Delimiting species boundaries within the Neotropical bamboo Otatea (Poaceae: Bambusoideae) using molecular, morphological and ecological data

Molecular Phylogenetics and Evolution

Volumn 54, Issue 2, 2010, Pages 344-356

  Ruiz Sanchez, Eduardo ^a   Sosa, Victoria ^a  

^a INSTITUTO DE ECOLOGÍA   (Mexico)

Author keywords

Diagnostic characters; Ecological niche modeling; Molecular parsimony; Morphology tree based analysis; Niche divergence; Statistical parsimony network

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COLOMBIA; DNA SEQUENCE; ECOSYSTEM; GENETICS; HAPLOTYPE; HISTOLOGY; MEXICO; MOLECULAR EVOLUTION; PHYLOGENY; POACEAE; POPULATION GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION;

COLOMBIA; DNA, CHLOROPLAST; DNA, PLANT; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETICS, POPULATION; HAPLOTYPES; MEXICO; MODELS, BIOLOGICAL; PHYLOGENY; POACEAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

BAMBUSOIDEAE; OTATEA; POACEAE;

EID: 73349102159     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.10.035     Document Type: Article

References (80)

1. Anderson R.P., Lew D., and Peterson A.T. Evaluating predictive models of species' distributions: criteria for selecting optimal models. Ecol. Mod. 162 (2003) 211-232
2. Bänfer G., Moog U., Fiala B., Mohamed M., Weising K., and Blattner F.R. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals. Mol. Ecol. 15 (2006) 4409-4424
3. Barraclough T.G., and Vogler A.P. Detecting the geographical pattern of speciation from species-level phylogenies. Am. Nat. 155 (2000) 419-434
4. Bond J.E., and Stockman A.K. An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structure. Syst. Biol. 57 (2008) 628-646
5. Bouchenak-Khelladi Y., Salamin N., Savolainen V., Forest F., van der Bank M., Chase M.W., and Hodkinson T.R. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol. Phylogenet. Evol. 47 (2008) 488-505
6. Bremer K. Branch support and tree stability. Cladistics 10 (1994) 295-304
7. Brower A.V.Z., DeSalle R., and Vogler A.P. Gene trees, species trees, and Systematics: A cladistic perspective. Annu. Rev. Ecol. Syst. 27 (1996) 423-450
8. Carstens B.C., and Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56 (2007) 400-411
9. Carstens B.C., and Knowles L.L. Shifting distributions and speciation: species divergence during rapid climate change. Mol. Ecol. 16 (2007) 619-627
10. Chase M.W., and Hills H.H. Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon 40 (1991) 215-220
11. Clark L.G., and Cortés G. A new species of Otatea from Chiapas, Mexico. Bamboo Sci. Cult. 18 (2004) 1-6
12. Clark L.G., Davidse G., and Ellis R. Natural hybridization in bamboos: evidence from [Chusquea] sect. [Swallenochloa] (Poaceae: Bambusoideae). Nat. Geo. Res. 5 (1989) 459-476
13. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1999
14. Cota-Sánchez H.J., Remarchuk K., and Ubayasena K. Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue. Plant Mol. Biol. Rep. 24 (2006) 161-167
15. Degnan J.H., and Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Gen. 2 (2006) e68 10.1371/journal.pgen.0020068
16. Elith J., Graham C.H., Anderson R.P., Dudik M., Ferrier S., Guisan A., Hijmans R.J., Huettmann F., Leathwick J.R., Lehmann A., Li J., Lohmann L.G., Loiselle B.A., Manion G., Moritz C., Nakamura M., Nakazawa Y., Overton J.M., Peterson A.T., Phillips S.J., Richardson K., Scachetti-Pereira R., Schapire R.E., Soberon J., Williams S., Wisz M.S., and Zimmermann N.E. Novel methods improve prediction of species' distributions from occurrence data. Ecography 29 (2006) 129-151
17. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladisticis 10 (1994) 315-319
18. Flagel L.E., Rapp R.A., Grover C.E., Widrlechner M.P., Hawkins J., Grafenberg J.L., and Álvarez I. Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea. Am. J. Bot. 95 (2008) 756-765
19. Goloboff, P., 1999. NONA (NO NAME) ver. 2 Published by the author, Tucumán, Argentina.
20. Goloboff, P.A., Farris, J.S., Nixon, K., 2003. TNT: Tree Analysis Using New Technology, Version 1.0. Program and Documentation. Available from: .
21. Gómez-Zurita J., and Vogler A.P. Testing introgressive hybridization hypothesis using statistical network analysis of nuclear and cytoplasmatic haplotypes in the leaf beetle Timarcha goettingensis species complex. J. Mol. Evol. 62 (2006) 421-433
22. Graham C.H., Ron S.R., Santos J.C., Schneider C.J., and Moritz C. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58 (2004) 1781-1793
23. Gray D.A., Huang H., and Knowles L.L. Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests. Mol. Ecol. 17 (2008) 3836-3855
24. Guo Z.H., and Li D.Z. Phylogenetics of the Thamnocalamus group and its allies (Gramineae: Bambusoideae) inferred from the sequences of GBSSI gene and ITS spacer. Mol. Phylogenet. Evol. 30 (2004) 1-12
25. Guo Z.H., Chen Y.Y., Li D.Z., and Yang J.B. Genetic variation and evolution of the alpine bamboos (Poaceae: Bambusoideae) using DNA sequence data. J. Plant Res. 114 (2001) 315-322
26. Guo Z.H., Chen Y.Y., and Li D.Z. Phylogenetic studies on Thamnocalamus group and its allies (Bambusoideae: Poaceae) based on ITS sequence data. Mol. Phylogenet. Evol. 2 (2002) 20-30
27. Guzmán R., Anaya M.C., and Santana F.J. El género Otatea (Bambusoideae), en México y Centroamérica. Boletín del Instituto de Botánica 5 (1984) 2-20
28. Hendrixson B.E., and Bond J.E. Testing species boundaries in the Antrodiateus unicolor complex (Aranae: Megalomorphae: Antrodiaetidae): "Paraphyly" and criptic diversity. Mol. Phylogenet. Evol. 36 (2005) 405-416
29. Hijmans R.J., Cameron S.E., Parra J.L., Jones P.G., and Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25 (2005) 1965-1978
30. Hodkinson T.R., Renvoize S.A., Ni Chonghaile G., Stapleton C.M.A., and Chase M.W. A comparison of ITS nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae). J. Plant Res. 113 (2000) 259-269
31. Hudson R.R., and Coyne J.A. Mathematical consequences of the genealogical species concept. Evolution 56 (2002) 1557-1565
32. Jakob S.S., and Blattner F.R. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol. Biol. Evol. 23 (2006) 1602-1612
33. Jakob S.S., Ihlow A., and Blattner F.R. Combined ecological niche modeling and molecular phylogeography revealed the evolutionary history of Hordeum marinum (Poaceae)-Niche differentiation, loss of genetic diversity, and speciation in Mediterranean Quaternary refugia. Mol. Ecol. 16 (2007) 1713-1727
34. Judziewicz E.J., Clark L.G., Londoño X., and Stern M.J. American Bamboos (1999), Smithsonian Institution Press, New York
35. Kelchner S.A., and Clark L.G. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Mol. Phylogenet. Evol. 8 (1997) 385-397
36. Knowles L.L., and Carstens B.C. Delimiting species without monophyletic gene trees. Syst. Biol. 56 (2007) 887-895
37. Kozak K.H., Grahahm C.H., and Wiens J.J. Integrating GIS-based environmental data into evolutionary biology. Trends Ecol. Evol. 23 (2008) 141-148
38. Lahaye, R., Savolainen, V., Duthoit, S., Maurin, O., van der Bank, M., 2008. A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system. Available from Nature Precedings: .
39. Leaché A.D., and Mulcahy D.M. Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California. Mol. Ecol. 16 (2007) 5216-5233
40. Leavitt D.H., Bezy R.L., Crandall K.A., and Sites Jr. J.W. Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae). Mol. Ecol. 16 (2007) 4455-4481
41. Lihová J., Kučera J., Perný M., and Marhold K. Hybridization between two polyploid Cardamine (Brassicaceae) species in north-western Spain: discordance between morphological and genetic variation patterns. Ann. Bot. 99 (2007) 1083-1096
42. Londoño X., and Clark L.G. Eight new taxa and two new reports of Bambuseae (Poaceae: Bambuseae) from Colombia. Novon 8 (1998) 408-428
43. Londoño X., and Clark L.G. A revision of the Brazilian bamboo genus Eremocaulon (Poaceae: Bambuseae: Guaduinae). Syst. Bot. 27 (2002) 703-721
44. Mable B.K. Why polyploidy is rarer in animals than in plants?. Biol. J. Linn. Soc. 82 (2004) 453-466
45. Maddison W.P. Gene trees in species trees. Syst. Biol. 46 (1997) 523-536
46. McGuire J.A., Linkem C.W., Koo M.S., Hutchison D.W., Lappin A.K., Orange D.I., Lemos-Espinal J., Riddle B.R., and Jaeger J.F. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61 (2007) 2879-2897
47. Mulcahy D.G. Phylogeography and species boundaries of the western North American Nigthsnake (Hypsiglena torquata): Revisiting the subspecies concept. Mol. Phylogenet. Evol. 46 (2008) 1095-1115
48. Nixon, K.C., 1999-2002. WinClada ver. 1.0000 Published by the author, Ithaca, NY, USA.
49. Pan J., Zhang D., and Sang T. Molecular phylogenetic evidence for the origin of a diploid hybrid of Paeonia (Paeoniaceae). Am. J. Bot. 94 (2007) 400-408
50. Pearson R.G., Raxworthy C.J., Nakamura M., and Peterson A.T. Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. J. Biogeogr. 34 (2007) 102-117
51. Peng S., Yang H.Q., and Li D.Z. Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): evidence from GBSSI and ITS sequences. Taxon 57 (2008) 799-810
52. Phillips S.J., Anderson R.P., and Schapire R.E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190 (2006) 231-259
53. Pollard D.A., Iver V.N., Moses A.M., and Eisen M.B. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Gen. 2 (2006) e173 10.1371/journal.pgen.0020173
54. Rambaut, A., 2002. Se-Al sequence alignment editor, v2.0a11. Department of Zoology, University of Oxford, Oxford.
55. Raxworthy C.J., Martínez-Meyer E., Horning N., Nussbaum R.A., Schneider G.E., Ortega-Huerta M.A., and Peterson A.T. Predicting distributions of known and unknown reptile species in Madagascar. Nature 426 (2003) 837-841
56. Raxworthy C.J., Ingram C.M., and Pearson R.G. Species delimitation applications for ecological niche modeling: a review and empirical evaluation using Phelsuma day gecko groups from Madagascar. Syst. Biol. 56 (2007) 907-923
57. Rieseberg L.H. Hybrid origins of plant species. Annu. Rev. Ecol. Syst. 28 (1997) 359-389
58. Rieseberg J.H., Wood T.E., and Baack E.J. The nature of plant species. Nature 440 (2006) 524-527
59. Rieseberg L.H., and Willis J.H. Plant speciation. Science 317 (2007) 910-914
60. Rissler L.J., and Apodaca J.J. Ecological niche models and phylogeography help uncover cryptic biodiversity. Syst. Biol. 56 (2007) 924-942
61. Ruiz-Sanchez E., Sosa V., and Mejía-Saules M.T. Phylogenetics of Otatea inferred from morphology and chloroplast DNA sequence data and recircumscription of Guaduinae (Poaceae: Bambusoideae). Syst. Bot. 33 (2008) 277-283
62. Shaw J., Lickey E.B., Schilling E.E., and Small R.L. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare. III. Am. J. Bot. 94 (2007) 275-288
63. Shrestha S., Adkins S.W., Graham G.C., and Loch D.S. Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences. Aust. Syst. Bot. 16 (2003) 165-176
64. Silvertwon J. The evolutionary maintenance of sexual reproduction: evidence from the ecological distribution of asexual reproduction in clonal plants. Int. J. Plant Sci. 169 (2008) 157-188
65. Sites J.W., and Marshall J.C. Delimiting species: a renaissance issue in systematic biology. Trends Ecol. Evol. 18 (2003) 462-470
66. Sites J.W., and Marshall J.C. Operational criteria for delimiting species. Annu. Rev. Ecol. Evol. Syst. 35 (2004) 199-227
67. Soltis D.E., Soltis P.S., Schemske D.W., Hancock J.F., Thompson J.N., Husband B.C., and Judd W.S. Autopolyploidy in angiosperms: have we grossly underestimated the number of species?. Taxon 1 (2007) 13-30
68. Stockman A.K., and Bond J.E. Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability. Mol. Ecol. 16 (2007) 3374-3392
69. Stockman A.K., Danell R.M., and Bond J.E. D-NOVL: A program to simulate overlap between two niche-based distribution models. Mol. Ecol. Resour. 8 (2008) 290-294
70. Stockwell D.R.B., and Noble I.R. Induction of sets of rules from animal distribution data: a robust and informative method of analysis. Math. Comp. Simul. 33 (1992) 385-390
71. Stockwell D.R., and Peters D. The GARP modeling system: problems and solutions to automated spatial prediction. Int. J. Geogr. Inform. Sys. 13 (1999) 143-158
72. Sungkaew S., Stapleton C.M.A., Salamin N., and Hodkinson T.R. Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. J. Plant Res. 122 (2008) 95-108
73. Sun Y., Xia N., and Lin R. Phylogenetic analysis of Bambusa (Poaceae: Bambusoideae) based on internal transcribed spacer sequences of nuclear ribosomal DNA. Biochem. Genet. 43 (2005) 603-612
74. Trewick S.A. DNA barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 24 (2008) 240-254
75. Triplett, J.K., Clark, L.G., 2009. Molecular phylogenetics of Pleioblastus sensu stricto (Poaceae: Bambusoideae) and allies in the Japanese Archipelago. Botany 2009. Utah.
76. van der Niet T., and Linder H.P. Dealing with incongruence in the quest for the species tree: a case study from the orchid genus Satyrium. Mol. Phylogent. Evol. 47 (2008) 154-174
77. White T.J., Bruns Y., Lee S., and Taylor J. Amplification and direct sequencing of fungal RNA genes for phylogenetics. In: Innis M., Gelfand D., Sninsky J., and White T. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, San Diego 315-322
78. Wiens J.J., and Graham C.H. Niche conservatism: integrating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Syst. 36 (2005) 519-539
79. Wiens J.J., and Penkrot T.A. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51 (2002) 69-91
80. Yang H.Q., Yang J.B., Peng Z.H., Gao J., Yang Y.M., Peng S., and Li D.Z. A molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trn L-F DNA sequences. Mol. Phylogenet. Evol. 48 (2008) 809-824