Coding and noncoding plastid DNA in palm systematics

American Journal of Botany

Volumn 88, Issue 6, 2001, Pages 1103-1117

  Asmussen, Conny B ^a   Chase, Mark W ^a,b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b JODRELL LABORATORY   (United Kingdom)

Author keywords

Arecaceae; Coding and noncoding plastid DNA; Molecular systematics; Palmae; Phylogeny; rbcl; rps16 intron; trnl trnf

Indexed keywords

ARECACEAE; CALAMOIDEAE; CEROXYLEAE; CEROXYLOIDEAE; CYCLOSPATHEAE; LILIOPSIDA; PHYTELEPHANTOIDEAE;

EID: 0347420076     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.2307/2657094     Document Type: Article

References (57)

1. ALBERT, V. A., A. BACKLUND, K. BREMER, M. W. CHASE, J. R. MANHART, B. D. MISHLER, AND K. C. NIXON. 1994. Functional constraints and rbcL evidence for land plant phylogeny. Annals of the Missouri Botanical Garden 81: 534-567.
2. APG (ANGIOSPERM PHYLOGENY GROUP). 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85: 531-553.
3. ASMUSSEN, C. B. 1999a. Toward a chloroplast DNA phylogeny of the Geonomeae (Palmae). In A. Henderson and F. Borchsenius [eds.], Evolution, variation, and classification of palms. Memoirs of The New York Botanical Garden 83: 121-129.
4. _. 1999b. Relationships of tribe Geonomeae (Arecaceae) based on plastid rps16 DNA sequences. Acta Botanica Venezuelica 22: 65-76.
5. _, W. J. BAKER, AND J. DRANSFIELD. 2000. Phylogeny of the palm family (Arecaceae) based on rps16 intron and trnL-trnF plastid DNA sequences. In K. L. Wilson and D. A. Morrison [eds.], Systematics and evolution of monocots, 525-537. CSIRO Publishing, Collingwood, Victoria, Australia.
6. BAKER, W. J., C. B. ASMUSSEN, S. BARROW, J. DRANSFIELD, AND T. A. HEDDERSON. 2000. A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from the trnL-trnF region. Plant Systematics and Evolution 219: 111-126.
7. _, T. A. HEDDERSON, AND J. DRANSFIELD. 2000. Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Molecular Phvlogenetics and Evolution 14: 195-217.
8. BARFOD, A. S. 1991. A monographic study of the subfamily Phytelephantoideae (Arecaceae). Opera Botanica 105: 1-73.
9. BARROW, S . 1999a. A monograph of Phoenix L. (Palmae: Coryphoideae). Kew Bulletin 53: 513-575.
10. _. 1999b. Systematic studies in Phoenix L. (Palmae: Coryphoideae). In A. Henderson and F. Borchsenius [eds.], Evolution, variation, and classification of palms. Memoirs of the New York Botanical Garden 83: 215-223.
11. BAYER, C., M. F. FAY, A. Y. D. BRUIJN, V. SAVOLAINEN, C. M. MORTON, K. KUBITZKI, W. S. ALVERSON, AND M. W. CHASE. 1999. Support for an expanded family concept of Malvaceae within a recircumscribed order Malvales: a combined analysis of plastid atpB and rbcL DNA sequences. Botanical Journal of the Linnean Society 129: 267-303.
12. CHASE, M. W., AND V. A. ALBERT. 1998. A perspective on the contribution of plastid rbcL DNA sequences to angiosperm phylogenies. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II, 488-507. Kluwer Academic Publishers, Boston, Massachusetts, USA.
13. _, A. Y. DE BRUIJN, G. REEVES, A. V. COX, P. J. RUDALL, M. A. T. JOHNSON, AND L. E. EGUIARTE. 2000. Phylogenetics of Asphodelaceae (Asparagales): an analysis of plastid rbcL and trnL-F DNA sequences. Annals of Botany. 86: 935-956.
14. _, AND A. V. COX. 1998. Gene sequences, collaboration and analysis of large data sets. Australian Systematic Botany 11: 215-229.
15. _, M. R. DUVALL, H. G. HILLS, J. G. CONRAN, A. V. COX, L. E. EGUIARTE, J. HARTWELL, M. F. FAY, L. R. CADDICK, K. M. CAMERON, AND S. HOOT. 1995a. Molecular phylogenetics of Lilianae. In P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries [eds.], Monocotyledons: systematics and evolution, 109-137. Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
16. _, D. E. SOLTIS, P. S. SOLTIS, P. J. RUDALL, M. F. FAY, W. J. HAHN, S. SULLIVAN, J. JOSEPH, M. MOLVRAY, P. J. KORES, T. J. GIVNISH, K. J. SYTSMA, AND J. C. PIRES. 2000. Higher-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. In K. L. Wilson and D. A. Morrison [eds.], Systematics and evolution of monocots, 3-16. CSIRO Publishing, Collingwood, Victoria, Australia.
17. _, D. W. STEVENSON, P. WILKIN, AND P. J. RUDALL. 1995b. Monocot systematics: a combined analysis. In P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries [eds.], Monocotyledons: systematics and evolution, 685-730. Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
18. _, ET AL. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 528-580.
19. COX, A. V., A. M. PRIDGEON, V. A. ALBERT, AND M. W. CHASE. 1997. Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): nuclear rDNA ITS sequences. Plant Systematics and Evolution 208: 197-223.
20. DOYLE, J. D., AND J. I. DAVIS. 1998. Homology in molecular phylogenetics: a parsimony perspective. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II, 101-131. Kluwer Academic Publishers, Boston, Massachusetts, USA.
21. _, AND J. L. DOYLE. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
22. DRANSFIELD, J., I. K. FERGUSON, AND N. W. UHL. 1990. The coryphoid palms: patterns of variation and evolution. Annals of the Missouri Botanical Garden 77: 802-815.
23. _, AND N. W. UHL. 1986. An outline of a classification of palms. Principes 30: 3-11.
24. _, AND _. 1990. The coryphoid palms: patterns of variation and evolution. Annals of the Missouri Botanical Garden 77: 802-815.
25. _, AND _. 1998. Palmae. In K. Kubitzki [ed.], The families and genera of vascular plants, vol. IV, Flowering plants: monocotyledons, 306-389. Springer-Verlag, Berlin, Germany.
26. DUVALL, M. R., M. T. CLEGG, M. W. CHASE, W. D. CLARK, W. J. KRESS, H. G. HILLS, L. E. EGUIARTE, J. F. SMITH, B. S. GAUT, E. A. ZIMMER, AND G. H. LEARN. 1993a. Phylogenetic hypotheses for the monocotyledons constructed from rbcL sequences data. Annals of the Missouri Botanical Garden 80: 607-619.
27. _, G. H. LEARN, L. E. EGUIARTE, AND M. T. CLEGG. 1993b. Phylogenetic analysis of rbcL sequences identifies Acorus calamus as the primal extant monocotyledon. Proceedings of the National Academy of Sciences, USA 90: 4641-4644.
28. FAY, M. F., C. BAYER, W. S. ALVERSON, A. Y. DE BRUIJN, AND M. W. CHASE. 1998. Plastid rbcL sequence data indicate a close affinity between Diegodendron and Bixa. Taxon 47: 43-50.
29. _, S. M. SWENSEN, AND M. W. CHASE. 1997. Taxonomic affinities of Medusagyne oppositifolia (Medusagynaceae). Kew Bulletin 52: 111-120.
30. FITCH, W. M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Systematic Zoology 20: 406-416.
31. GAUT, B. S., B. R. MORION, B. C. MCCAIG, AND M. T. CLEGG. 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proceedings of the National Academy of Sciences, USA 93: 10274-10279.
32. HILLIS, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Systematic Biology 47: 3-8.
33. HIRATSUKA, J., H. SHIMADA, R. WHITTIER, T. ISHIBASHI, M. SAKAMOTO, M. MORI, C. KONDO, Y. HONJI, C.-R. SUN, B.-Y. MENG, Y-Q. LI, A. KANNO, Y. NISHIZAWA, A. HIRAI, K. SHINOZAKI, AND M. SUGIURA. 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermoleeular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molecular and General Genetics 217: 185-194.
34. 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 Systematics and Evolution 213: 259-287.
35. KELCHNER, S. A., AND L. G. CLARK. 1997. Molecular evolution and phy-logenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8: 385-397.
36. _, AND J. F. WENDEL. 1996. Hairpins create minute inversions in noncoding regions of chloroplast DNA. Current Genetics 30: 259-262.
37. LINDER, H. P., AND E. A. KELLOGG. 1995. Phylogenetic patterns in the commelinid clade. In P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries [eds.], Monocotyledons: systematics and evolution, 473-496. Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
38. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade version 3.04. Sinauer, Sunderland, Massachusetts, USA.
39. MARTIUS, C. F. P. VON. 1824. Palmarum familia ejusque genera. Lindauer, Munich, Germany.
40. MOORE, H. E. 1973. The major groups of palms and their distribution. Gentes Herbarum 11: 27-141.
41. _, AND N. W. UHL. 1982. Major trends of evolution in palms. Botanical Review 48: 1-69.
42. NISHIZAWA, Y., AND A. HIRAI. 1987. Nucleotide sequence and expression of the gene for the large subunit of rice ribulose 1,5-biphosphate carboxylase. Japanese Journal of Genetics 62: 389-395.
43. OLMSTEAD, R. G., H. J. MICHAELS, K. M. SCOTT, AND J. D. PALMER. 1992. Monophyly of the Asteridae and the identification of their major lineages inferred from DNA sequences of rbcL. Annals of the Missouri Botanical Garden 79: 249-265.
44. OXELMAN, B., M. LIDÉN, AND D. BERGLUND. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206: 393-410.
45. PRIDGEON, A. M., R. M. BATEMAN, A. V. COX, J. R. HAPEMAN, AND M. W. CHASE. 1997. Phylogenetics of subtribe Orchidinae (Orchidoideae, Orchidaceae) based on nuclear ITS sequences. 1. Intergeneric relationships and polyphyly of Orchis sensu lato. Lindleyana 12: 89-109.
46. RICHARDSON, J. E., M. F. FAY, Q. C. B. CRONK, D. BOWMAN, AND M. W. CHASE. 2000. A molecular phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences. American Journal of Botany 87: 1309-1324.
47. SMITH, J. F., W. J. KRESS, AND E. A. ZIMMER. 1993. Phylogenetic analysis of the Zingiberales based on rbcL sequences. Annals of the Missouri Botanical Garden 80: 620-630.
48. SOLTIS, D. E., AND P. S. SOLTIS. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. In D. E. Soltis, P. S. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II, 1-42. Kluwer Academic Publishers, Boston, Massachusetts, USA.
49. STEVENSON, D. W., AND H. LOCONTE. 1995. Cladistic analysis of monocot families. In P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries [eds.], Monocotyledons: systematics and evolution, 543-578. Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
50. SWOFFORD, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA.
51. TABERLET, P., L. GIELLY, G. PAUTOU, AND J. BOUVET. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
52. UHL, N. W., AND J. DRANSFIELD. 1987. Genera Palmarum: a classification of palms based on the work of H. E. Moore, Jr. International Palm Society and L. H. Bailey Hortorium, Lawrence, Kansas, USA.
53. _, AND _. 1999. Genera Palmarum after ten years. In A. Henderson and F. Borchsenius [eds.], Evolution, variation, and classification of palms. Memoirs of the New York Botanical Garden 83: 245-253.
54. _, _, J. I. DAVIS, M. A. LUCKOW, K. S. HANSEN, AND J. J. DOYLE. 1995. Phylogenetic relationships among palms: cladistic analyses of morphological and chloroplast DNA restriction site variation. In P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries [eds.], Monocotyledons: systematics and evolution. 623-661. Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
55. VENDRAMIN, G. G., L. LELLI, P. ROSSI, AND M. MORGANTE. 1996. A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology 5: 595-598.
56. WILSON, M. A., B. GAUT, AND M. T. CLEGG. 1990. Chloroplast DNA evolves slowly in the palm family (Arecaceae). Molecular Biology and Evolution 7: 303-314.
57. ZONA, S. 1996. Roystonea (Arecaceae: Arecoideae). Flora Neotropica 71: 1-36.