z. Yang 1994 Estimating the pattern of nucleotide substitution J. Molec. Evol. 39 105 111
65. Z. Yang 1998 Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution Molec. Biol. Evol. 15 568 573
66. Z. Yang 2000 Phylogenetic analysis by maximum likelihood (PAML). Version 3.0 University College London London
67. Z. Yang R. Nielsen 1998 Synonymous and nonsynonymous rate variation in nuclear genes of mammals J. Molec. Evol. 46 409 418
68. Z. Yang N. Goldman A. Friday 1995 Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem Syst. Biol. 44 384 399
69. E. A. Zimmer E. H. Roalson L. E. Skog J. K. Boggan A. Indurm 2002 Phylogenetic relationships in the Gesnerioideae (Gesneriaceae) based on nrDNA ITS and cpDNA trnL-F and trnE-T spacer region sequences Amer. J. Bot. 89 296 311