Evidence of transoceanic dispersion of the genus Vanilla based on plastid DNA phylogenetic analysis

Molecular Phylogenetics and Evolution

Volumn 55, Issue 2, 2010, Pages 621-630

  Bouetard, Anthony ^a   Lefeuvre, Pierre ^a,b   Gigant, Rodolphe ^a   Bory, Séverine ^a   Pignal, Marc ^c   Besse, Pascale ^a   Grisoni, Michel ^a  

^a UNIVERSITÉ DE LA RÉUNION   (France)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

Bayesian analysis; Gondwanan vicariance; Molecular dating; Orchidaceae; Phylogeography; psaB; psbB; psbC; rbcL; Transoceanic dispersion; Vanilla

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; PHYLOGENY; VANILLA;

BAYES THEOREM; DNA, CHLOROPLAST; DNA, PLANT; EVOLUTION, MOLECULAR; GEOGRAPHY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VANILLA;

AVES; MAGNOLIOPHYTA; MYA; ORCHIDACEAE;

EID: 77950299361     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.01.021     Document Type: Article

References (64)

1. Arditti J., and Ghani A.K.A. Numerical and physical properties of orchid seeds and their biological implications. New Phytologist 145 (2000) 367-421
2. Bory S., Da Silva D., Risterucci A.M., Grisoni M., Besse P., and Duval M.F. Development of microsatellite markers in cultivated vanilla: polymorphism and transferability to other Vanilla species. Scientia Horticulturae 115 (2008) 420-425
3. Bory S., Grisoni M., Duval M.F., and Besse P. Biodiversity and preservation of vanilla: present state of knowledge. Genetic Resources and Crop Evolution 55 (2008) 551-571
4. Bory S., Lubinsky P., Risterucci A.M., Noyer J.L., Grisoni M., Duval M.-F., and Besse P. Patterns of introduction and diversification of Vanilla planifolia (Orchidaceae) in Reunion Island (Indian Ocean). American Journal of Botany 95 (2008) 805-815
5. Bouriquet, G., 1954. Le vanillier et la vanille dans le monde. Encyclopédie Biologique XLVI. Lechevalier, Paris VI.
6. Cameron, K.M., 1999. Biogeography of Vanilloideae (Orchidaceae). In: 16th International Botanical Congress, 1-7 August 1999, St. Louis, Missouri (abstract).
7. Cameron, K.M., 2000. Gondwanan biogeography of Vanilloideae (Orchidaceae). 3rd Southern Connection Congress, 17-22 January 2000, Canterbury, New Zealand (abstract).
8. Cameron K.M. Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae. Molecular Phylogenetic and Evolution 31 (2004) 1157-1180
9. Cameron, K.M., 2005. Recent advances in the systematic biology of Vanilla and related orchids (Orchidaceae: subfamily Vanilloideae). In: 1st International Vanilla Congress, 11-12 November 2003, Princeton, NJ, USA (Poster).
10. Cameron K.M. On the value of nuclear and mitochondrial gene sequences for reconstructing the phylogeny of vanilloid orchids (Vanilloideae, Orchidaceae). Annals of Botany 104 (2009) 377-385
11. Cameron, K.M., in press. Vanilloid orchids systematics and evolution. In: Odoux, E., Grisoni, M. (Eds.), Vanilla. Medicinal and Aromatic Plants - Industrial profiles. Taylor and Francis, NY.
12. Cameron K.M., and Chase M.W. Phylogenetic relationships of Pogoniiae (Vanilloideae, Orchidaceae): an herbaceous example of the eastern north America-eastern Asia phylogeographic disjunction. Journal of Plant Research 112 (1999) 317-329
13. Cameron K.M., and Chase M.W. Nuclear 18S rDNA sequences of Orchidaceae confirm the subfamilial status and circumscription of Vanilloideae. In: Wilson K.L., and Morrison D.A. (Eds). Monocots, Systematics and Evolution (2000), CSIRO, Collingwood, Victoria, Australia 457-464
14. Cameron K.M., Chase M.W., Whitten W.M., Kores P.J., Jarrell D.C., Albert V.A., Yukawa T., Hills H.G., and Goldman D.H. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. American Journal of Botany 86 (1999) 208-224
15. Cameron K.M., and Molina M.C. Photosystem II gene sequences of psbB and psbC clarify the phylogenetic position of Vanilla (Vanilloideae, Orchidaceae). Cladistics 22 (2006) 239-248
16. Chang C.C., Lin H.C., Lin I.P., Chow T.Y., Chen H.H., Chen W.H., Cheng C.H., Lin C.Y., Liu S.M., Chang C.C., and Chaw S.M. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Molecular Biology and Evolution 23 (2006) 279-291
17. Chaterjee S., and Scotese C.R. The break-up of Gondwana and the evolution and biogeography of the Indian plate. Proceedings of the Indian National Science Academy A 65 (1999) 397-425
18. Clegg M.T., and Zurawski G. Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Soltis P., Soltis D., and Doyle J. (Eds). Molecular Systematics of Plants (1992), Chapman and Hall, New York, NY
19. Conran J.G., Bannister J.M., and Lee D.E. Earliest orchid macrofossils: early Miocene Dendrobium and Earina (Orchidaceae: Epidendroideae) from New Zealand. American Journal of Botany 96 (2009) 466-474
20. Crane P.R., Friis E.M., and Pedersen K.R. The origin and early diversification of angiosperms. Nature 374 (1995) 27-33
21. Cuenca A., Asmussen-Lange C.B., and Borchsenius F. A dated phylogeny of the palm tribe Chamaedoreeae supports Eocene dispersal between Africa, North and South America. Molecular Phylogenetics and Evolution 46 (2008) 760-775
22. Davis C.C., Anderson W.R., and Donoghue M.J. Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences. American Journal of Botany 88 (2001) 1830-1846
23. Davis C.C., Bell C.D., Mathews S., and Donoghue M.J. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proceedings of the National Academy of Sciences USA 99 (2002) 6833-6837
24. Doyle J.A., and Thomas A.L. Phylogeny and geographic history of Annonaceae. Géographie Physique et Quaternaire 51 (1997) 353-361
25. Drummond A.J., Ho S.Y.W., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biology 4 (2006) e88
26. Freudenstein J.V., van den Berg C., Goldman D.H., Kores P.J., Molvray M., and Chase M.W. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. American Journal of Botany 91 (2004) 149-157
27. Greiner S., Wang X., Herrmann R.G., Rauwolf U., Mayer K., Haberer G., and Meurer J. The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data. Molecular Biology and Evolution 25 9 (2008) 2019-2030
28. Grisoni M., Moles M., Besse P., Bory S., Duval M.-F., and Kahane R. Towards an international plant collection to maintain and characterize the endangered genetic resources of vanilla. Acta Horticulturae (ISHS) 760 (2007) 83-91
29. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systems biology 52 (2003) 696-704
30. Hall T.A. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
31. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
32. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5 (2004) 150-163
33. Lavin M., Thulin M., Labat J.-N., and Pennington R.T. Africa, the odd man out: molecular biogeography of Dalbergioid Legumes (Fabaceae) suggests otherwise. Systematic Botany 25 (2000) 449-467
34. Lubinsky P., Van Dam M., and Van Dam A. Pollination of Vanilla and evolution in Orchidaceae. Orchids 75 (2006) 926-929
35. Magallon S., and Castillo A. Angiosperm diversification through time. American Journal of Botany 96 (2009) 10.3732/ajb.0800060
36. McLoughlin S. The break up history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Australian Journal of Botany 49 (2001) 271-300
37. Morley, R.J., 2000. Origin and evolution of tropical rain forests. John Wiley and Sons, Chichester, UK, 378p.
38. Morley R.J. Interplate dispersal paths for megathermal angiosperms. Perspectives in Plant Ecology, Evolution and Systematics 6 (2003) 5-20
39. Morley R.J., and Dick C.W. Missing fossils, molecular clocks, and the origin of the Melastomataceae. American Journal of Botany 90 (2003) 1638-1644
40. Muellner A.N., Samuel R., Chase M.W., Pannell C.M., and Greger H. Aglaia (Meliaceae): an evaluation of taxonomic concepts based on DNA data and secondary metabolites. American Journal of Botany 92 (2005) 534-543
41. Muellner A.N., Savolainen V., Samuel R., and Chase M.W. The mahogany family "out-of-Africa": divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Molecular Phylogenetics and Evolution 40 (2006) 236-250
42. Okumura S., Sawada M., Park Y.W., Hayashi T., Shimamura M., Takase H., and Tomizawa K. Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts. Transgenic Research 15 (2006) 637-646
43. Olmstead R., and Palmer J. Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany 81 (1994) 1205-1224
44. Palmer J., Jansen R., Michaels H., Chase M., and Manhart J. Chloroplast DNA variation and plant phylogeny. Annals of the Missouri Botanical Garden 75 (1988)
45. Pennington R.T., and Dick C.W. The role of immigrants in the assembly of the South American rainforest tree flora. Philosophical Transactions of the Royal Society B: Biological Sciences 359 (2004) 1611-1622
46. Portères, R., 1954. Le genre Vanilla et ses espèces. In: Bouriquet, G. (Ed.), Le vanillier et la vanille dans le monde, Paul Lechevailer, Paris, pp. 94-290.
47. Rambaut, R., Drummond, A.J., 2004. Tracer v1.3. Available from: http://evolve.zoo.ox.ac.uk/software.html.
48. Ramirez S.R., Gravendeel B., Singer R.B., Marshall C.R., and Pierce N.E. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator. Nature 448 (2007) 1042-1045
49. Renner S.S. Multiple Miocene Melastomataceae dispersal between Madagascar, Africa and India. Philosophical Transactions of the Royal Society B: Biological Sciences 359 (2004) 1485-1494
50. Rolfe R.A. A revision of the genus Vanilla. Journal of the Linnean Society 32 (1896) 439-478
51. Rozas J., Sánchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
52. Rozen S., and Skaletsky H.J. PRIMER3 on the WWW for general users and for biologist programmers. In: Krawetz S., and Misener S. (Eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology (2000), Humana Press, Totowa, NJ 365-386. http://fokker.wi.mit.edu/primer3/ Source code available from: http://fokker.wi.mit.edu/primer3/
53. Sanmartìn I., and Ronquist H.E.F. Patterns of animal dispersal, vicariance and diversification in the Holarctic. Biological Journal of the Linnean Society 73 (2001) 345-390
54. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16 (1999) 1114-1116
55. Soto Arenas, M.A., 1999. Filogeografia y recursos genéticos de las vainillas de México, Herbario de la Asociación Mexicana de Orquideología, México.
56. Soto Arenas M.A. Vanilla. In: Pridgeon A.M., Cribb P.J., Chase M.W., and Rasmussen F.N. (Eds). Genera Orchidacearum: Orchidoideae (2003), Oxford University Press, USA 321-334
57. Steel M., and McKenzie A. Properties of phylogenetic trees generated by Yule-type speciation models. Mathematical Biosciences 170 (2001) 91-112
58. Stern W.L., and Judd W.S. Comparative vegetative anatomy and systematics of Vanilla (Orchidaceae). Botanical journal of the Linnean Society 131 (1999) 353-382
59. Sun G., Ji Q., Dilcher D.L., Zheng S., Nixon K.C., and Wang X. Archaefructaceae, a new basal Angiosperm family. Science 296 (2002) 899-904
60. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22 (1994) 4673-4680
61. Van Bocxlaer I., Roelants K., Biju S.D., Nagaraju J., and Bossuyt F. Late Cretaceous vicariance in Gondwanan amphibians. PLoS One 1 (2006) e74
62. Von Balthazar M., Pedersen K.R., Crane P.R., Stampanoni M., and Friis E.M. Potomacanthus lobatus gen. et sp. nov., a new flower of probable Lauraceae from the Early Cretaceous (Early to Middle Albian) of eastern North America. American Journal of Botany 94 (2007) 2041-2053
63. Zerega N.J.C., Clement W.L., Datwyler S.L., and Weiblen G.D. Biogeography and divergence times in the mulberry family (Moraceae). Molecular Phylogenetics and Evolution 37 (2005) 402-416
64. Zhang L.-B., Simmons M.P., and Renner S.S. A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia. Molecular Phylogenetics and Evolution 44 (2007) 1057-1067