More characters or more taxa for a robust phylogeny - Case study from the coffee family (Rubiaceae)

Systematic Biology

Volumn 48, Issue 3, 1999, Pages 413-435

  Bremer, Birgitta ^a   Jansen, Robert K ^b   Oxelman, Bengt ^a   Backlund, Maria ^a   Lantz, Henrik ^a   Kim, Ki Joong ^b,c  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c Yeungnam University   (South Korea)

Author keywords

Bootstrap; Morphology; ndhF; Phylogeny; rbcL; RFLP; Rubiaceae; Subfamilies; Support

Indexed keywords

APOCYNACEAE; ASTERACEAE; CINCHONOIDEAE; COPTOSAPELTA; IXOROIDEAE; LARDIZABALACEAE; LUCULIA; MAGNOLIOPHYTA; RUBIACEAE; RUBIOIDEAE; SAXIFRAGACEAE; SOLANACEAE;

PLANT DNA;

ARTICLE; CLASSIFICATION; COFFEE; GENETICS; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

COFFEE; DNA, PLANT; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

EID: 0033183681     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351599260085     Document Type: Article

References (87)

1. ALBERT, V. A., M. W. CHASE, AND B. D. MISHLER. 1993. Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Mo. Bot. Gard. 80:752-766.
2. ALLARD, M. W., AND J. M. CARPENTER. 1996. On weighting and congruence. Cladistics 12:183-198.
3. ANDERSSON, L. 1993. Pollen characteristics of the tribes Calycophylleae, Cinchoneae and Hillieae (Rubiaceae). Nord. J. Bot. 13:405-417.
4. ANDERSSON, L., AND C. PERSSON. 1991. Circumscription of the tribe Cinchoneae (Rubiaceae) - a cladistic approach. Plant Syst. Evol. 178:65-94.
5. ANDREASEN, K., B. G. BALDWIN, AND B. BREMER. 1999. Phylogenetic utility of the internal transcribed spacer of nuclear ribosomal DNA in the subfamily Ixoroideae (Rubiaceae). Plant Syst. Evol. 217:119-131.
6. ANDREASEN, K., AND B. BREMER. 1996. Phylogeny of the subfamily Ixoroideae (Rubiaceae). Opera Bot. Belg. 7:119-138.
7. ANNALS OF THE MISSOURI BOTANICAL GARDEN. 1995. Alternative genes for phylogenetic reconstruction in plants. Ann. Missouri Bot. Gard. 82(2).
8. ARNASON, U., A. GULLBERG, A. JANKE, AND X. XU. 1996. Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J. Mol. Evol. 43:650-661.
9. BACKLUND, M., B. OXELMAN, AND B. BREMER. 1999. Phylogenetic relationships within the Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae. Am. J. Bot. (in press).
10. BARRETT, M., M. J. DONOGHUE, AND E. SOBER. 1991. Against consensus. Syst. Zool. 40:486-493.
11. BARRETT, M., M. J. DONOGHUE, AND E. SOBER. 1993. Crusade? A reply to Nelson. Syst. Biol. 42:216-217.
12. BREMEKAMP, C. E. B. 1966. Remarks on the position, the delimitation and the subdivision of the Rubiaceae. Acta Bot. Neerl. 15:1-33.
13. BREMER, B. 1996a. Combined and separate analyses of morphological and molecular data in the plant family Rubiaceae. Cladistics 12:21-40.
14. BREMER, B. 1996b. Phylogenetic studies within Rubiaceae and relationships to other families based on molecular data. Opera Bot. Belg. 7:33-50.
15. BREMER, B., K. ANDREASEN, AND D. OLSSON. 1995. Subfamilial and tribal relationships in the Rubiaceae based on rbcL sequence data. Ann. Mo. Bot. Gard. 82:383-397.
16. BREMER, B., AND R. K. JANSEN. 1991. Comparative restriction site mapping of the chloroplast DNA implies new phylogenetic relationships within the Rubiaceae. Am. J. Bot. 78:198-213.
17. BREMER, K., R. K. JANSEN, P. O. KARIS, M. KÄLLERSJÖ, AND S. C. KEELEY. 1992. A review of the phylogeny and classification of the Asteraceae. Nord. J. Bot. 12:141-148.
18. BREMER, B., AND L. STRUWE. 1992. Phylogeny of the Rubiaceae and the Loganiaceae: Congruence or conflict between morphological and molecular data? Am. J. Bot. 79:1171-1184.
19. BREMER, B., AND M. THULIN. 1998. Collapse of Isertieae, re-establishment of Mussaendeae, and a new genus of Sabiceeae (Rubiaceae): Phylogenetic relationships based on rbcL data. Plant Syst. Evol. 211:71-92.
20. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDELL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
21. CHASE, M. W., AND J. D. PALMER. 1989. Chloroplast DNA systematics of lilioid monocots: Resources, feasibility, and an example from the Orchidaceae. Am. J. Bot. 76:1720-1730.
22. CHASE, M. W., D. E. SOLTIS, R. G. OLMSTEAD, D. MORGAN, D. H. LES, B. D. MISHLER, M. R. DUVALL, R. A. PRICE, H. G. HILLS, Y.-L. QIU, K. A. KRON, J. H. RETTIG, E. CONTI, J. D. PALMER, J. R. MANHART, K. J. SYTSMA, H. J. MICHAELS, W. J. KRESS, K. G. KAROL, W. D. CLARK, M. HEDRÉN, B. S. GAUT, R. K. JANSEN, K. J. KIM, C. F. WIMPEE, J. F. SMITH, G. R. FURNIER, S. H. STRAUSS, Q. XIANG, G. M. PLUNKETT, P. S. SOLTIS, S. SWENSEN, S. E. WILLIAMS, P. A. GADEK, C. J. QUINN, L. E. EGUIARTE, E. GOLDENBERG, G. H. J. LEARN, S. W. GRAHAM, S. C. H. BARRETT, S. DAYANANDAN, AND V. A. ALBERT. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mo. Bot. Gard. 80:528-581.
23. CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
24. DE JUSSIEU, A. L. 1789. Genera plantarum. Viduam Herissant, Paris.
25. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
26. DOEBLEY, J., M. DURBIN, E. GOLDBERG, M., M. T. CLEGG, AND D. P. MA. 1990. Evolutionary analysis of the large subunit of carboxylas (rbcL) nucleotide sequence among the grasses (Gramineae). Evolution 44:1097-1108.
27. DOWNIE, S. R., D. S. KATZ-DOWNIE, AND K. J. CHO. 1997. Relationships in the Caryophyllales as suggested by phylogenetic analyses of partial chloroplast DNA ORF2280 homologue sequences. Am. J. Bot. 84:253-273.
28. DOYLE, J. J., J. L. DOYLE, J. A. BALLENGER, E. E. DICKSON, T. KAJITA, AND H. OHASHI. 1997. A phylogeny of the chloroplast gene rbcL in the Leguminosae: Taxonomic correlations and insights into the evolution of nodulation. Am. J. Bot. 84:541-554.
29. EERNISSE, D. J., AND A. G. KLUGE. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10:1170-1195.
30. ENDRESS, M. E., B. SENNBLAD, S. NILSSON, L. CIVEYREL, M. W. CHASE, S. HUYSMANS, E. GRAFSTRÖM, AND B. BREMER. 1996. A phylogenetic analysis of Apocynaceae s. str. and some related taxa in Gentianales: A multidisciplinary approach. Opera Bot. Belg. 7:59-102.
31. FARRIS, J. S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18:374-385.
32. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
33. FERNHOLM, B., K. BREMER, AND H. JÖRNVALL, eds. 1989. The hierarchy of life - molecules or morphology in phylogenetic analysis. Excerta Medica, Amsterdam.
34. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem. Syst. Biol. 47:9-17.
35. GIVNISH, T. J., AND SYTSMA, K. J. 1997. Homoplasy in molecular vs. morphological data: The likelihood of correct phylogenetic inference. Pages 55-101 in Molecular evolution and adaptive radiation. (T. J. Givnish, and K. J. Sytsma, eds.) Cambridge University Press, Cambridge, England.
36. HILLIS, D. M. 1987. Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18:23-42.
37. HILLIS, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
38. HOLM, S. 1979. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6:65-70.
39. HOLMGREN, P. K., N. H. HOLMGREN, AND L. C. BARNETT. 1990. Index herbariorum, 8th ed. New York Botanical Garden, New York.
40. HOOT, S. B., A. CULHAM, AND P. R. CRANE. 1995. The utility of atpB gene sequences in resolving phylogenetic relationships: Comparisons with rbcL and 18S ribosomal DNA sequences in the Lardizabalaceae. Ann. Mo. Bot. Gard. 82:194-207.
41. IGERSHEIM, A. 1993. The character states of the caribbean monotypic endemic Strumpfia (Rubiaceae). Nord. J. Bot. 13:545-559.
42. JANSEN, R. K., AND J. D. PALMER. 1987. A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84:5818-5822.
43. JANSEN, R. K., J. L. WEE, AND D. MILLIE. 1998. Comparative utility of chloroplast restriction site and DNA sequence data for phylogenetic studies in plants. Pages 87-100. Molecular systematics of plants, 2nd ed. In D. Soltis, P. Soltis, and J. Doyle, (eds.), Chapman and Hall: New York.
44. JOHNSON, L. A., J. L. SCHULTZ, D. E. SOLTIS, AND P. S. SOLTIS. 1996. Monophyly and generic relationships of Polemoniaceae based on matK sequences. Am. J. Bot. 83:1207-1224.
45. JOHNSON, L. A. AND D. E. SOLTIS. 1995. Phylogenetic interference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK. sequences. Ann. Mo. Bot. Gard. 82:149-175.
46. KÄLLERSJÖ, M., J. S. FARRIS, M. W. CHASE, B. BREMER, M. F. FAY, C. J. HUMPHRIES, G. PETERSEN, O. SEBERG, AND K. BREMER. 1998. Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants. Plant Syst. Evol. 213:259-287.
47. KIM, J. 1998. Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47:43-60.
48. KIM, K. J., AND R. K. JANSEN. 1995. ndhF sequence evolution and the major clades in the sunflower family. Proc. Natl. Acad. Sci. USA 92:10379-10383.
49. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
50. KLUGE, A. G., AND A. J. WOLF. 1993. Cladistics: What's in a word? Cladistics 9:183-199.
51. MANEN, J.-F., AND A. NATALI. 1996. The chloroplast atpB-rbcL spacer in Rubiaceae. Opera Bot. Belg. 7:51-57.
52. MIYAMOTO, M. M. 1983. Frogs of the Eleutherodactylus rugulosus group: A cladistic study of allozyme, morphological, and karyological data. Syst. Zool. 32:109-124.
53. MIYAMOTO, M. M. 1985. Consensus cladograms and general classifications. Cladistics 1:186-189.
54. MIYAMOTO, M. M., AND W. M. FITCH. 1995. Testing species phylogeny and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
55. MORGAN, D. R., AND D. E. SOLTIS. 1993. Phylogenetic relationships among members of Saxifragaceae sensu lato based on rbcL sequence data. Ann. Mo. Bot. Gard. 80:631-660.
56. NADOT, S., G. BITTAR, L. CARTER, R. LACROIX, AND B. LEJEUNE. 1995. A phylogenetic analysis of Monocotyledons based on the chloroplast gene rps4, using parsimony and a new numerical phenetic method. Mol. Phylogenet. Evol. 4:257-282.
57. NATALI, A., J.-F. MANEN, AND F. EHRENDORFER. 1996. Tribal, generic and specific relationships in the Rubioideae-Rubieae (Rubiaceae) based on sequence data of the cpDNA intergene spacer. Opera Bot. Belg. 7:193-203.
58. NELSON, G. 1993. Why crusade against consensus? A reply to Barrett, Donoghue, and Sober. Syst. Biol. 42:215-216.
59. NICKRENT, D. L., AND D. E. SOLTIS. 1995. A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann. Mo. Bot. Gard. 82:208-234.
60. OLMSTEAD, R. G., B. BREMER, K. M. SCOTT, AND J. D. PALMER. 1993. A parsimony analysis of the Asteridae sensu lato based on rbcL sequences. Ann. Mo. Bot. Gard. 80:700-722.
61. OLMSTEAD, R. G., AND J. D. PALMER. 1994. Chloroplast DNA systematics: A review of methods and data analysis. Am. J. Bot. 81:1205-1224.
62. OLMSTEAD, R. G., AND P. A. REEVES. 1995. Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences. Ann. Mo. Bot. Gard. 82:176-193.
63. OLMSTEAD, R. G., AND J. A. SWEERE. 1994. Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. 43:467-481.
64. PAGE, R. D. M. 1996. On consensus, confidence, and "total evidence." Cladistics 12:83-92.
65. PATTERSON, C. 1987. Molecules and morphology in evolution: Conflict or compromise. Cambridge University Press, Cambridge.
66. POE, S., AND SWOFFORD, D. L. 1999. Taxon sampling revisited. Nature 398:299-300.
67. RICE, E. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
68. ROBBRECHT, E. 1988. Tropical woody Rubiaceae. Opera Bot. Belg. 1:1-271.
69. ROBBRECHT, E. 1993. Supplement to the 1988 outline of the classification of the Rubiaceae Index to genera. Opera Bot. Belg. 6:173-196.
70. ROBBRECHT, E., AND C. PUFF. 1986. A survey of the Gardenieae and related tribes (Rubiaceae). Bot. Jahrb. Syst., Pflanzengesch. Pflanzengeog. 108:63-137.
71. SANDERSON, M. J. 1989. Confidence limits on phylogenies: The bootstrap revisited. Cladistics 5:113-129.
72. SANDERSON, M. J., AND M. J. DONOGHUE. 1989. Patterns of variation in level of homoplasy. Evolution 43:1781-1795.
73. SCHUMANN, K., ed. 891. Rubiaceae. Die natürlichen Pflanzenfamilien 4 (4). Wilhelm Engelmann, Leipzig, Germany.
74. SENNBLAD, B., AND B. BREMER. 1996. The familial and subfamilial relationships of Apocynaceae and Asclepiadaceae evaluated with rbcL data. Plant Syst. Evol. 202:153-175.
75. SMITH, J. F. 1996. Tribal relationships within Gesneriaceae: A cladistic analysis of morphological data. Syst. Bot. 21:497-513.
76. SMITH, J. F., W. J. KRESS, AND E. A. ZIMMER. 1993. Phylogenetic analysis of the Zingiberales based on rbcL sequences. Ann. Mo. Bot. Gard. 80:620-630.
77. SOKAL, R. R., AND K. SHAO. 1985. Characters stability in 39 data sets. Syst. Zool. 34:83-89.
78. SOLTIS, D. E., P. S. SOLTIS, M. T. CLEGG, AND M. DURBIN. 1990. rbcL sequence divergence and phylogenetic relationships in Saxifragaceae sensu lato. Proc. Natl. Acad. Sci. USA 87:4640-4644.
79. SOLTIS, D. E., Q.-Y. XIANG, AND L. HUFFORD. 1995. Relationships and evolution of Hydrangeaceae based on rbcL sequence data. Am. J. Bot. 82:504-514.
80. SOUZA-CHIES, T. T., G. BITTAR, S. NADOT, L. CARTER, E. BESIN, AND B. LEJEUNE. 1997. Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Syst. Evol. 204:109-123.
81. STEVENS, P. 1997. How to interpret botanical classifications - suggestions from history. BioScience 47:243-250.
82. SWOFFORD, D. L. 1993. PAUP: Phylogenetic Analysis Using Parsimony. Version 3.1.1. Computer program. Illinois Natural History Survey, Champaign.
83. SYTSMA, K. J. 1990. DNA and morphology: Inference of plant phylogeny. Trends Ecol. Evol. 5:104-110.
84. SYTSMA, K. J., AND B. A. SCHAAL. 1985. Phylogenetics of the Lisianthus skinneri (Gentianaceae) species complex in Panama using DNA restriction fragment analysis. Evolution 37:594-608.
85. VERDCOURT, B. 1958. Remarks on the classification of the Rubiaceae. Bull. Jard. Bot. l'État 28:209-281.
86. WAGSTAFF, S. J., AND R. G. OLMSTEAD. 1997. Phylogeny of Labiateae and Verbenaceae inferred from rbcL sequences. Syst. Bot. 22:165-177.
87. WILSON, M. A., B. GAUT, AND M. T. CLEGG. 1990. Chloroplast DNA evolves slowly in the palm family (Arecaceae). Mol. Biol. Evol. 7:303-314.