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 Systematics and Evolution

Volumn 213, Issue 3-4, 1998, Pages 259-287

  Källersjö, Mari ^a   Farris, James S ^a   Chase, Mark W ^b   Bremer, Birgitta ^c   Fay, Michael F ^b   Humphries, Christopher J ^d   Petersen, Gitte ^e   Seberg, Ole ^e   Bremer, Kåre ^c  

^a SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^b JODRELL LABORATORY   (United Kingdom)

^c UPPSALA UNIVERSITY   (Sweden)

^d DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

DNA sequences; Flowering plants; Green plants; Land plants; Large data sets; Parsimony jackknifing; Phylogenetic analysis; rbcL; Seed plants

Indexed keywords

CYANOBACTERIA; EMBRYOPHYTA; LILIOPSIDA; MAGNOLIOPHYTA; SPERMATOPHYTA; VIRIDIPLANTAE;

EID: 0032420129     PISSN: 03782697     EISSN: None     Source Type: Journal    
DOI: 10.1007/bf00985205     Document Type: Article

References (65)

1. ALBERT, V. A., WILLIAMS, S. E., CHASE, M. W., 1992: Carnivorous plants: phylogeny and structural evolution. - Science 257: 1491-1495.
2. _ BACKLUND, A., BREMER, K., CHASE, M. W., MANHART, J., MISHLER, B. D., NIXON, K. C., 1994: Functional history and rbcL evidence for land plant phylogeny. - Ann. Missouri Bot. Gard. 81: 534-567.
3. ALVERSON, W. S., KAROL, K. G., BAUM, D.A., CHASE, M. W., SWENSEN, S. M., MCCOURT, R., SYTSMA, K. J., 1998: Circumscription of the Malvales and relationship to other Rosidae: evidence from rbcL sequence data. - Amer. J. Bot. (in press).
4. ANDERBERG, A. A., STÅHL, B., KÄLLERSJÖ, M., 1998: Phylogenetic interrelationships in the Primulales inferred from rbcL sequence data. - Pl. Syst. Evol. 211: 93-102.
5. BACKLUND, A., BREMER, B., 1998: Phylogeny of the Asteridae s.str. based on rbcL sequences, with particular reference to the Dipsacales. - Pl. Syst. Evol. 207: 225-254.
6. BAYER, C., CHASE, M. W., FAY, M. F., 1998: Muntingiaceae, a new family of dicotyledons with malvalean affinities. - Taxon 47: 37-42.
7. BREMER, B., 1996: Phylogenetic studies within Rubiaceae and relationships to other families based on molecular data. - Opera Bot. Belg. 7: 33-50.
8. BREMER, K., 1985: Summary of green plant phylogeny and classification. - Cladistics 1: 369-385.
9. _ 1988: The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. - Evolution 42: 795-803.
10. _ 1994: Branch support and tree stability. - Cladistics 10: 295-304.
11. CHASE, M. W., SOLTIS, D. E., OLMSTEAD, R. G., MORGAN, D., LES, D. H., MISHLER, B. D., DUVALL, M. R., PRICE, R. Q., 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., HEDRÉN, M., GAUT, B. 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., SWENSEN S., WILLIAMS, S. E., GADEK, P. A., QUINN, C. J., EGUIARTE, L. E., GOLENBERG, E., LEARN, G. H., Jr., 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.
12. _ DUVALL, M. R., HILLS, H. G., CONRAN, J. G., COX, A. V., EGUIARTE, L. E., HARTWELL, J., FAY, M. F., CADDICK, L. R., CAMERON, K. M., HOOT, S., 1995a: Molecular phylogenetics of Lilianae. - In RUDALL, P. J., CRIBB, P. J., CUTLER, D. F., HUMPHRIES, C. J., (Eds): Monocotyledons: systematics and evolution, pp. 109-137. - Richmond: Royal Botanic Gardens, Kew.
13. _ STEVENSON, D. W., WILKIN, P., RUDALL, P. J., 1995b: Monocot systematics: a combined analysis. - In RUDALL, P. J., CRIBB, P. J., CUTLER, D. F., HUMPHRIES, C. J., (Eds): Monocotyledons: systematics and evolution, pp. 685-730. - Richmond: Royal Botanic Gardens, Kew.
14. _ RUDALL, P. J., CONRAN, J. G., 1996: New circumscriptions and a new family of asparagoid lilies: genera formerly included in Anthericaceae. - Kew Bull. 51: 667-680.
15. CONTI, E., LITT, A., SYTSMA, K. J., 1996: Circumscription of Myrtales and their relationships to other rosids: evidence from rbcL sequence data. - Amer. J. Bot. 83: 221-233.
16. CRONQUIST, A., 1981: An integrated system of classification of flowering plants. - New York: Columbia University Press.
17. DAHLGREN, R. M. T., CLIFFORD, H. T., 1982: The monocotyledons: a comparative study. - London: Academic Press.
18. _ YEO, P. F., CLIFFORD, H. T., 1985: The families of the monocotyledons. - Berlin, Heidelberg, New York: Springer.
19. DOYLE, J. A., DONOGHUE, M. J., ZIMMER, E. A., 1994: Integration of morphological and ribosomal RNA data on the origin of angiosperms. - Ann. Missouri Bot. Gard. 81: 419-450.
20. DUVALL, M. R., CLEGG, M. T., CHASE, M. W., CLARK, W. D., KRESS, W. J., HILLS, H. G., EGUIARTE, L. E., SMITH, J. F., GAUT, B. S., ZIMMER, E. A., LEARN, G. H. Jr., 1993: Phylogenetic hypotheses for the monocotyledons constructed from rbcL sequence data. - Ann. Missouri Bot. Gard. 80: 607-619.
21. FARRIS, J. S., 1988: Hennig86, version 1.5. Computer program and documentation. - Port Jefferson, New York.
22. _ 1996: 'Jac. Version 4.4.' - Stockholm: Swedish Museum of Natural History.
23. _ ALBERT, V. A., KÄLLERSJÖ, M., LIPSCOMB, D., KLUGE, A. G., 1996: Parsimony jackknifing outperforms neighbor-joining. - Cladistics 12: 99-124.
24. _ GOLOBOFF, P., KÄLLERSJÖ, M., OXELMAN, B., 1998: Improving the bootstrap. - Cladistics (in press).
25. FAY, M. F., SWENSEN, S. M., CHASE, M. W., 1997: Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). - Kew Bull. 52: 111-120.
26. FELSENSTEIN, J., 1985: Confidence limits on phylogenies: an approach using the bootstrap. - Evolution 39: 783-791.
27. FERNANDO, E. S., GADEK, P. A., CRAYN, D. M., QUINN, C. J., 1993: Rosid affinities of Surianaceae: molecular evidence. - Molec. Phylogenet. Evol. 2: 344-350.
28. _ _ QUINN, C. J., 1995: Simaroubaceae, an artificial construct: evidence from rbcL sequence variation. - Amer. J. Bot. 82: 92-103.
29. GOLENBERG, E. M., GIANNASI, D. E., CLEGG, M. T., SMILEY, C. J., DURBIN, M., HENDERSON, D., ZURAWSKI, G., 1990: Chloroplast DNA sequence from a miocene Magnolia species. - Nature 344: 656-658.
30. GOLOBOFF, P., 1993: Pee-Wee and NONA. Computer programs and documentation. - New York.
31. GUSTAFSSON, M. H. G., BREMER, K., 1997: The circumscription and systematic position of Carpodetaceae. - Austral. Syst. Bot. 10: 855-862.
32. _ BACKLUND, A., BREMER, B., 1996: Phylogeny of the Asterales sensu lato based on rbcL sequences with particular reference to the Goodeniaceae. - Pl. Syst. Evol. 199: 217-242.
33. HASEBE, M., WOLF, P. G., PRYER, K. M., UEDA, K., ITO, M., SANO, R., GASTONY, G. J., YOKOYAMA, J., MANHART, J. R., MURAKAMI, N., CRANE, E. H., HAUFLER, C. H., HAUK, W. D., 1995: Fern phylogeny based on rbcL nucleotide sequences. - Amer. Fern J. 85: 134-181.
34. HUBER H., 1969: Die Samenmerkmale und Verwandtschaftsverhältnisse der Liliiflorae. - Mitt. Bot. Staatssamml. München 8: 219-538.
35. JEFFREY, C., 1982: Kingdoms, codes and classification. - Kew Bull. 37: 403-416.
36. KÄLLERSJÖ, M., FARRIS, J. S., KLUGE, A. G., BULT, C., 1992: Skewness and permutation. - Cladistics 8: 275-287.
37. KRON, K. A., CHASE, M. W., 1993: Systematics of the Ericaceae, Empetraceae, Epacridaceae and related taxa based upon rbcL sequence data. - Ann. Missouri Bot. Gard. 80: 735-741.
38. KUMAR, S., TAMURA, K., NEI, M., 1993: MEGA: molecular evolutionary genetic analysis. Computer program and documentation. - University Park: Pennsylvania State University.
39. MANHART, J. R., 1994: Phylogenetic analysis of green plant rbcL sequences. - Molec. Phylogenet. Evol. 3: 114-127.
40. MATTOX, K. R., STEWART, K. D., 1984: Classification of the green algae: a concept based on comparative cytology. - In IRVINE, D. E. G., JOHN, D., (Eds): The systematics of green algae, pp. 29-72. - London: Academic Press.
41. MISHLER, B. D., LEWIS, L. A., BUCHHEIM, M. A., RENZAGLIA, K. S., GARBARY, D. J., DELWICHE, C. F., ZECHMAN, F. W., KANTZ, T. S., CHAPMAN, R. L., 1994: Phylogenetic relationships of the 'green algae' and 'bryophytes'. - Ann. Missouri Bot. Gard. 81: 451-483.
42. MORGAN, D. R., SOLTIS, D. E., 1993: Phylogenetic relationships among members of Saxifragaceae sensu lato based on rbcL sequence data. - Ann. Missouri Bot. Gard. 80: 631-660.
43. _ SOLTIS, D. E., ROBERTSON, K. R., 1994: Systematic and evolutionary implications of rbcL sequence variation in Rosaceae. - Amer. J. Bot. 81: 890-903.
44. MORTON, C. M., CHASE, M. W., KAROL, K. G., 1997a: Taxonomic affinities of Physena (Physenaceae) and Asteropeia (Asteropeiaceae). - Bot. Rev. 63: 231-239.
45. _ _ KRON, K. A., SWENSEN, S. A., 1997b: A molecular evaluation of the monophyly of the order Ebenales based upon rbcL sequence data. - Syst. Bot. 21: 567-586.
46. _ MORI, S. A., PRANCE, G. T., KAROL, K. G., CHASE, M. W., 1997c: Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequences and morphological data. - Amer. J. Bot. 84: 530-540.
47. NIXON, K. C., CREPET, W. L., STEVENSON, D., FRIIS, E. M., 1994: A reevaluation of seed plant phylogeny. - Ann. Missouri Bot. Gard. 81: 484-533.
48. 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.
49. _ 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.
50. PLUNKETT, G. M., SOLTIS, D. E., SOLTIS, P. S., 1996: Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences. - Amer. J. Bot. 83: 399-415.
51. PRICE, R. A., Palmer, J. D., 1993: Phylogenetic relationships of the Geraniaceae and Geraniales from rbcL sequence comparisons. - Ann. Missouri Bot. Gard. 80: 661-671.
52. QIU, Y.-L., CHASE, M. W., LES, D. H., PARKS, C. R., 1993: Molecular phylogenetics of the Magnoliidae: cladistic analyses of nucleotide sequences of the plastid gene rbcL. - Ann. Missouri Bot. Gard. 80: 587-606
53. RICE K. A., DONOGHUE, M. J., OLMSTEAD, R. G., 1997: Analyzing large date sets: rbcL 500 revisited. - Syst. Biol. 46: 554-563.
54. RITLAND, K., CLEGG, M. T., 1987: Evolutionary analyses of plant DNA sequences. - Amer. Naturalist 130: S74-S100.
55. RODMAN, J. E., PRICE, R. A., KAROL, K., CONTI, E., SYTSMA, K. J., PALMER, J. D., 1993: Nucleotide sequences of the rbcL gene indicate monophyly of mustard oil plants. - Ann. Missouri Bot. Gard. 80: 686-699.
56. RUDALL, P. J., CUTLER, D. F., 1995: Asparagales: a reappraisal. - In RUDALL, P. J., CRIBB, P. J., CUTLER, D. F., HUMPHRIES, C. J., (Eds): Monocotyledons: systematics and evolution, pp. 157-168. - Richmond: Royal Botanic Gardens, Kew.
57. _ CHASE, M. W., 1996: Systematics of Xanthorrhoeaceae sensu lato: evidence for polyphyly. - Telopea 6: 629-647.
58. SANDERSON, M. J., 1989: Confidence limits on phylogenies: the bootstrap revisited. - Cladistics 5: 113-129.
59. SAVOLAINEN, V., SPICHIGER, R., MANEN, J.-F., 1997: Polyphyletism of Celastrales deduced from a chloroplast noncoding DNA region. - Molec. Phylogenet. Evol. 7: 145-157.
60. SHEAHAN, M. C., CHASE, M. W., 1996: A phylogenetic analysis of Zygophyllaceae R. BR. based on morphological, anatomical and rbcL sequence data. - Bot. J. Linn. Soc. 122: 279-300.
61. 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.
62. SWOFFORD, D., 1993: PAUP, phylogenetic analysis using parsimony, version 3.1.1. - Champaign, Illinois: Illinois Natural History Survey.
63. TAKHTAJAN, A. L., 1994: New families of the monocotyledons. - Bot. Zhurn. 79: 65-66.
64. WOLF, P. G., 1995: Phylogenetic analyses of rbcL and nuclear ribosomal RNA gene sequences in Dennstaedtiaceae. -Amer. Fern J. 85: 306-327.
65. ZURAWSKI, G., CLEGG, M. T., 1987: Evolution of higher-plant chloroplast DNA-coded genes: implications for structure-function and phylogenetic studies. - Ann. Rev. Pl. Physiol. 38: 391-418.