A phylogeny of the violaceae (malpighiales) inferred from plastid DNA sequences: Implications for generic diversity and intrafamilial classification

Systematic Botany

Volumn 39, Issue 1, 2014, Pages 239-252

  Wahlert, Gregory A ^a   Marcussen, Thomas ^b   De Paula Souza, Juliana ^c   Feng, Min ^d   Ballard, Harvey E ^e  

^a UNIVERSITY OF UTAH   (United States)

^b Monrads Gate 21A   (Norway)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

^d INSTITUTE OF BOTANY   (China)

^e OHIO UNIVERSITY   (United States)

Author keywords

Non monophyletic genus; RbcL; Rinorea; TrnL trnLF; Viola; Zygomorphy

Indexed keywords

EID: 84894595624     PISSN: 03636445     EISSN: 15482324     Source Type: Journal    
DOI: 10.1600/036364414X678008     Document Type: Article

References (61)

1. Álvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference.Molecular Phylogenetics and Evolution29: 417-434.
2. Angiosperm Phylogeny Group. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105-121.
3. Baillon, H. E. 1873. Violacées. Pp. 265-356 inHistoire des Plantesvol. 4. Paris: L. Hachette et Cie.
4. Ballard, H. E. Jr. 1996.Phylogenetic relationships and infrageneric groups in Viola(Violaceae) based on morphology, chromosome numbers, natural hybridization and Internal Transcribed Spacer (ITS) sequences.Ph. D. thesis. Madison, Wisconsin: University of Wisconsin.
5. Ballard, H. E. Jr., J. Paula-Souza, and G. A. Wahlert. 2013. Violaceae. InThe Families and Genera of Vascular Plants, ed. K. Kubitzki, in review. Berlin: Springer-Verlag.
6. Ballard, H. E. Jr., K. J. Sytsma, and R. R. Kowal. 1999. Shrinking the violets: Phylogenetic relationships of infrageneric groups inViola (Violaceae) based on internal transcribed DNA sequences.Systematic Botany23: 439-458.
7. Bentham, G. and J. D. Hooker. 1862.Genera Plantarum,vol. 1, part 1. London: Reeve and Co.
8. Beuzenberg, E. J. 1961. Observations on sex differentiation and cytotaxonomy of the New Zealand species of the Hymenantherinae (Violaceae).New Zealand Journal of Science4: 337-349.
9. Brizicky, G. K. 1961. The genera of Violaceae in the southeastern United States.Journal of the Arnold Arboretum42: 321-333.
10. Chase, M. W. and J. L. Reveal. 2009. A phylogenetic classification of the land plants to accompany APG III. Botanical Journal of the Linnean Society161: 122-127.
11. Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, R. A. Price, H. G. Hills, Y. L. Qiu, K. A. Kron, J. H. Rettig, E. Conti, J. D. Palmer, J. R. Manhart, K. J. Sytsma, H. J. Michaels, W. J. Kress, K. G. Karol, W. D. Clark, M. Hedren, B. S. Gaut, R. K. Jansen, K. J. Kim, C. F. Wimpee, J. F. Smith, G. R. Furnier, S. H. Strauss, Q. Y. Xiang, G. M. Plunkett, P. S. Soltis, S. M. Swensen, S. E. Williams, P. A. Gadek, C. J. Quinn, L. E. Eguiarte, E. Golenberg, G. H. Learn, S. W. Graham, S. C. H. Barrett, S. Dayanandan, and V. A. Albert. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid generbcL. Annals of the Missouri Botanical Garden80: 528-580.
12. Connor, H. E. and E. Edgar. 1987. Name changes in the indigenous flora, 1960-1986 and Nomina Nova IV, 1983-1986.New Zealand Journal of Botany25: 115-170.
13. Doyle, J. J. and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue.Phytochemical Bulletin19: 11-15.
14. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research32: 1792-1797.
15. Edwards, K., C. Johnstone, and C. Thompson. 1991. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Research19: 1349.
16. Farris, J. S., M. Källersjo ̈, A. G. Kluge, and C. Bult. 1995. Constructing a significance test for incongruence.Systematic Biology44: 570-572.
17. Fay, M. F., S. M. Swensen, and M. W. Chase. 1997. Affinities of Medusagyne oppositifolia(Medusagynaceae).Kew Bulletin52: 111-120.
18. Feng, M. 2005.Floral morphogenesis and molecular systematics of the family Violaceae.Ph. D. thesis. Athens, Ohio: Ohio University.
19. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap.Evolution39: 783-791.
20. Gingins de la Sarraz, F. C. J. de. 1823. Mémoire sur la Famille des Violacées.Mémoires de la Sociétéde Physique et d́Histoire naturelle de Genéve2: 1-28.
21. Green, P. S. 1970. Notes relating to the floras of Norfolk and Lord Howe Islands. I.Journal of the Arnold Arboretum51: 204-220.
22. Harris, S. A. and R. Ingram. 1991. Chloroplast DNA and biosystematics: the effects of intraspecific diversity and plastid transmission. Taxon 40: 393-412.
23. Hekking, W. H. A. 1988. Monograph 46. Violaceae Part I -Rinoreaand Rinoreocarpus. Flora Neotropica Monograph26: 1-207.
24. Hoffmann, M. H., J. Paula-Souza, A. Fläshchendräger, and M. Röser. 2010. The gynoecium of maleAnchietea pyrifolia(Violaceae): Preserved structure with a new function.Flora205: 429-433.
25. Hoyos-Gómez, S. E. 2011.Towards an understanding of the basal evolution of Violaceae from an anatomical and morphological perspective.Master's thesis. St. Louis, Missouri: University of Missouri.
26. Jobb, G., A. von Haeseler, and K. Strimmer. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology4: 18.
27. Kumar, S., A? . Skjæveland, R. S. J. Orr, P. Enger, T. Ruden, B.-H. Mevik, F. Burki, A. Botnen, and K. Shalchian-Tabrizi. 2009. AIR: A batchoriented web program package for construction of supermatrices ready for phylogenomic analyses.BMC Bioinformatics10: 357.
28. Kuntze, O. 1891.Revisio Generum Plantarum,vol. 1. Leipzig: Arthur Felix.
29. Marcussen, T., K. Blaxland, M. D. Windham, K. E. Haskins, and F. Armstrong. 2011. Establishing the phylogenetic origin, history and age of the narrow endemicViola guadalupensis(Violaceae).American Journal of Botany98: 1-11.
30. Marcussen, T., K. S. Jakobsen, J. Danihelka, H. E. Ballard, K. Blaxland, A. K. Brysting, and B. Oxelman. 2012. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). Systematic Biology61: 107-126.
31. Marcussen, T., B. Oxelman, A. Skog, and K. S. Jakobsen. 2010. Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola(Violaceae). BMC Evolutionary Biology10: 1.
32. Mark, P. J. L., A. H. Wortley, and C. A. Furness. 2012. Not a shrinking violet: pollen morphology of Violaceae (Malpighiales).Grana51: 181-193.
33. Mayers, A. M. and E. M. Lord. 1983. Comparative flower development in the cleistogamous species of Viola odorata. I. A growth rate study. American Journal of Botany70: 1548-1555.
34. Melchior, H. 1925a. Violaceae. Pp. 329-377 inDie Natürlichen Pflanzenfamilien21, eds. H. G. A. Engler and K. A. Prantl. Leipzig: Wilhelm Engelmann.
35. Melchior, H. 1925b. III. Die phylogenetishe Entwicklung der Violaceen und die natürlichen Verwandtschaftsverha ̈ltnisse ihrer Gattungen. Feddes Repertorium Specierum Novarum Regni Vegetabilis. 36(Beiheft.): 83-125.
36. Mitchell, A. D., P. B. Heenan, B. G. Murray, B. P. J. Molloy, and P. J. de Lange. 2009. Evolution of the south-western Pacific genusMelicytus (Violaceae): evidence from DNA sequence data, cytology and sex expression.Australian Systematic Botany22: 143-157.
37. Miyaji, Y. 1913. Untersuchungen über die Chromosomenzahlen bei einigen Viola-Arten.Botanical Magazine Tokyo27: 443-460. [in Japanese].
38. Molloy, B. P. J. and A. P. Druce. 1994. A new species name inMelicytus (Violaceae) from New Zealand. New Zealand Journal of Botany32: 113-118.
39. Müller, K. 2005. SeqState-primer design and sequence statistics for phylogenetic DNA data sets.Applied Bioinformatics4: 65-69.
40. Nieuwland, J. A. and R. M. Kaczmarek. 1914. Studies inViola. I. Proposed segregates ofViola. American Midland Naturalist3: 207-217.
41. Paula-Souza, J. and V. C. Souza. 2003.Hybanthopsis, a new genus of Violaceae from Eastern Brazil.Brittonia55: 209-213.
42. Paula-Souza, J. 2009.Estudos Filogenéticos em Violaceae com ěnfase na Tribo Violeaee Revisão Taxonǒmica dos Gěneros Lianescentes de Violaceae na Região Neotropical. Ph. D. thesis. São Paulo: Universidade de São Paulo.
43. Reiche, K. F. and P. H. W. Taubert. 1895. Violaceae. Pp. 322-336 inDie Natürlichen Pflanzenfamilien.1 st . ed. Teil 3, Heft 6, eds. H. G. A. Engler and K. A. Prantl. Leipzig: Wilhelm Engelmann.
44. Rieseberg, L. H., M. A. Hanson, and C. T. Philbrick. 1992. Androdioecy is derived from dioecy in Datiscaceae: evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments.Systematic Botany17: 324-336.
45. Ronquist, F. and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models.Bioinformatics19: 1572-1574.
46. Simmons, M. P. and H. Ochoterena. 2000. Gaps as characters in sequencebased phylogenetic analyses.Systematic Biology49: 369-381.
47. Smith, J. F., K. J. Sytsma, J. S. Shoemaker, and R. L. Smith. 1992. A qualitative comparison of total cellular DNA extraction protocols. Phytochemical Bulletin23: 2-9.
48. Strimmer, K. and A. Rambaut. 2002. Inferring confidence sets of possibly misspecified gene trees.Proceedings. Biological Sciences269: 137-142.
49. Souza, J. P. 2002.Levantamento das espécies deHybanthusJacq. do Brasil. Master's thesis: São Paulo: Universidade de São Paulo.
50. Master's thesis: São Paulo: Universidade de São Paulo. Swofford, D. L. 2002. PAUP Phylogenetic Analysis Using Parsimony, vers. 4.0b10. Sinauer Associates, Sunderland, MA.
51. 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 Reporter17: 1105-1109.
52. Plant Molecular Biology Reporter17: 1105-1109. Taylor, F. H. 1972. The secondary xylem of the Violaceae: a comparative study.Botanical Gazette (Chicago, Ill.)133: 230-242.
53. Thiers, B. 2013. Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden's Virtual Herbarium. http://sweetgum.nybg.org/ih/.
54. Tokuoka, T. 2008. Molecular phylogenetic analysis of Violaceae (Malpighiales) based on plastid and nuclear DNA sequences.Journal of Plant Research121: 253-260.
55. Turner, B. L. and L. K. Escobar. 1991. Documented chromosome numbers 1991: 1. Chromosome numbers inHybanthus(Violaceae). Sida14: 501-503.
56. Wahlert, G. A. 2010.Phylogeny, biogeography, and a taxonomic revision of Rinorea(Violaceae) from Madagascar and the Comoro Islands. Ph. D. thesis. Athens, Ohio: Ohio University.
57. Wahlert, G. A. and H. E. Ballard Jr. 2009. A new zygomorphic-flowered Rinorea(Violaceae) from the Neotropics.Novon19: 416-420.
58. Wahlert, G. A. and H. E. Ballard Jr. 2012. A phylogeny ofRinorea (Violaceae) inferred from plastid DNA sequences with an emphasis on the African and Malagasy species.Systematic Botany37: 964-973.
59. Wurdack, K. J. and C. C. Davis. 2009. Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life.American Journal of Botany96: 1551-1570.
60. Xi, Z., B. R. Ruhfel, H. Schaefer, A. M. Amorim, M. Sugumarane, K. J. Wurdack, P. K. Endress, M. L. Matthews, P. F. Stevens, S. Mathews, and C. C. Davis. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences USA109: 17519-17524.
61. Yockteng, R., H. E. Ballard Jr., G. Mansion, I. Dajoz, and S. Nadot. 2003. Relationships among pansies (ViolasectionMelanium)investigated using ITS and ISSR markers.Plant Systematics and Evolution241: 153-170.