Phylogenetics of Puya (Bromeliaceae): Placement, major lineages, and evolution of Chilean species

American Journal of Botany

Volumn 97, Issue 2, 2010, Pages 337-356

  Jabaily, Rachel Schmidt ^a   Sytsma, Kenneth J ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Andes; Bromeliaceae; Chile; Chloroplast capture; CIPRES; MatK; PHYC; Phytochrome C; Puya; Rps16; TrnS trnG

Indexed keywords

ADAPTIVE RADIATION; CHLOROPLAST; DIVERGENCE; DNA; ENVIRONMENTAL CONDITIONS; HYBRIDIZATION; INTROGRESSION; MONOCOTYLEDON; PHYLOGENETICS; PHYTOGEOGRAPHY;

BROMELIACEAE; PUYA;

EID: 76349122243     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.0900107     Document Type: Article

References (90)

1. Amico, G. C., R. Vidal-Russell, and D. L. Nickrent. 2007. Phylogenetic relationships and ecological speciation in the mistletoe Tristerix (Loranthaceae): The infl uence of pollinators, dispersers, and hosts. American Journal of Botany 94: 558-567.
2. Anderson, B., W. W. Cole, and S. C. H. Barrett. 2005. Specialized bird perch aids cross-pollination. Nature 435: 41-42.
3. Ané, C., B. Larget, D. A. Baum, S. D. Smith, and A. Rokas. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24: 412-426.
4. Arroyo, M. T. K., F. A. Squeo, J. J. Armesto, and C. Villagrá n. 1988. Effects of aridity on plant diversity in the northern Chilean Andes: Results of a natural experiment. Annals of the Missouri Botanical Garden 75: 55-78.
5. Barfuss, M. H. J., R. Samuel, W. Till, and T. F. Stuessy. 2005. Phylogenetic relationships in subfamily Tillandsioideae (Bromeliaceae) based on DNA sequence data from seven plastid regions. American Journal of Botany 92: 337-351.
6. Baum, D. A., R. L. Small, and J. F. Wendel. 1998. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology 47: 181-207.
7. Baum, D. A., K. J. Sytsma, and P. C. Hoch. 1994. A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences. Systematic Botany 19: 363-388.
8. Benzing, D. H. 2000. Bromeliaceae: Profi le of an adaptive radiation. Cambridge University Press, New York, New York, USA.
9. Berry, P. E., W. J. Hahn, K. J. Sytsma, J. C. Hall, and A. Mast. 2004. Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on non-coding nuclear and chloroplast DNA data. American Journal of Botany 91: 601-614.
10. Bremer, K. 1994. Branch support and tree stability. Cladistics 10: 295-304.
11. Brown, G. K., and A. J. Gilmartin. 1989. Chromosome numbers in Bromeliaceae. American Journal of Botany 76: 657-665.
12. Catalán, P., E. A. Kellogg, and R. G. Olmstead. 1997. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Molecular Phylogenetics and Evolution 8: 150-166.
13. Come, H. P., and R. J. Abbott. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55: 1943-1962.
14. Crayn, D. M., R. G. Terry, A. C. Smith, and K. Winter. 2000. Molecular systematic investigations in Pitcairnioideae (Bromeliaceae) as a basis for understanding the evolution of crassulacean acid metabolism (CAM). 2000. In K. L. Wilson and D. A. Morrison [eds.], Monocots: Systematics and evolution, 569-579. CSIRO, Melbourne, Australia.
15. Crayn D. M., K. Winter, and J. A. C. Smith. 2004. Multiple origins of crassulacean acid metabolism and the epiphytic habit in the Neotropical family Bromeliaceae. Proceedings of the National Academy of Sciences, USA 101: 3703-3708.
16. Cuénoud, P., L. Savolainen, W. Chatrou, M. Powell, R. J. Grayer, and M. W. Chase. 2002. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 89: 132-144.
17. Davis, C. C., W. R. Anderson, and M. J. Donoghue. 2001. Phylogeny of Malpighiaceae: Evidence from chloroplast ndhF and trnL-F nucleotide sequences. American Journal of Botany 88: 1830-1846.
18. Denton, A. L., B. L. McConaughy, and B. D. Hall. 1998. Usefulness of RNA polymerase II: Coding sequences for estimation of green plant phylogeny. Molecular Biology and Evolution 15: 1082-1085.
19. Ezcurra, C. 2002. Phylogeny, morphology, and biogeography of Chuquiraga, an Andean-Patagonian genus of Asteraceae-Barnadesioideae. Botanical Review 68: 153-170.
20. Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5: 417-419.
21. Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1994. Testing signifi cance of incongruence. Cladistics 10: 315-319.
22. Felsenstein, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22: 240-249.
23. Felsenstein, J. 1985. Confi dence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
24. Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics 22: 521-565.
25. Friar, E. A., L. M. Prince, J. M. Cruse-Sanders, M. E. McGlaughlin, C. A. Butterworth, and B. G. Baldwin. 2008. Hybrid origin and genomic mosaicism of Dubautia scabra (Hawaiian silversword alliance; Asteraceae, Madiinae). Systematic Botany 33: 589-597.
26. Gaut, B. S., S. V. Muse, W. D. Clark, and M. T. Clegg. 1992. Relative rates of nucleotide substitution at the rbcL locus in monocotyledonous plants. Journal of Molecular Evolution 35: 292-303.
27. Gitaí, J., R. Horres, and A. M. Benko-Iseppon. 2005. Chromosomal features and evolution of Bromeliaceae. Plant Systematics and Evolution 253: 65-80.
28. Givnish, T. J., K. C. Millam, P. E. Berry, and K. J. Sytsma. 2007. Phylogeny, adaptive radiation, and historical biogeography of Bromeliaceae inferred from ndhF sequence data. In J. T. Columbus, E. A. Friar, C. W. Hamilton, J. M. Porter, L. M. Prince, and M. G. Simpson [eds.], Monocots: Comparative biology and evolution: Poales. Rancho Santa Ana Botanic Garden, Claremont, California, USA.
29. Hall, J. C., K. J. Sytsma, and H. H. Iltis. 2002. Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data. American Journal of Botany 89: 1826-1842.
30. Hershkovitz, M. A., M. T. K. Arroyo, C. Bell, and L. F. Hinojosa. 2006b. Phylogeny of Chaetanthera (Asteraceae: Mutisieae) reveals both ancient and recent origins of the high elevation lineages. Molecular Phylogenetics and Evolution 41: 594-605.
31. Hershkovitz, M. A., C. C. Hernández-Pellicer, and M. T. K. Arroyo. 2006a. Ribosomal DNA evidence for the diversifi cation of Tropaeolum sect. Chilensia (Tropaeolaceae). Plant Systematics and Evolution 260: 1-24.
32. Hipp, A. L., J. C. Hall, and K. J. Sytsma. 2004. Congruence versus phylogenetic accuracy: Revisiting the incongruence length difference test. Systematic Biology 53: 81-89.
33. Hornung-Leoni, C. T., and V. Sosa. 2008. Morphological phylogenetics of Puya subgenus Puya (Bromeliaceae). Botanical Journal of the Linnean Society 156: 93-110.
34. Horres, R., K. Schulte, K. Weising, and G. Zizka. 2007. Systematics of Bromelioideae (Bromeliaceae)-Evidence from molecular and anatomical studies. Aliso 23: 27-43.
35. Horres, R., G. Zizka, G. Kahl, and K. Weising. 2000. Molecular phylogenetics of Bromeliaceae: Evidence from trnL (UAA) intron sequences of the chloroplast genome. Plant Biology 2: 306-315.
36. Hughes, C., and R. Eastwood. 2006. Island radiation on a continental scale: Exceptional rates of plant diversifi cation after uplift of the Andes. Proceedings of the National Academy of Sciences, USA 103: 10334-10339.
37. Jabaily, R. S., B. Larget, and K. J. Sytsma. 2008. Bayesian AFLP approach to phylogenetic relationships of Puya (Bromeliaceae). In Botany Without Borders: Annual meeting of the Botanical Society of America, Vancouver, British Columbia, Canada, abstract 447. Website http://2008.botanyconference.org/engine/search/index.php?func=detail&aid=447.
38. Johow, F. 1898. Ueber Ornithophilie in der chilenischen Flora. Sitzungsber. Akademie der Wissenschaften zu Berlin 28: 338-341.
39. Katinas, L., and J. V. Crisci. 2000. Cladistic and biogeographic analyses of the genera Moscharia and Polyachyrus (Asteraceae, Mutisieae). Systematic Botany 25: 33-46.
40. Katinas, L., J. V. Crisci, R. S. Jabaily, C. Williams, J. Walker, B. Drew, J. M. Bonifacino, and K. J. Sytsma. 2008. Evolution of secondary heads in Nassauviinae (Asteraceae, Mutisieae). American Journal of Botany 95: 229-240.
41. Katinas, L., J. J. Morrone, and J. V. Crisci. 1999. Track analysis reveals the composite nature of the Andean biota. Australian Journal of Botany 47: 111-130.
42. Kim, S.-T., and M. J. Donoghue. 2008. Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae). Systematic Botany 33: 77-86.
43. Klak, C., G. Reeves, and T. Hedderson. 2004. Unmatched tempo of evolution in southern African semi-desert ice plants. Nature 427: 63-65.
44. Linder, C. R., and L. H. Rieseberg. 2004. Reconstructing patterns of reticulate evolution in plants. American Journal of Botany 91: 1700-1708.
45. Luebert, F., J. Wen, and M. O. Dillon. 2009. Systematic placement and biogeographical relationships of the monotypic genera Gypothamnium and Oxyphyllum (Asteraceae: Mutisioideae) from the Atacama Desert. Botanical Journal of the Linnean Society 159: 32-51.
46. Luteyn, J. L. 1999. Páramos: A checklist of plant diversity, geographical distribution, and botanical literature. New York Botanical Garden Press, Bronx, New York, USA.
47. Luther, H. 2004. An alphabetical list of bromeliad binomials, 9th ed. Bromeliad Society International, Sarasota, Florida, USA.
48. Martin, C. E. 1994. Physiological ecology of the Bromeliaceae. Botanical Review 60: 1-82.
49. Mez, C. 1896. Bromeliaceae. In C. Martius [ed.], Flora brasiliensis, vol. 3, part 3, 635-816. F. Fleischer, Leipzig, Germany.
50. Mez, C. 1934-1935. Bromeliaceae. In A. Endler [ed.], Das Pfl anzenreich, vol. 4, 1-667. W. Engelmann, Leipzig, Germany.
51. Myers, N., R. A. Mittermeier, C. G. Mittermeier, G. A. B. Da Fonseca, and J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
52. Nixon, K. C., and J. I. Davis. 1991. Polymorphic taxa, missing values and cladistic analysis. Cladistics 7: 233-241.
53. Oxelman, B., M. Liden, and D. Berglund. 1997. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). Plant Systematics and Evolution 206: 393-410.
54. Palma, R. E., P. A. Marquet, and D. Boric-Bargetto. 2005. Interand intraspecifi c phylogeography of small mammals in the Atacama Desert and adjacent areas of northern Chile. Journal of Biogeography 32: 1931-1941.
55. Posada, D., and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14: 817-818.
56. Rambaut, A. 2003. Sequence alignment editor (Se-Al), version 2.0a11carbon [computer program]. Website http://tree.bio.ed.ac.uk/software/seal/ [accessed 2005].
57. Rex, M., K. Schulte, G. Zizka, J. Peters, R. Vásquez, P. L. Ibisch, and K. Weising. 2009. Phylogenetic analysis of Fosterella L.B. Sm. (Pitcairnioideae, Bromeliaceae) based on four chloroplast DNA regions. Molecular Phylogenetics and Evolution 51: 472-485.
58. Richardson, J. E., R. T. Pennington, T. D. Pennington, and P. M. Hollingsworth. 2001. Rapid diversifi cation of a species-rich genus of neotropical rain forest trees. Science 293: 2242-2245.
59. Roalson, E. H., and E. A. Friar. 2004. Phylogenetic analysis of nuclear alcohol dehydrogenase (Adh) gene family in Carex section Acrocystis (Cyperaceae) and combined analyses of Adh and nuclear ribosomal ITS and ETS sequences for inferring species relationships. Molecular Phylogenetics and Evolution 33: 671-686.
60. Robinson, H., and D. C. Taylor. 1999. A rejection of Pepinia (Bromeliaceae: Pitcairnioideae) and taxonomic revisions. Harvard Papers in Botany 4: 203-217.
61. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
62. Rundel, P. W., and M. O. Dillon. 1998. Ecological patterns in the Bromeliaceae of the lomas formations of coastal Chile and Peru. Plant Systematics and Evolution 212: 261-278.
63. Samuel, R., H. Kathriarachchi, P. Hoffmann, M. H. J. Barfuss, K. J. Wurdack, C. C. Davis, and M. W. Chase. 2005. Molecular phylogenetics of Phyllanthaceae: Evidence from plastid matK and nuclear PHYC sequences. American Journal of Botany 92: 132-141.
64. Scherson, R. A., R. Vidal, and M. J. Sanderson. 2008. Phylogeny, biogeography, and rates of diversifi cation of New World Astragalus (Leguminosae) with an emphasis on South American radiations. American Journal of Botany 95: 1030-1039.
65. Schulte, K., M. H. J. Barfuss, and G. Zizka. 2009. Phylogenetics of Bromelioideae (Bromeliaceae) inferred from nuclear and plastid DNA loci reveals the evolution of the tank habit within the subfamily. Molecular Phylogenetics and Evolution 51: 327-339.
66. Schulte, K., and G. Zizka. 2008. Multi locus plastid phylogeny of Bromelioideae (Bromeliaceae) and the taxonomic utility of petal appendages and pollen characters. Candollea 63: 209-225.
67. Sharkey, M. J., and J. W. Leathers. 2001. Majority does not rule: The trouble with majority-rule consensus trees. Cladistics 17: 282-284.
68. Shaw, J., E. B. Lickey, J. T. Beck, S. B. Farmer, W. Liu, J. Miller, K. C. Siripun, C. T. Winder, E. E. Schilling, and R. L. Small. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
69. Shaw, J., E. B. Lickey, J. T. Beck, E. E. Schilling, and R. L. Small. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany 94: 275-288.
70. Simpson, B. B. 1975. Pleistocene changes in the fl ora of the high tropical Andes. Paleobiology 1: 273-294.
71. Simpson Vuilleumier, B. B. 1971. Pleistocene changes in the fauna and fl ora of South America. Science 173: 771-774.
72. Smith, L. B. 1968. Notes on Bromeliaceae, XXVIII. Phytologia 16: 461.
73. Smith, L. B., and R. J. Downs. 1974. Pitcairnioideae (Bromeliaceae). Flora Neotropica 14: 1-662.
74. Smith, R. L., and K. J. Sytsma. 1990. Evolution of Populus nigra (sect. Aigeiros): Introgressive hybridization and the chloroplast contribution of Populus alba (sect. Populus). American Journal of Botany 77: 1176-1187.
75. Smith, S. A., and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in fl owering plants. Science 322: 86-89.
76. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688-2690.
77. Stamatakis, A., P. Hoover, and J. Rougemont. 2008. A fast bootstrapping algorithm for the RAxML Web servers. Systematic Biology 57: 758-771.
78. Swofford, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony ((*and other methods), version 4.0b10. Sinauer, Sunderland, Massachusetts, USA.
79. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplifi cation of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
80. Templeton, A. R. 1983. Convergent evolution and nonparamateric inferences from restriction data and DNA sequences. In B. S. Weir [ed.], Statistical analysis of DNA sequence data, 151-179. Marcel Dekker, New York, New York, USA.
81. Terry, R. G., G. K. Brown, and R. G. Olmstead. 1997. Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF. American Journal of Botany 84: 664-670.
82. Varadarajan, G. S. 1990. Patterns of geographic distribution and their implications on the phylogeny of Puya (Bromeliaceae). Journal of the Arnold Arboretum 71: 527-552.
83. Varadarajan, G. S., and A. J. Gilmartin. 1988. Taxonomic realignments within the subfamily Pitcairnioideae (Bromeliaceae). Systematic Botany 13: 294-299.
84. Weigend, M., M. Gottschling, S. Hoot, and M. Ackermann. 2004. A preliminary phylogeny of Loasaceae subfam. Loasoideae (Angiospermae: Cornales) based on trnL (UAA) sequence data, with consequences for systematics and historical biogeography. Organisms, Diversity & Evolution 4: 73-90.
85. Wendel, J. F., and J. J. Doyle. 1998. Phylogenetic incongruence: Window into genome history and molecular evolution. In P. S. Soltis, D. E. Soltis, and J. J. Doyle [eds.], Molecular systematics of plants II, 265-296. Kluwer, Boston, Massachusetts, USA.
86. Wheeler, W. 1996. Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12: 1-10.
87. Wittmack, L. 1888. Bromeliaceae. In A. Engler and K. Prantl [eds.], Die Nat ü rlichen Pfl anzenfamilien, vol. II, part 4, 32-59. W. Engelmann, Leipzig, Germany.
88. Yang, Z., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolution 14: 717-724.
89. Yoder, A. D., J. A. Irwin, and B. A. Payseur. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology 50: 408-424.
90. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence data sets under the maximum likelihood criterion. Ph.D. dissertation, University of Texas at Austin, Austin, Texas, USA.