A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods

American Journal of Botany

Volumn 98, Issue 8, 2011, Pages 1356-1365

  Tepe, Eric J ^a,b   Farruggia, Frank T ^a   Bohs, Lynn ^a  

^a UNIVERSITY OF UTAH   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

Author keywords

Bayesian Estimation of Species trees (BEST); Concatenation; COSII markers; Herpystichum; Matrix representation using parsimony (MRP); Solanaceae; Solanum; Species tree; Supertree

Indexed keywords

PLANT DNA; SPACER DNA; VEGETABLE PROTEIN;

BAYESIAN ANALYSIS; COMPARATIVE STUDY; DICOTYLEDON; GENETIC MARKER; PARSIMONY ANALYSIS; PHYLOGENY; PLASTID; RELATEDNESS; TOPOLOGY;

ARTICLE; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; PLANT LEAF; PLASTID; SOLANACEAE;

BASE SEQUENCE; CELL NUCLEUS; DNA, INTERGENIC; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENETIC MARKERS; GENETIC VARIATION; MODELS, GENETIC; PHYLOGENY; PLANT LEAVES; PLANT PROTEINS; PLASTIDS; SEQUENCE ANALYSIS, DNA; SOLANACEAE;

SOLANACEAE; SOLANUM; SOLANUM EVOLVULIFOLIUM;

EID: 81855168112     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1000516     Document Type: Article

References (80)

1. Anderson, G. J., C. Martine, J. Prohens, and F. Nuez. 2006. Solanum perlongistylum and S. catilliflorum, new endemic Peruvian species of Solanum, section Basarthrum, are close relatives of the domesticated pepino, S. muricatum. Novon 16: 161-167.
2. Averof, M., A. Rokas, K. H. Wolfe, and P. M. Sharp. 2000. Evidence for a high frequency of double-nucleotide substitutions. Science 287: 1283-1286.
3. Baldwin, B. G. 2005. Origin of the serpentine-endemic herb Layia discoidea from the widespread L. glandulosa (Compositae). Evolution 59: 2473-2479.
4. Baum, D. A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.
5. Bininda-Emonds, O. R. P. 2004. Phylogenetic supertrees: Combining information to reveal the tree of life. Kluwer, Dordrecht, Netherlands.
6. Bohs, L. 2004. A chloroplast DNA phylogeny of Solanum section Lasiocarpa. Systematic Botany 29: 177-187.
7. Bohs, L. 2005. Major clades in Solanum based on ndhF sequence data. In R. C. Keating, V. C., Hollowell, and T. B. Croat [eds.], A festschrift for William G. D'Arcy: The legacy of a taxonomist, 27-49. Missouri Botanical Garden Press, St. Louis, Missouri, USA.
8. Bohs, L. 2007. Phylogeny of the Cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data. Taxon 56: 1012-1026.
9. Borchsenius, F. 1997. Patterns of plant species endemism in Ecuador. Biodiversity and Conservation 6: 379-399.
10. Comes, H. P., and R. J. Abbott. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55: 1943-1962.
11. Crawford, D. J. 2010. Progenitor-derivative species pairs and plant speciation. Taxon 59: 1413-1423.
12. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology 52: 477-487.
13. Darlu, P., and G. Lecointre. 2002. When does the incongruence length difference test fail? Molecular Biology and Evolution 19: 432-437.
14. Degnan, J. H., and N. A. Rosenberg. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24: 332-340.
15. De Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879-886.
16. Dolphin, K., R. Belshaw, C. D. L. Orme, and D. L. J. Quicke. 2000. Noise and incongruence: Interpreting results of the incongruence length difference test. Molecular Phylogenetics and Evolution 17: 401-406.
17. Dowton, M., and A. D. Austin. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy: The behavior of the incongruence length difference test in mixed-model analyses. Systematic Biology 51: 19-31.
18. Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Systematic Biology 52: 665-673.
19. Farris, S. J., M. Källersjö, A. G. Kluge, and C. Bult. 1994. Testing significance of incongruence. Cladistics 10: 315-319.
20. Gottlieb, L. D. 2003. Rethinking classic examples of recent speciation in plants. New Phytologist 161: 71-82.
21. Grant, V. 1981. Plant speciation, 2nd ed. Columbia University Press, New York, New York, USA.
22. Green, M. J., D. A. Thompson, and D. J. MacKenzie. 1999. Easy and effi-cient DNA extraction from woody plants for the detection of phytoplasmas by polymerase chain reaction. Plant Disease 83: 482-485.
23. Hamilton, M. B. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8: 521-523.
24. 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.
25. Hörandl, E., and T. F. Stuessy. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641-1653.
26. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
27. Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
28. Knowles, L. L., and B. C. Carstens. 2007. Delimiting species without monophyletic gene trees. Systematic Biology 56: 887-895.
29. Koopman, M. M., and D. A. Baum. 2010. Isolating nuclear genes and identifying lineages without monophyly: An example of closely related species from southern Madagascar. International Journal of Plant Sciences 171: 761-771.
30. Leaché, A. D., and B. Rannala. 2011. The accuracy of species tree estimation under simulation: A comparison of methods. Systematic Biology 60: 126-137.
31. Levin, D. A. 1993. Local speciation in plants: the rule, not the exception. Systematic Botany 18: 197-208.
32. Levin, R. A., N. R. Myers, and L. Bohs. 2006. Phylogenetic relationships among the " spiny solanums " (Solanum subgenus Leptostemonum, Solanaceae). American Journal of Botany 93: 157-169.
33. Levin, R. A., K. Watson, and L. Bohs. 2005. A four-gene study of evolutionary relationships in Solanum section Acanthophora. American Journal of Botany 92: 603-612.
34. Levin, R. A., A. Whelan, and J. S. Miller. 2009. The utility of nuclear conserved ortholog set II (COSII) genomic regions for specieslevel phylogenetic inference in Lycium (Solanaceae). Molecular Phylogenetics and Evolution 53: 881-890.
35. Liu, L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543 www.stat.osu. edu/~dkp/BEST/.
36. Liu, L., and D. K. Pearl. 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56: 504-514.
37. Liu, L., D. K. Pearl, and S. V. Edwards. 2003. BEST 2.3 manual. Website http://www.stat.osu.edu/~dkp/BEST/help/.
38. Maddison, W. P., and D. R. Maddison. 2009. Mesquite: A modular system for evolutionary analysis, version 2.6. Website http:// mesquiteproject.org.
39. Mason-Gamer, R. J., and E. A. Kellogg. 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Systematic Biology 45: 524-545.
40. Mayr, E. 1942. Systematics and the origin of species. Columbia University Press, New York, New York, USA.
41. Mutke, J., and W. Barthlott. 2005. Patterns of vascular plant diversity at continental to global scales. Biologiske Skrifter 55: 521-531.
42. Myers, N. 1988. Threatened biotas: " Hot spots " in tropical forests. Environmentalist 8: 187-208.
43. 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.
44. Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Website http:// www.csit.fsu.edu/~nylander/.
45. Paape, T., B. Igic, S. D. Smith, R. Olmstead, L. Bohs, and J. R. Kohn. 2008. A 15-Myr-old genetic bottleneck. Molecular Biology and Evolution 25: 655-663.
46. Peralta, I. E., S. Knapp, and D. M. Spooner. 2008. Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Systematic Botany Monographs 84: 1-186.
47. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808.
48. Prohens, J., G. J. Anderson, J. M. Blanca, J. Cañizares, E. Zuriaga, and F. Nuez. 2006. The implications of AFLP data for the systematics of the wild species of Solanum section Basarthrum. Systematic Botany 31: 208-216.
49. Rambaut, A. 1996. Se-Al: Sequence Alignment Editor. Computer program and documentation distributed by the author, website http:// evolve.zoo.ox.ac.uk/.
50. Rieseberg, L. H. 1991. Homoploid reticulate evolution in Helianthus (Asteraceae): Evidence from ribosomal genes. American Journal of Botany 78: 1218-1237.
51. Rieseberg, L. H., and L. Brouillet. 1994. Are many plant species polyphyletic? Taxon 43: 21-32.
52. Rieseberg, L. H., R. Carter, and S. Zona. 1990. Molecular tests of the hypothesized hybrid origin of two diploid Helianthus species (Asteraceae). Evolution 44: 1498-1511.
53. Rodríguez, F., and D. M. Spooner. 2009. Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploid species. Systematic Botany 34: 207-219.
54. Rodríguez, F., F. Wu, C. Ané, S. Tanksley, and D. M. Spooner. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evolutionary Biology 9: 191.
55. Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
56. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
57. Sanderson, M. J., and H. B. Shaffer. 2002. Troubleshooting molecular phylogenetic analyses. Annual Review of Ecology and Systematics 33: 49-72.
58. Sang, T., D. J. Crawford, and T. F. Stuessy. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136.
59. Seelanan, T., A. Schnabel, and J. F. Wendel. 1997. Congruence and consensus in the cotton tribe (Malvaceae). Systematic Botany 22: 259-290.
60. Shaw, J., E. B. Lickey, J. T. Beck, S. B. Farmer, W. Liu, J. Miller, K. C. Sirpun, 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.
61. Shaw, J., E. B. Lickey, 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.
62. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of loglikelihoods with applications for phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
63. Simmons, M. P., K. M. Pickett, and M. Miya. 2004. How meaningful are Bayesian support values? Molecular Biology and Evolution 21: 188-199.
64. Spooner, D. M. 2009. DNA barcoding will frequently fail in complicated groups: An example in wild potatoes. American Journal of Botany 96: 1177-1189.
65. Spooner, D. M., G. J. Anderson, and R. K. Jansen. 1993. Chloroplast DNA evidence for the interrelationships of tomatoes, potatoes, and pepinos. American Journal of Botany 80: 676-688.
66. Spooner, D. M., F. Rodríguez, Z. Polgár, H. E. Ballard Jr., and S. H. Jansky. 2008. Genomic origins of potato polyploids: GBSSI gene sequencing data. Plant Genome 48: S27-S36.
67. Stern, S., T. Weese, and L. Bohs. 2010. A three-gene evolutionary study of Solanum section Androceras. Systematic Botany 35: 885-893.
68. Sullivan, J. 1996. Combining data with different distributions of amongsite rate variation. Systematic Biology 45: 375-380.
69. Swofford, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b10. Sinauer, Sunderland, Massachussets, USA.
70. 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: 1105-1110.
71. Tepe, E. J., and L. Bohs. 2009. Three new species of Solanum section Herpystichum (Solanaceae) from Ecuador. Journal of the Botanical Research Institute of Texas 3: 511-519.
72. Tepe, E. J., and L. Bohs. 2010. A molecular phylogeny of Solanum sect. Pteroidea (Solanaceae) and the utility of COSII markers in resolving relationships among closely related species. Taxon 59: 733-743.
73. Tepe, E. J., and L. Bohs. 2011. A revision of Solanum section Herpystichum. Systematic Botany 36(4): in press.
74. Vargas, P., B. G. Baldwin, and L. Constance. 1998. Nuclear ribosomal DNA evidence for a western North American origin of Hawaiian and South American species of Sanicula (Apiaceae). Proceedings of the National Academy of Sciences, USA 95: 235-240.
75. Weese, T. L., and L. Bohs. 2007. A three-gene phylogeny of the genus Solanum (Solanaceae). Systematic Botany 32: 445-463.
76. Weese, T. L., and L. Bohs. 2010. Eggplant origins: Out of Africa, into the Orient. Taxon 59: 49-56.
77. White, T. J., T. Bruns, S. Lee, and J. W. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White. [eds.], PCR protocols: A guide to methods and applications, 315-322. Academic Press, San Diego, California, USA.
78. Wiens, J. J. 1998. Combining data sets with different phylogenetic histories. Systematic Biology 47: 568-581.
79. Wu, F., L. A. Mueller, D. Crouzillat, V. Pétiard, and S. D. Tanksley. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade. Genetics 174: 1407-1420.
80. Yoder, A. D., J. A. Irwin, and B. A. Payseur. 2001. Failure of the PHT to determine data combinability for slow loris phylogeny. Systematic Biology 50: 408-424.