Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences

American Journal of Botany

Volumn 101, Issue 1, 2014, Pages 92-103

  Eserman, Lauren A ^a   Tiley, George P ^b   Jarret, Robert L ^c   Leebens Mack, Jim H ^a   Miller, Richard E ^d  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d SOUTHEASTERN LOUISIANA UNIVERSITY   (United States)

Author keywords

Character evolution; Chloroplast genomes; Convolvulaceae; Divergence time estimation; Ipomoea; Ipomoeeae; Morning glories; Phylogenetics; Plastid sequences

Indexed keywords

CHLOROPLAST; DICOTYLEDON; FLOWER; PHYLOGENETICS; PHYLOGENY; PLASTID; TOPOLOGY;

ARTICLE; CHARACTER EVOLUTION; CHLOROPLAST GENOME; CHLOROPLAST GENOMES; CONVOLVULACEAE; DIVERGENCE TIME ESTIMATION; GENETIC VARIABILITY; GENETICS; IPOMOEA; IPOMOEEAE; MOLECULAR GENETICS; MORNING GLORIES; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; PLASTID SEQUENCES; TIME;

CHARACTER EVOLUTION; CHLOROPLAST GENOMES; CONVOLVULACEAE; DIVERGENCE TIME ESTIMATION; IPOMOEA; IPOMOEEAE; MORNING GLORIES; PHYLOGENETICS; PLASTID SEQUENCES;

BASE SEQUENCE; CONVOLVULACEAE; GENETIC VARIATION; GENOME, CHLOROPLAST; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; TIME FACTORS;

EID: 84892568483     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1300207     Document Type: Article

References (114)

1. Ahimsa-Müller, M. A., A. Markert, S Hellwig, V Knoop, U Steiner, C Drewke and E Leistner. 2007. Clavicipitaceous fungi associated with ergoline alkaloid-containing Convolvulaceae. Journal of Natural Products 70: 1955-1960.
2. Austin, D. F. 1975. Typifi cation of the New World subdivisions of Ipomoea L. (Convolvulaceae). Taxon 24: 107-110.
3. Austin, D. F. 1978. The Ipomoea batatas complex. I. Taxonomy. Bulletin of the Torrey Botanical Club 105: 114-129.
4. Austin, D. F. 1979. An infrageneric classifi cation for Ipomoea (Convolvulaceae). Taxon 28: 359-361.
5. Austin, D. F. 1980. Additional comments on infrageneric taxa in Ipomoea (Convolvulaceae). Taxon 29: 501-502.
6. Austin, D. F. 1988. Nomenclatural changes in the Ipomoea batatas Complex (Convolvulaceae). Taxon 37: 184-185.
7. Austin, D. F. 1997. Dissolution of Ipomoea series Anisomerae (Convolvulaceae). Journal of the Torrey Botanical Society 124: 140-159.
8. Austin, D.F. 2000. The search for "kaladana" (Ipomoea, Convolvulaceae). Economic Botany 54: 114-118.
9. Austin, D. F. 2005. The enigmatic "salsa da rua"-Ipomoea asarifolia (Convolvulaceae). Ethnobotany 17: 41-48.
10. Austin, D. F. 2007. Merremia dissecta (Convolvulaceae): Condiment, medicine, ornamental, and weed-A review. Economic Botany 61: 109-120.
11. Austin, D. F., and S Demissew. 1997. Unique fruits and generic status of Stictocardia (Convolvulaceae). Kew Bulletin 52: 161-169.
12. Austin, D. F., K. Kitajima, Y Yoneda and L Qian. 2001. A putative tropical American plant, Ipomoea nil (Convolvulaceae), in pre-Columbian Japanese art. Economic Botany 55: 515-527.
13. Austin, D. F., D. A. Powell and D. H. Nicolson. 1978. Stictocardia tili-ifolia (Convolvulaceae) re-evaluated. Brittonia 30: 195-198.
14. Baucom, R. S., S. M. Chang, J. M. Kniskern, M. D. Rausher and J. R. S tinchcombe. 2011. Morning glory as a powerful model in ecological genomics: Tracing adaptation through both natural and artifi cial selection. Heredity 107: 377-385.
15. Boyce, P. 2008. A taxonomic revision of Biarum. Curtis's Botanical Magazine 25: 2-17.
16. Bremer K, E Friis and B Bremer. 2004. Molecular phylogenetic dating of asterid fl owering plants shows early Cretaceous diversifi cation. Systematic Biology 53: 496-505.
17. Cabrera, L. I., G. A. Salazar, M. W. Chase, S. J. Mayo, J Bogner and P Dávila. 2008. Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA. American Journal of Botany 95: 1153-1165.
18. Choisy, J. D. 1833. Convolvulaceas orientales. Memoires de la Societe de Physique et d'Historie Naturelle de Geneve 6: 430-431.
19. Clegg, M. T., and M. L. Durbin. 2003. Tracing fl oral adaptations from ecology to molecules. Nature Reviews. Genetics 4: 206-215.
20. Darling A E, B Mau and N T Perna. 2010. Progressive mauve: Multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147.
21. Darriba, D., G. L. Taboada, R Doallo and D Posada. 2012. jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772.
22. Diaz J, P Schmiediche and D. F. Austin. 1996. Polygon of crossability between eleven species of Ipomoea section Batatas (Convolvulaceae). Euphytica 88: 189-200.
23. Dillon MO, T Tu, L Xie, V Quipuscoa Silvestre and J Wen. 2009. Biogeographic diversifi cation in Nolana (Solanaceae), a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America. Journal of Systematics and Evolution 47: 457-476.
24. Drummond, A. J., S. Y. W. Ho, M. J. Phillips and A Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
25. Drummond, A. J., M. A. Suchard, D Xie and A Rambaut. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
26. Edgar, R. C. 2004a. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
27. Edgar, R. C. 2004b. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
28. Eich, E. 2008. Solanaceae and Convolvulaceae secondary metabolites: Biosynthesis, chemotaxonomy, biological and economic significance: A handbook. Springer, Berlin, Germany.
29. Geneious. 2013. Geneious version 6.0.5 created by Biomatters. Available from http://www.geneious.com.
30. Geological Society of America. 2012. Geologic time scale. Available at http://www.geosociety.org/science/timescale/.
31. Graham, A. 2010. Late Cretaceous and Cenozoic history of Latin American vegetation and terrestrial environments. Missouri Botanical Garden Press, St. Louis, Missouri, USA.
32. Graham A and D. M. Jarzen. 1969. Studies in neotropical paleobotany. I. The Oligocene communities of Puerto Rico. Annals of the Missouri Botanical Garden 56: 308-357.
33. Grisebach, A. H. R. 1864. Convolvulaceae. In A. H. R. Grisebach [ed.], Flora of the British West Indian Islands, 466-475. Lovell Rheeve & Co., London, UK.
34. Hallier H. 1893. Versuch einer natuerlichen Gliederung der Convolvulaceen auf morphologischer und anatomischer Grundlage. Botanische Jahrbuecher fuer Systematik 16: 453-591.
35. Ho, S. Y. W. and M. J. Phillips. 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58: 367-380.
36. Hofmann A. 1961. Die Wirkstoffe der mexikanischen Zauberdroge "Ololiuqui". Planta Medica 9: 354-367.
37. Hofmann, A. 2006. LSD-mein Sorgenkind, die Entdeckung einer Wunderdroge, 12th ed. Deutscher Taschenbuch Verlag, München, Germany.
38. Horak, M.J., and LM Wax. 1991. Growth and development of big-root morning glory (Ipomoea pandurata). Weed Technology 5: 805-810.
39. House, H. D. 1908. The North American species of the genus Ipomoea. Annals of the New York Academy of Sciences 18: 181-263.
40. Huelsenbeck J P, B Larget, R. E. Miller and F Ronquist. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51: 673-688.
41. Huelsenbeck, J. P. and F Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
42. Jansen, R. K., L. A. Raubeson, JL Boore, CW de Pamphilis, T. W. Chumley, R. C. Haberle, S K Wyman et al. 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology 395: 348-384.
43. Jones, K. N., and J S Reithel. 2001. Pollinator-mediated selection on a fl ower color polymorphism in experimental populations of Antirrhinum (Schrophulariaceae). American Journal of Botany 88: 447-454.
44. Knapp, S. 2002. Tobacco to tomatoes: A phylogenetic perspective on fruit diversity in the Solanaceae. Journal of Experimental Botany 53: 2001-2022.
45. Kucht S., J. Gross, Y Hussein, T Grothe, U Keller, S Basar, W.A. König et al. 2004. Elimination of ergoline alkaloids following treatment of Ipomoea asarifolia (Convolvulaceae) with fungicides. Planta 219: 619-625.
46. Langmead B, C Trapnell, M Pop and S. L. Salzberg. 2009. Ultrafast and memory-effi cient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.1-R25.10.
47. Legoux, O. 1978. Quelques especes de pollen caracteristiques du Neogene de Nigeria. Bulletin des Centres de Recherches Exploration-Production Elf-Aquitaine 2: 265-317.
48. Lewis, P. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.
49. Liu K, S Raghavan, S Nelesen, C. R. Linder and T. J. Warnow. 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324: 1561-1564.
50. Liu, K., T. J. Warnow, M. T. Holder, S M Nelesen, J Yu, A. P. Stamatakis and C. R. Linder. 2012. SATe-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylo-genetic trees. Systematic Biology 61: 90-106.
51. Lohse M, O Drechsel and R Bock. 2007. OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics 52: 267-274.
52. Lohse M, O Drechsel, S Kahlau and R Bock. 2013. OrganellarGenomeDRAW-A suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41: W575-W581.
53. Mabberley, D. 2008. Mabberley's plant book, 3rd ed. Cambridge University Press, Cambridge, UK.
54. Maddison, W. P., and D. R. Maddison. 2011. Mesquite: A modular system for evolutionary analysis, version 2.75. Computer program and documentation distributed by the authors, website: http://mesquiteproject.org [accessed 22 March 2013].
55. Manos, P. S., R. E. Miller and P Wilkin. 2001. Phylogenetic analysis of Ipomoea, Argyreia, Stictocardia, and Turbina suggests a generalized model of morphological evolution in morning glories. Systematic Botany 26: 585-602.
56. Mansion G, G Rosenbaum, N Schoenenberger, G Bacchetta, J.A. Rosselló and E Conti. 2008. Phylogenetic analysis informed by geological history supports multiple, sequential invasions of the Mediterranean Basin by the angiosperm family Araceae. Systematic Biology 57: 269-285.
57. Martin, H. A. 2000. Re-assignment of the affi nities of the fossil pollen type Tricolpites trioblatus Mildenhall and Pocknall to Wilsonia (Convolvulaceae) and a reassessment of the ecological interpretations. Review of Palaeobotany and Palynology 111: 237-251.
58. Martin, H. A. 2001. The family Convolvulaceae in the Tertiary of Australia: Evidence from pollen. Australian Journal of Botany 49: 221-234.
59. Martínez-Hernández E and E Ramírez-Arriaga. 1999. Palinostratigrafi a de la region de Tepexi de Rodriguez, Puebla, Mexico-Implicaciones cronoestratigrafias. Revista Mexicana de Ciencias Geológicas 16: 187-207.
60. McDonald, J. A. 1989. Neotypifi cation of Ipomoea jalapa (Convol-vulaceae). Taxon 38: 135-138.
61. McDonald, J. A. 1991. Origin and diversity of Mexican Convolvulaceae. Anales del Instituto de Biología Universidad Nacional Autónoma de México serie Botánica 62: 65-82.
62. McDonald, J. A. 1994. Convolvulaceae II. In V. Sosa [ed.], Flora de Veracruz, vol. 77, 1-133. Instituto de Ecología, A. C., Xalapa, Veracruz, Mexico.
63. McDonald, J. A., and D F Austin. 1990. Changes and additions in Ipomoea section Batatas (Convolvulaceae). Brittonia 42: 116-120.
64. McDonald, J. A., D. R. Hansen, J. R. McDill and B B Simpson. 2011. A phylogenetic assessment of breeding systems and fl oral morphology of North American Ipomoea (Convolvulaceae). Journal of the Botanical Research Institute of Texas 5: 159-177.
65. M cDonald, J. A., and T. J. Mabry. 1992. Phylogenetic systematics of New World Convolvulaceae based on chloroplast DNA restriction site variation. Plant Systematics and Evolution 180: 243-259.
66. McNeal, J. R., J. V. Kuehl, JL Boore and C. W. dePamphilis. 2007. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biology 7: 57.
67. Miller, R. E., T. R. Buckley and P. S. Manos. 2002. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Systematic Biology 51: 740-753.
68. Miller, R. E., J. A. McDonald and P. S. Manos. 2004. Systematics of Ipomoea subgenus Quamoclit based on ITS sequence data and a Bayesian phylogenetic analysis. American Journal of Botany 91: 1208-1218.
69. Miller, R. E., M. D. Rausher and P. S. Manos. 1999. Phylogenetic sys-tematics of Ipomoea (Convolvulaceae) based on ITS and waxy sequences. Systematic Botany 24: 209-227.
70. Montenegro Á, C Avis and A. Weaver. 2008. Modeling the prehistoric arrival of the sweet potato in Polynesia. Journal of Archaeological Science 35: 355-367.
71. Moore, M. J., P. S. Soltis, C. D. Bell, J. G. Burleigh and D. E. Soltis 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversifi cation of eudicots. Proceedings of the National Academy of Sciences, USA 107: 4623-4628.
72. Muller, J. 1981. Fossil pollen records of extant angiosperms. Botanical Review 47: 1-142.
73. Noda N, M Ono, K Miyahara and T Kawasaki. 1987. Resin glyco-sides I. Isolation and structure elucidation of orizabin-I, II, III, and IV. Genuine resin glycosides from the root of Ipomoea orizabensis. Tetrahedron 43: 3889-3902.
74. Olmstead R G, L Bohs, H.A. Migid, E Santiago-Valentin, V.F. Garcia and S. M. Collier. 2008. A molecular phylogeny of the Solanaceae. Taxon 57: 1159-1181.
75. van Ooststroom, S. J., and Leyden. 1953. Convolvulaceae. In C. van Stennis [ed.], Flora Malesiana, 459-489. Noordhoff-Kolff N. V., Djakarta, Indonesia.
76. Ozias-Akins P., and R L Jarret. 1994. Nuclear DNA content and ploidy levels in the genus Ipomoea. Journal of the Society for Horticultural Science 119: 110-115.
77. de Pares Regali MS., N. Uesugui and AS. DE Santos. 1974a. Palinologia dos sedimentos meso-cenozóicas do Brasil (I). Boletim Técnico da Petrobrás, Rio de Janeiro 17: 177-191.
78. de Pares Regali MS, N Uesugui and AS de Santos. 1974b. Palinologia dos sedimentos meso-cenozóicas do Brasil (II). Boletim Técnico da Petrobrás, Rio de Janeiro 17: 263-301.
79. Rambaut A and A. J. Drummond. 2007. Tracer v1.4. Computer program and documentation distributed by the author, website http:// beast.bio.ed.ac.uk/Tracer [accessed 22 March 2013].
80. Ratan, A. 2009. Assembly algorithms for next-generation sequence data. Ph.D. dissertation, Pennsylvania State University, University Park, Pennsylvania, USA.
81. Rausher, M.D. 2008. Evolutionary transitions infloral color. International Journal of Plant Sciences 169: 7-21.
82. Ree, R. H., and S. A. Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and clado-genesis. Systematic Biology 57: 4-14.
83. Richards, C. L., B. C. Carstens and L Knowles. 2007. Distribution modeling and statistical phylogeography: An integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography 34: 1833-1845.
84. Roberty, G. 1952. Genera Convolvulacearum. Candollea 14: 11-65.
85. Robinson J. T., H. Thorvaldsdóttir, W Winckler, M Guttman, E. S. Lander, G. Getz and J. P. Mesirov. 2011. Integrative genomics viewer. Nature Biotechnology 29: 24-26.
86. Ronquist F, M Teslenko, P Van Der Mark, D.L. Ayres, A Darling, S Höhna, B Larget et al. 2012. MrBayes 3.2: Effi cient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
87. Roullier C, L Benoit, D. B. McKey and V Lebot. 2013a. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. Proceedings of the National Academy of Sciences, USA 110: 2205-2210.
88. Roullier C, R Kambouo, J Paofa, D McKey and V Lebot. 2013b. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity. Heredity 110: 594-604.
89. Roullier C., G. Rossel, D Tay, D. McKey and V Lebot. 2011. Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces. Molecular Ecology 20: 3963-3977.
90. Schardl, C. L., and K Clay. 1997. Evolution of mutualistic endophytes from plant pathogens. In G. C. Carroll and P. Tudzynski [eds.], The Mycota V: Plant relationships, 221-238. Springer-Verlag, Berlin, Germany.
91. Schardl C L, A Leuchtmann and M. J. Spiering. 2004. Symbioses of grasses with seedborne fungal endophytes. Annual Review of Plant Biology 55: 315-340.
92. Schardl, C. L., C. A. Young, U Hesse, S. G. Amyotte, K Andreeva, P.J. Calie, DJ Fleetwood et al. 2013. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLOS Genetics 9: e1003323.
93. Sequencher. 2012. Sequencher version 5.0. Sequence analysis software, Gene Codes Corp., Ann Arbor, MI USA. Available at http://www.genecodes.com.
94. Shinners, L. 1979. Convolvulaceae. In D. S. Correll, and M. C. Johnston [eds.], Manual of the vascular plants of Texas. University of Texas at Dallas, Texas Research Foundation, Richardson, Texas, USA.
95. Smith, S.D., and D.A. Baum. 2007. Systematics of Iochrominae (Solanaceae): Patterns in fl oral diversity and interspecifi c crossability. Acta Horticulturae 745: 241-254.
96. Smith, S. D., R. E. Miller, S. P. Otto, R. G. Fitzjohn and M. D. Rausher 2010. The effects of fl ower color transitions on diversifi cation rates in morning glories (Ipomoea subg. Quamoclit, Convolvulaceae). Proceedings of the Darwin 2000 Beijing International Conference 186-210.
97. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
98. Stefanovic, S., D. F. Austin and R. G. Olmstead. 2003. Classifi cation of Convolvulaceae: A phylogenetic approach. Systematic Botany 28: 791-806.
99. Stefanovic S, L Krueger and R. G. Olmstead. 2002. Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci. American Journal of Botany 89: 1510-1522.
100. Steiner U, S Leibner, C.L. Schardl, A Leuchtmann and E Leistner 2011. Periglandula, a new fungal genus within the Clavicipitaceae and its association with Convolvulaceae. Mycologia 103: 1133-1145.
101. Streisfeld, M. A., and J R Kohn. 2005. Contrasting patterns of fl oral and molecular variation across a cline in Mimulus aurantiacus. Evolution 59: 2548-2559.
102. Streisfeld, M. A., and M D Rausher. 2009. Genetic changes contributing to the parallel evolution of red fl oral pigmentation among Ipomoea species. New Phytologist 183: 751-763.
103. Streisfeld, M. A., and M. D. Rausher. 2011. Population genetics, pleiot-ropy, and the preferential fi xation of mutations during adaptive evolution. Evolution 65: 629-642.
104. Swofford, D. L. 2003. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA.
105. Thorvaldsdóttir, H., J. T. Robinson and J. P. Mesirov. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefi ngs in Bioinformatics 14: 178-192.
106. Tripp, E. A., and P S Manos. 2008. Is fl oral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae). Evolution 62: 1712-1737.
107. Verdcourt, B. 1963. Convolvulaceae. In C. E. Hubbard and E. Milne-Redhead [eds.], Flora of tropical East Africa, 1-162. Whitefriars Press, London, UK.
108. Verdcourt, B. 1957. Typifi cation of the subdivisions of Ipomoea L. (Convolvulaceae) with particular regard to the East African species. Taxon 6: 150-152.
109. Wessinger, C. A., and M. D. Rausher. 2012. Lessons from fl ower colour evolution on targets of selection. Journal of Experimental Botany 63: 5741-5749.
110. Wikström N, V Savolainen and M. W. Chase. 2001. Evolution of the angiosperms: Calibrating the family tree. Proceedings of the Royal Society 268: 2211-2220.
111. Wilkin, P. 1999. A morphological cladistic analysis of the Ipomoeeae (Convolvulaceae). Kew Bulletin 54: 853-876.
112. Wyman S. K., R. K. Jansen and J L Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252-3255.
113. Zerbino, D. R., and E Birney. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
114. Zufall, R. A., and M. D. Rausher. 2004. Genetic changes associated with fl oral adaptation restrict future evolutionary potential. Nature 428: 847-850.