Phylogenetic signal common to three data sets: Combining data which initially appear heterogeneous

Plant Systematics and Evolution

Volumn 221, Issue 3-4, 2000, Pages 179-198

  Smith, James F ^a  

^a BOISE STATE UNIVERSITY   (United States)

Author keywords

Congruence; Gesneriaceae; Morphology; NdhF; Phylogeny; RbcL

Indexed keywords

EMBRYOPHYTA; GESNERIACEAE;

EID: 0033934242     PISSN: 03782697     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF01089293     Document Type: Article

References (93)

1. Adams E. N. (1972) Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390-397.
2. The Angiosperm Phylogeny Group. (1998) An ordinal classification for the families of flowering plants. Ann. Missouri Bot. Gard. 85: 531-553.
3. Ballard J. W. O., Thayer M. K., Newton Jr. A. F., Grismer E. R. (1998) Data sets, partitions, and characters: philosophies and procedures for analyzing multiple data sets. Syst. Biol. 47: 367-396.
4. Barrett M., Donoghue M. J., Sober E. (1991) Against consensus. Syst. Zool. 40: 486-493.
5. Bentham G. (1876) Gesneriaceae. In: Hooker J. D. (ed.). Genera Plantarum, G. Bentham, pp. 990-1025.
6. Boggan J. K. (1991) A morphological study and cladistic analysis of Sinningia and associated genera with particular reference to Lembocarpus, Lietzia, Paliavana, and Vanhouttea (Gesneriaceae: Gloxinieae) M. S. thesis, Cornell University, Ithaca, NY.
7. Bremer B. (1996) Combined and separate analysis of morphological and molecular data in the plant family Rubiaceae. Cladistics 12: 21-40.
8. Bremer K. (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803.
9. Bremer K. (1990) Compatible component consensus. Cladistics 6: 369-372.
10. Bremer K. (1994) Branch support and tree stability. Cladistics 10: 295-304.
11. Brower A. V. Z., DeSalle R., Vogler A. (1996) Gene trees, species trees, and systematics: A cladistic perspective. Annu. Rev. Ecol. Syst. 27: 423-450.
12. Bull J. J., Huelsenbeck J. P., Cunningham C. W., Swofford D. L., Waddell P. J. (1993) Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42: 384-397.
13. Burtt B. L. (1962) Studies in the Gesneriaceae of the Old World XXIV: Tentative keys to the tribes and genera. Notes Roy. Bot. Gard., Edinburgh 24: 205-220.
14. Burtt B. L. (1977) Classification above the genus, as exemplified by Gesneriaceae, with parallels from other groups. Plant Syst. Evol., Suppl. 1: 97-109.
15. Burtt B. L., Wiehler H. (1995) Classification of the family Gesneriaceae. Gesneriana 1: 1-A.
16. Chase M. W., Soltis D. E., Olmstead R. G., Morgan D., Les D. H., Mishler B. D., Duvall M. R., Price R. A., Hills H. G., Qiu Y-L., Kron K. A., Rettig J. H., Conti E., Palmer J. D., Manhart J. R., Sytsma K. J., Michaels H. J., Kress W. J., Karol K. G., Clark W. D., Hedren M. B., Gaut S., Jansen R. K., Kim K-J., Wimpee C. F., Smith J. F., Furnier G. R., Strauss S. H., Xiang Q-Y., Plunkett G. M., Soltis P. S., Williams S. E., Gadek P. A., Quinn C. J., Eguiarte L. E., Golenberg E., Learn G. H., Graham S. W., Barrett S. C. H., Dayanandan S., Albert V. A. (1993) Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard. 80: 528-580.
17. Chase M. W., Cox A. V., Soltis D. E., Soltis P. S., Mort M. E., Savolainen V., Reeves G., Hoot S. B., Morton C. M. (1997) Large DNA sequence matrices, phylogenetic signal, and feasibility: an empirical approach. Amer. J. Bot. 84: 181.
18. Crisci J. V., Cigliano M. M., Morrone J. J., Roig-Juent S. (1991) Historical biogeography of southern South America. Syst. Zool. 40: 152-171.
19. Cronquist A. (1981) An integrated system of classification of flowering plants. Columbia University Press, New York.
20. Day W. H. E., Estabrook G. F., McMorris F. R. (1998) Measuring the phylogenetic randomness of biological data sets. Syst. Biol. 47: 604-616.
21. Donoghue M. J. (1994) Progress and prospects in reconstructing plant phylogeny. Ann. Missouri Bot. Gard. 81: 405-418.
22. Donoghue M. J., Olmstead R. G., Smith J. F., Palmer J. D. (1992) Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Missouri Bot. Gard. 79: 333-345.
23. Doyle J. J. (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot. 17: 144-163.
24. Eernisse D. J., Kluge A. J. (1993) Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10: 1170-1195.
25. Faith D. P. (1991) Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40: 366-375.
26. Farris S. J. (1970) Methods for computing Wagner trees. Syst. Zool. 19: 83-92.
27. Farris S. J., Kluge A. G., Eckardt M. J. (1970) A numerical approach to phylogenetic systematics. Syst. Zool. 19: 172-191.
28. Farris S. J., Källersjö M., Kluge A. G., Bult C. (1994a) Permutations. Cladistics 10: 65-76.
29. Farris S. J., Källersjö M., Kluge A. G., Bult C. (1994b) Testing significance of incongruence. Cladistics 10: 315-319.
30. Felsenstein J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
31. Fritsch K. (1893-1894) Gesneriaceae. In: A. Engler & K. Prantl. Die Natürlichen Pflanzenfamilien Vol. 4(3b). Leipzig: Wilhelm Engelmann, pp. 133-185.
32. Givnish T. J., Sytsma K. J. (1997a) Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference. In: Givnish T. J., Sytsma K. J. (eds.) Molecular Evolution and Adaptive Radiation. Cambridge University Press, New York, pp. 55-101.
33. Givnish T. J., Sytsma K. J. (1997b) Consistency, characters, and the likelihood of correct phylogenetic inference. Mol. Phyl. Evol. 7: 320-330.
34. Graham S. W., Kohn J. R., Morton B. R., Eckenwalder J. E., Barrett S. C. H. (1998) Phylogenetic congruence and discordance among one morphological and three molecular data sets from Pontederiaceae. Syst. Biol. 47: 545-567.
35. Heywood V. H. (1978) Flowering Plants of the World. Prentice Hall, Englewood Cliffs, NJ.
36. Hillis D. M., Huelsenbeck J. P. (1992) Signal, noise, and reliability in molecular phylogenetic analyses. J. Heredity 83: 189-195.
37. Huelsenbeck J. P., Hillis D. M. (1993) Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42: 247-264.
38. Huelsenbeck J. P., Bull J. J., Cunningham C. W. (1996) Combining data in phylogenetic analysis. Trends Ecol. Evol. 11: 152-158
39. Innis M. A., Myambo K. B., Gelfand D. H., Brow M. A. D. (1988) DNA sequencing and direct sequencing of polymerase chain reaction-amplified DNA. Proc. Natl. Acad. Sci., USA 85: 9436-9440.
40. Ivanina L. I. (1965) Application of the carpological method to the taxonomy of Gesneriaceae. Notes Roy. Bot. Gard., Edinburgh 26: 383-402.
41. Johnson L. A., Soltis D. E. (1998) Assessing congruence: empirical examples from molecular data. In: Soltis D. E., Soltis P. S., Doyle J. J. (eds.) Molecular Systematics of Plants II DNA Sequencing. Kluwer Academic Publishers, Norwell Massachusetts, pp. 297-328.
42. Källersjö M., Farris J. S., Kluge A. G., Bult C. (1992) Skewness and permutation. Cladistics 8: 275-287.
43. Kim K.-J., Jansen R. K. (1994) Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Plant Syst. Evol. 190: 157-185.
44. Kluge A. G. (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38: 7-25.
45. Kress W. J. (1986) The systematic distribution of vascular epiphytes: an update. Selbyana 9: 2-22.
46. Kvist L. P. (1990) Revision of Heppiella (Gesneriaceae). Syst. Bot. 15: 720-735.
47. Lavin M. (1993) Biogeography and systematics of Poitea (Leguminosae). Syst. Bot. Monogr. 37: 1-87.
48. Lutzoni F. M. (1997) Phylogeny of liehen- and non-lichen-forming Omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Syst. Biol. 46: 373-406.
49. Madison M. (1977) Vascular epiphytes: their systematic occurrence and salient features. Selbyana 2: 1-13.
50. Maddison D. R. (1991) The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 40: 315-328.
51. Mason-Gamer R. J., Kellogg E. A. (1996) Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae. Syst. Biol. 45: 524-545.
52. Miyamoto M. M. (1981) Congruence among character sets in phylogenetic studies of the frog genus Leptodactylus. Syst. Zool. 30: 281-290.
53. Miyamoto M. M., Fitch W. M. (1995) Testing species phytogenies and phylogenetic methods with congruence. Syst. Biol. 44: 64-76.
54. Möller M., Cronk Q. C. B. (1997) Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences. Amer. J. Bot. 84: 956-965.
55. Munro S. L., Linder H. P. (1998) The phylogenetic position of Prionium (Juncaceae) within the order Juncales based on morphological and rbcL sequence data. Syst. Bot. 23: 43-56.
56. Neigel J. E., Avise J. C. (1986) Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In: Karlin S., Nevo E. (eds.) Evolutionary processes and theory. Academic Press, New York, pp. 515-534.
57. Nelson G. (1979) Cladistic analysis and synthesis: principles and definitions with a historical note on Adanson's Famille des Plantes (1763-1764). Syst. Zool. 28: 1-21.
58. Olmstead R. G., Palmer J. D. (1994) Chloroplast DNA systematics: A review of methods and data analysis. Amer. J. Bot. 81: 1205-1224.
59. Olmstead R. G., Sweere J. A. (1994) Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. 43: 467-481.
60. Olmstead R. G., Reeves P. A. (1995) Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences. Ann. Missouri Bot. Gard. 82: 176-193.
61. Olmstead R. G., Bremer B., Scott K. M., Palmer J. D. (1993). A parsimony analysis of the Asteridae Sensu Lato based on rbcL sequences. Ann. Missouri Bot. Gard. 80: 700-722.
62. Olmstead R. G., Michaels H. J., Scott K. M., Palmer J. D. (1992). Asteridae monophyly and major lineages of Asteridae inferred from rbcL sequences. Ann. Missouri Bot. Gard. 79: 249-265.
63. Pennington R. T. (1996) Molecular and morphological data provide phylogenetic resolution at different hierarchical levels in Andira. Syst. Biol. 45: 496-515.
64. Poe S. (1996) Data set incongruence and the phylogeny of Crocodilians. Syst. Biol. 45: 393-414.
65. Rieseberg L. H., Brunsfeld S. J. (1992) Molecular evidence and plant introgression. In: Soltis P. S., Soltis D. E., Doyle J. J. (eds.) Molecular systematics of plants. Chapman and Hall New York, pp. 151-176.
66. Rodman J. E., Soltis P. S., Soltis D. E., Sytsma K. J., Karol K. G. (1998) Parallel evolution of glucosinolate biosynthesis inferred from congruent nuclear and plastid gene phylogenies. Amer. J. Bot. 85: 997-1006.
67. Rodrigo A. G., Kelly-Borges M., Bergquist P. R., Bergquist P. L. (1993) A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N. Z. J. Bot. 31: 257-268.
68. Sanderson M. J. (1989) Confidence limits in phylogenies: the bootstrap revisited. Cladistics 5: 113-129.
69. Sanderson M. J., Donoghue M. J. (1989) Patterns of variation in levels of homoplasy. Evolution 43: 1781-1795.
70. Sanderson M. J., Donoghue M. J. (1996) The relationship between homoplasy and confidence in a phylogenetic tree. In: Sanderson M. J., Hufford L. (eds.) Homoplasy: The recurrence of similarity in evolution. Academic Press, San Diego, pp. 67-90.
71. Seelanen T., Schnabel A., Wendel J. F. (1997) Congruence and consensus in the cotton tribe (Malvaceae) Syst. Bot. 22: 259-290.
72. Smith J. F. (1996) Tribal relationships within the Gesneriaceae: A cladistic analysis of morphological data. Syst. Bot. 21: 497-514.
73. Smith J. F., Sytsma K. J. (1994a) Evolution in the Andean epiphytic genus Columnea (Gesneriaceae): Part I. morphological variation. Syst. Bot. 19: 220-235.
74. Smith J. F., Sytsma K. J. (1994b) Evolution in the Andean epiphytic genus Columnea (Gesneriaceae): Part II. chloroplast DNA restriction site variation. Syst. Bot. 19: 317-336.
75. Smith J. F., Sytsma K. J. (1994c) Molecules and morphology: congruence of data in Columnea (Gesneriaceae). Plant Syst. Evol. 194: 37-52.
76. Smith J. F., Carroll C. L. (1997) Phylogenetic relationships of the Episcieae (Gesneriaceae) based on ndhF sequences. Syst. Bot. 22: 713-724.
77. Smith J. F., Atkinson S. (1998) Phylogenetic analysis of the tribes Gloxinieae and Gesnerieae (Gesneriaceae): Data from ndhF Sequences. Selbyana 19: 122-131.
78. Smith J. F., Sytsma K. J., Shoemaker J. S., Smith R. L. (1992) A qualitative comparison of total cellular DNA extraction protocols. Phytochem. Bull. Bot. Soc. Amer. 23: 2-9.
79. Smith J. F., Kress W. J., Zimmer E. A. (1993) Phylogenetic analysis of the Zingiberales based on rbcL sequences. Ann. Missouri Bot. Gard. 80: 620-630.
80. Smith J. F., Wolfram J. C., Brown K. D., Carroll C. L., Denton D. S. (1997a) Tribal relationships in the Gesneriaceae: Evidence from DNA sequences of the chloroplast gene ndhF. Ann. Missouri Bot. Gard. 84: 50-66.
81. Smith J. F., Brown K. D., Carroll C. L., Denton D. S. (1997b) Familial placement of Cyrtandromoea, Titanotrichum, and Sanango: Three problematic genera of the Lamiales. Taxon 46: 65-74.
82. Smith J. F., Kresge M., Möller M., Cronk Q. C. B. (1998) The African violets (Saintpaulia) are members of Streptocarpus subgenus Streptocarpella (Gesneriaceae): Combined evidence from chloroplast and nuclear ribosomal genes. Edin. J. Bot. 55: 1-11.
83. Soltis D. E., Soltis P. S., Collier T. G., Edgerton M. L. (1991) Chloroplast DNA variation within and among genera of the Heuchera group (Saxifragaceae); Evidence for chloroplast transfer and paraphyly. Amer. J. Bot. 78: 1091-1112.
84. Soltis D. E., Soltis P. S., Chase M. W., Mort M. E., Savolainen V., Hoot S., Morton C. M. (1997) Inferring complex phylogenies: an empirical approach using three large DNA data sets for angiosperms. Amer. J. Bot. 84: 232.
85. Soltis D. E., Soltis P. S., Mort M. E., Chase M. W., Savolainen V., Hoot S. B., Morton C. M. (1998) Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms. Syst. Biol. 47: 32-42.
86. Steele K. P., Vilgalys R. (1994) Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene mat K. Syst. Bot. 19: 126-142.
87. Swofford D. L. (1991) When are phylogeny estimates from molecular and morphological data incongruent? In: Miyamoto M. M., Cracraft J. (eds.) Phylogenetic analysis of DNA sequences. Oxford University Press, New York, pp. 295-333.
88. Swofford D. L. (1993) PAUP: Phylogenetic analysis using parsimony, version 3.1.1 Computer program distributed by the Illinois Natural History Survey, Champaign, Illinois.
89. Swofford D. L., Maddison W. P. (1987) Reconstructing ancestral character states under Wagner parsimony. Math. Biosci. 87: 199-229.
90. Sytsma K. J. (1990) DNA and morphology: inference of plant phylogeny. Trends Ecol. Evol. 5: 104-110.
91. Wendel J. F., Doyle J. J. (1998) Phylogenetic incongruence: window into genome history and molecular evolution. In: Soltis D. E., Soltis P. S., Doyle J. J. (eds.) Molecular Systematics of Plants II DNA Sequencing. Kluwer Academic Publishers, Norwell Massachusetts, pp. 265-296.
92. Wiehler H. (1983) A synopsis of the neotropical Gesneriaceae. Selbyana 6: 1-249.
93. Wiens J. J. (1998) Combining data sets with different phylogenetic histories. Syst. Biol. 47: 568-581.