A molecular phylogeny of Solanum sect. Pteroidea (Solanaceae) and the utility of COSII markers in resolving relationships among closely related species

Taxon

Volumn 59, Issue 3, 2010, Pages 733-743

  Tepe, Eric J ^a,b   Bohs, Lynn ^a  

^a UNIVERSITY OF UTAH   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

Author keywords

Bayesian estimation of species trees (best); Central america; Cosii markers; Phylogeny; Solanum section pteroidea; South america

Indexed keywords

BAYESIAN ANALYSIS; GENETIC MARKER; GEOGRAPHICAL DISTRIBUTION; HERB; PHYLOGENETICS; PHYLOGENY; STARCH; VINE;

ANDES; CENTRAL AMERICA;

EID: 77954525760     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.593006     Document Type: Article

References (59)

1. Anderson, G.J., Bernardello, G. & Schlehofer, M. 1999. Continuous variation among three species of Solanum sect. Anarrhichomenum (Solanaceae): The synonymy of S. carchiense and S. tetrapetalum with S. sodiroi. Kurtziana 27: 233-242.
2. Anderson, G.J., Prohens, J., Nuez, F. & Martine, C. 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.
3. Averof, M., Rokas, A., Wolfe, K.H. & Sharp, P.M. 2000. Evidence for a high frequency of double-nucleotide substitutions. Science 287: 1283-1286.
4. Baum, D.A. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56: 417-426.
5. Bitter, G. 1912. XVI. Weitere Polybotryon-Arten. Repert. Spec. Nov. Regni Veg. 11: 469-473.
6. Bitter, G. 1921. Aufteilung der Gattung Bassovia (im Dunalischen Sinne) zwischen Solanum, Capsicum und Lycianthes. Repert. Spec. Nov. Regni Veg. 18: 328-335.
7. Blanca, J.M., Prohens, J., Anderson, G.J., Zuriaga, E., Cañizares, J. & Nuez, F. 2007. AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): Implications for evolution and domestication. Amer. J. Bot. 94: 1219-1229.
8. Bohs, L. 2005. Major clades in Solanum based on ndhF sequence data. Pp. 27-49 in: Keating, R.C., Hollowell, V.C. & Croat T.B. (eds.), A festschrift for William G. D'Arcy: The legacy of a taxonomist. Monographs in Systematic Botany from the Missouri Botanical Garden 104. St. Louis: Missouri Botanical Garden Press.
9. Bohs, L., Weese, T., Myers, N., Lefgren, V., Thomas, N., van Wagenen, A. & Stern, S. 2007. Zygomorphy and heterandry in Solanum in a phylogenetic context. Acta Hort. 745: 201-223.
10. Child, A. 1979. A review of branching patterns in the Solanaceae. Pp. 345-356 in: Hawkes, J.G., Lester, R.N. & Skelding, A.D. (eds.), The biology and taxonomy of the Solanaceae. London: Academic Press.
11. Comes, H.P. & Abbott, R.J. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evolution 55: 1943-1962.
12. Cummings, M.P., Handley, S.A., Myers, D.S., Reed, D.L., Rokas, A. & Winka, K. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52: 477-487.
13. Danert, S. 1967. Die Verzweigung als infragenerisches Gruppenmerkmal in der Gattung Solanum. Kulturpflanze 15: 275-292.
14. Darlu, P. & Lecointre, G. 2002. When does the incongruence length difference test fail? Molec. Biol. Evol. 19: 432-437.
15. Degnan, J.H. & Rosenberg, N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24: 332-340.
16. Dolphin, K., Belshaw, R., Orme, C.D.L. & Quicke, D.L.J. 2000. Noise and incongruence: Interpreting results of the incongruence length difference test. Molec. Phylog. Evol. 17: 401-406.
17. Dowton, M. & Austin, A.D. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy: The behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51: 19-31.
18. Erixon, P., Svennblad, B., Britton, T. & Oxelman, B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52: 665-673.
19. Farris S.J., Källersjö, M., Kluge, A.G. & Bult, C. 1994. Testing significance of incongruence. Cladistics 10: 315-319.
20. Gatesy, J. & Baker, R.H. 2005. Hidden likelihood support in genomic data: Can forty-five wrongs make a right? Syst. Biol. 54: 483-492.
21. Green, M.J., Thompson, D.A. & MacKenzie, D.J. 1999. Easy and efficient DNA extraction from woody plants for the detection of phytoplasmas by polymerase chain reaction. Pl. Disease 83: 482-485.
22. Hipp, A.L., Hall, J.C. & Sytsma, K.J. 2004. Congruence versus phylogenetic accuracy: Revisiting the incongruence length difference test. Syst. Biol. 53: 81-89.
23. Horne, E.C., Kumpatla, S.P., Patterson, K.A., Gupta, M. & Thompson, S.A. 2004. Improved high-throughput sunflower and genomic DNA extraction and PCR fidelity. Pl. Molec. Biol. Reporter 22: 83a-83i.
24. Huelsenbeck, J.P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
25. Huson, D.H. & Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Molec. Biol. Evol. 23: 254-267.
26. Knapp, S. & Helgason, T. 1997. A revision of Solanum section Pteroidea: Solanaceae. Bull. Nat. Hist. Mus. London, Bot. 27: 31-73.
27. Levin, R.A., Myers, N.R. & Bohs, L. 2006. Phylogenetic relationships among the "spiny solanums" (Solanum subgenus Leptostemonum, Solanaceae). Amer. J. Bot. 93: 157-169.
28. Levin, R.A., Watson, K. & Bohs, L. 2005. A four-gene study of evolutionary relationships in Solanum section Acanthophora. Amer. J. Bot. 92: 603-612.
29. Levin, R.A., Whelan, A. & Miller, J.S. 2009. The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae). Molec. Phylog. Evol. 53: 881-890.
30. Liu, L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543.
31. Liu, L. & Pearl, D.K. 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56: 504-514.
32. Mason-Gamer, R.J. & Kellogg, E.A. 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45: 524-545.
33. Mueller, L.A., Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M.H., Ahrens, R., Wang, Y., Herbst, E.V., Keyder, E.R., Menda, N., Zamir, D. & Tanksley, S.D. 2005. The SOL Genomics Network: A comparative resource for Solanaceae biology and beyond. Pl. Physiol. 138: 1310-1317.
34. Nylander, J.A.A. 2004. MrModeltest, version 2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. www.csit.fsu.edu/~nylander/.
35. Peralta, I.E. & Spooner, D.M. 2005. Morphological characterization and relationships of wild tomatoes (Solanum L. section Lycopersicon). Pp. 227-257 in: Keating, R.C., Hollowell, V.C. & Croat T.B. (eds.), A festschrift for William G. D'Arcy: The legacy of a taxonomist. Monographs in Systematic Botany from the Missouri Botanical Garden 104. St. Louis: Missouri Botanical Garden Press.
36. Posada, D. & Buckley, T.R. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and bayesian approaches over likelihood ratio tests. Syst. Biol 53: 793-808.
37. Prohens, J., Anderson, G.J., Blanca, J.M., Cañizares, J., Zuriaga, E. & Nuez, F. 2006. The implications of AFLP data for the systematics of the wild species of Solanum section Basarthrum. Syst. Bot. 31: 208-216.
38. Rambaut, A. 1996. Se-Al: Sequence alignment editor. http://evolve.zoo.ox.ac.uk/.
39. Rodríguez, F. & Spooner, D.M. 2009. Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploid species. Syst. Bot. 34: 207-219.
40. Rodríguez, F., Wu, F., Ané, C., Tanksley, S. & Spooner, D.M. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evol. Biol. 9: 191. doi:10.1186/1471-2148-9-191.
41. Rokas, A., Williams, B.L., King, N. & Carroll, S.B. 2003. Genomescale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
42. Ronquist, F. & Huelsenbeck, J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
43. Sanderson, M.J. & Shaffer, H.B. 2002. Troubleshooting molecular phylogenetic analyses. Annual Rev. Ecol. Syst. 33: 49-72.
44. Seelanan, T., Schnabel, A. & Wendel, J.F. 1997. Congruence and consensus in the cotton tribe (Malvaceae). Syst. Bot. 22: 259-290.
45. Shimodaira, H. & Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications for phylogenetic inference. Molec. Biol. Evol. 16: 1114-1116.
46. Simmons, M.P., Pickett, K.M. & Miya, M. 2004. How meaningful are Bayesian support values? Molec. Biol. Evol. 21: 188-199.
47. Spooner, D.M. 2009. DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Amer. J. Bot. 96: 1177-1189.
48. Spooner, D.M., Anderson, G.J. & Jansen, R.K. 1993. Chloroplast DNA evidence for the interrelationships of tomatoes, potatoes, and pepinos. Amer. J. Bot. 80: 676-688
49. Spooner, D.M., Rodríguez, F., Polgár, Z., Ballard Jr., H.E. & Jansky, S.H. 2008. Genomic origins of potato polyploids: GBSSI gene sequencing data. Pl. Genome 48: S27-S36.
50. Sullivan, J. 1996. Combining data with different distributions of among-site rate variation. Syst. Biol. 45: 375-380.
51. Swofford, D.L. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sunderland, Massachusetts: Sinauer.
52. Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Molec. Biol. 17: 1105-1110.
53. Vargas, P., Baldwin, B.G. & Constance, L. 1998. Nuclear ribosomal DNA evidence for a western North American origin of Hawaiian and South American species of Sanicula (Apiaceae). Proc. Natl. Acad. Sci. U.S.A. 95: 235-240.
54. Weese, T.L. & Bohs, L. 2007. A three-gene phylogeny of the genus Solanum (Solanaceae). Syst. Bot. 32: 445-463.
55. White, T.J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315-322 in: Innis, M., Gelfand, D., Sninsky, J. & White, T. (eds.), PCR protocols: A guide to methods and applications. San Diego: Academic Press.
56. Wiens, J.J. 1998. Combining data sets with different phylogenetic histories. Syst. Biol. 47: 568-581.
57. Wu, F., Mueller, L.A, Crouzillat, D., Pétiard, V. & Tanksley, S.D. 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.
58. Yi, T., Miller, A.J. & Wen, J. 2004. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the northern hemisphere. Molec. Phylog. Evol. 33: 861-879.
59. Yoder A.D., Irwin, J.A. & Payseur, B.A. 2001. Failure of the PHT to determine data combinability for slow loris phylogeny. Syst. Biol. 50: 408-424.