Towards a species level phylogeny of symphoricarpos (caprifoliaceae), based on nuclear and chloroplast DNA

Systematic Botany

Volumn 35, Issue 2, 2010, Pages 442-450

  Bell, Charles D ^a  

^a University of New Orleans   (United States)

Author keywords

Caprifolieae; geranylgeranyl reductase; phylogenetics; single copy uclear genes; Symphoricarpos

Indexed keywords

CAPRIFOLIACEAE; DIPSACALES; LEYCESTERIA; LONICERA; SYMPHORICARPOS; TRIOSTEUM;

EID: 77954487836     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364410791638351     Document Type: Article

References (44)

1. Angiosperm Phylogeny Group (APG). 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri Botanical Garden 85:531-553.
2. Angiosperm Phylogeny Group II. 2003. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APGII. Botanical Journal of the Linnean Society 141:399-436.
3. Backlund, A. and N. Pyck. 1998. Diervillaceae and Linnaeaceae, two new families of Caprifolioides. Taxon 47:657-661.
4. *: A hierarchical likelihood ratio calculator for LINUX. New Haven: Yale University, Available at http://www.phylodiver sity.net/cbell/pornstar/.
5. Bell, C. D., E. J. Edwards, S.-T. Kim, and M. J. Donoghue. 2001. Dipsacales phylogeny based on chloroplast DNA sequences. Harvard Papers in Botany 6:481-499.
6. Bell, C. D. 2009. Caprifoliaceae. in The Jepson manual: higher plants of California, Volume 2. ed. B. G. Baldwin, S. Boyd, D. J. Keil, R. Patterson, T. J. Rosatti, and D. Wilken. Berkeley: University of California Press.
7. Donoghue, M. J., C. D. Bell, and R. C. Winkworth, 2003. The evolution of reproductive characters in Dipsacales. International Journal of Plant Sciences 164: S453-S464.
8. Donoghue, M. J., T. Eriksson, P. A. Reeves, and R. G. Olmstead. 2001. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany 6:459-479.
9. Doyle, J. J. and J. L. Doyle,. 1990. Isolation of plant DNA from fresh tissue. Focus (San Francisco, Calif.) 12:13-15.
10. Edwards, S. V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
11. Edwards, S. V., L. Liu, and D. K. Pearl. 2007. High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences USA 104:5936-5941.
12. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
13. Fulton, T., R. van der Hoeven, N. Eannetta, and S. Tanksley. 2002. Identification, analysis and utilization of a conserved ortholog set (COS) markers for comparative genomics in higher plants. The Plant Cell 14:1457-1467.
14. Gould, K. R. and M. J. Donoghue. 2000. Phylogeny and biogeography of Triosteum (Caprifoliaceae). Harvard Papers in Botany 5:157-166.
15. Hamilton, M. B. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8:521-523.
16. Holmgren, P. K., N. H. Holmgren, and L. C. Barnet (eds.). 1990. Index Herbariorum. part 1: the herbaria of the world, 8th edition. Bronx: New York Botanical Garden.
17. Jacobs, B., F. Lens, and E. Smets. 2009. Evolution of fruit and seed characters in the Diervilla and Lonicera clades (Caprifoliaceae, Dipsacales). Annals of Botany 104:253-276.
18. Jian, S., P. S. Soltis, M. A. Gitzendanner, M. Moore, A. Dhingra, R. Li, T. A. Hendry, Y.-L. Qui, C. D. Bell, and D. E. Soltis. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57:38-57.
19. Jones, G. N. 1940. A monograph of the genus Symphoricarpos. Journal of the Arnold Arboretum 21:201-252.
20. Lee, C. and J. Wen. 2004. Phylogeny of Panax using chloroplast trnC-trnD intergentic region and the utility of trnC-trnD in interspecific studies of plants. Molecular Phylogenetics and Evolution 31:894-903.
21. Li, M., J. Wunder, G. Bissoli, E. Scarponi, S. Gazzani, E. Barbaro, H. Saedler, and C. Varotto. 2008. Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics 24:727-745.
22. 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.
23. Liu, L., D. K. Pearl, R. T. Brumfield, and S. V. Edwards. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080-2091.
24. Maddison, W. P. 1997. Gene trees in species trees. Systematic Biology 46:523-536.
25. Maddison, W. P. and D. R. Maddison. 2000. MacClade 4: Interactive analysis of phylogeny and character evolution. Sunderland: Sinauer Associates.
26. Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldry. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47-67.
27. Poole, J. M., W. R. Carr, and D. M. Price. 2007. Rare plants of Texas: A field guide. College Station: Texas A & M University Press.
28. Ronquist, F. and J. P. Huelsenbeck. 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
29. Small, R. L. 2004. Phylogeny of Hibiscus sect. Muenchhusia (Malvaceae) based on chloroplast rpl16 and ndhF, and nuclear ITS and GBSSI sequences. Systematic Botany 29:385-392.
30. Smith, S. A. 2009. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographic analysis of the Northern Hemisphere plant clade Caprifolieae. Journal of Biogeography, doi: 10.1111/j.1365-2699. 2009.02160.x.
31. Smith, S. A. and M. J. Donoghue. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 332:86-89.
32. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
33. * and other methods), version b4. Sunderland: Sinauer Associates.
34. 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.
35. Tang, Y. and L. Li. 1994. The phytogeography of Caprifoliaceae s. str. with its implications for understanding eastern Asiatic flora. Acta Phytotaxonomica Sinica 32:197-218.
36. Theis, N., M. J. Donoghue, and J. Li. 2008. Phylogenetics of the Caprifolieae and Lonicera (Dipsacales) based on nuclear and chloroplast DNA sequences. Systematic Botany 33:776-783.
37. Urbatsch, L. E., B. G. Baldwin, and M. J. Donoghue. 2000. Phylogeny of the coneflowers and relatives (Heliantheae: Asteraceae) based on nuclear rDNA internal transcribed spacer (ITS) and chloroplast DNA restriction site data. Systematic Botany 25:539-565.
38. Wang, H., M. J. Moore, P. S. Solits, C. D. Bell, S. F. Brockington, A. Roolse, C. C. Davis, M. Latvis, S. Manchester, and D. E. Soltis. 2009. Phylogeny and diversification of rosids Inferred from nuclear and plastid genes. Proceedings of the National Academy of Sciences USA 106:3853-3858.
39. Weberling, F. 1989. Morphology of flowers and inflorescences. Cambridge: Cambridge University Press.
40. White, T. J., T. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pp. 315-322 in, PCR protocols: A guide to methods and applications, eds. M. Innis, D. Gelfand, J. Sninsky, and T. J. White, San Diego: Academic Press.
41. Winkworth, R. C., C. D. Bell, and M. J. Donoghue. 2008. Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection. Molecular Phylogenetics and Evolution 46:830-843.
42. Winkworth, R. C. and M. J. Donoghue. 2004. Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI. Molecular Phylogenetics and Evolution 33:109-126.
43. Wu, F., L. A. Mueller, D. Crouzillat, V. Petiard, and S. D. Tanksley. 2006. Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COSII) for comparative, evolutinonary and systematics studies: a test case in the euasterid plant clade. Genetics 174:1407-1420.
44. Young, N. D., K. E. Steiner, and C. W. de Pamphilis. 1999. The evolution of parasitism in Scrophulariaceae/Orobanchaceae: plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden 86:876-893.