Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers

Molecular Phylogenetics and Evolution

Volumn 69, Issue 3, 2013, Pages 740-763

  Turner, Barbara ^a   Munzinger, JérÔme ^b   Duangjai, Sutee ^c   Temsch, Eva M ^a   Stockenhuber, Reinhold ^d   Barfuss, Michael H J ^a   Chase, Mark W ^e,f   Samuel, Rosabelle ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b UMR AMAP   (France)

^c KASETSART UNIVERSITY   (Thailand)

^d UNIVERSITY OF ZURICH   (Switzerland)

^e JODRELL LABORATORY   (United Kingdom)

^f UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Endemism; Genome size; Island flora; Low copy nuclear markers; Molecular dating

Indexed keywords

CHLOROPLAST DNA; PLANT DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CELL NUCLEUS; CLASSIFICATION; DIOSPYROS; DIPLOIDY; DNA SEQUENCE; ECOSYSTEM; ENDEMISM; GENETIC MARKER; GENETICS; GENOME SIZE; ISLAND FLORA; LOW-COPY NUCLEAR MARKERS; MOLECULAR DATING; MOLECULAR EVOLUTION; NEW CALEDONIA; PHYLOGENY; PLANT GENOME;

ENDEMISM; GENOME SIZE; ISLAND FLORA; LOW-COPY NUCLEAR MARKERS; MOLECULAR DATING;

BAYES THEOREM; CELL NUCLEUS; DIOSPYROS; DIPLOIDY; DNA, CHLOROPLAST; DNA, PLANT; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENOME, PLANT; MODELS, GENETIC; NEW CALEDONIA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84884572836     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2013.07.002     Document Type: Article

References (85)

1. Alba R., Kelmsnson P.M., Cordonnier-Pratt M.-M., Pratt L.H. The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. Molecular Biology and Evolution 2000, 17:362-373.
2. APG III An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 2009, 161:105-121.
3. Baldwin B.G., Sanderson M.J. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences USA 1998, 95:9402-9406.
4. Bartish I.V., Antonelli A., Richardson J.E., Swenson U. Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae). Journal of Biogeography 2011, 38:177-190.
5. Basinger J.F., Christophel D.C. Fossil flowers and leaves of the Ebenaceae from the Eocene of southern Australia. Canadian Journal of Botany 1985, 63:1825-1843.
6. Bell C.D., Soltis D.E., Soltis P.S. The age and diversification of the angiosperms re-revisited. American Journal of Botany 2010, 97:1296-1303.
7. Bennett M.D., Leitch I.J. Genome size evolution in plants. The Evolution of the Genome 2005, 90-151. Elsevier, San Diego. T.R. Gregory (Ed.).
8. Bennett, M.D., Leitch, I.J., 2010. Angiosperm DNA C-Values Database (Release 7.0, December 2010). < http://www.kew.org/cvalues/.
9. Bennett J.R., Mathews S. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A1. American Journal of Botany 2006, 93:1039-1051.
10. Bremer K., Friis E.M., Bremer B. Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification. Systematic Biology 2004, 53:496-503.
11. Darriba D., Taboada G.L., Doallo R., Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nature Methods 2012, 9:772.
12. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. Molecular Biology and Evolution 2006, 29:1969-1973. (PLoS Biology 4, 699-710).
13. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 2012, 29:1969-1973.
14. Duangjai S., Wallnöfer B., Samuel R., Munzinger J., Chase M.W. Generic delimitation and relationships in Ebenaceae sensu lato: evidence from six plastid DNA regions. American Journal of Botany 2006, 93:1808-1827.
15. Duangjai S., Samuel R., Munzinger J., Forest F., Wallnöfer B., Barfuss M.H.J., Fischer G., Chase M.W. A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species. Molecular Phylogenetics and Evolution 2009, 52:602-620.
16. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
17. Emshwiller E., Doyle J.J. Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Molecular Phylogenetics and Evolution 1999, 12:310-319.
18. Espeland M., Murienne J. Diversity dynamics in New Caledonia: towards the end of the museum model?. BMC Evolutionary Biology 2011, 11:254.
19. Farris J.S., Källersjö M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics 1994, 10:315-319.
20. Ferreira M.A.R., Suchard M.A. Bayesian analysis of elapsed times in continuous-time Markov chains. The Canadian Journal of Statistics 2008, 36:355-368.
21. Forest F. Calibrating the Tree of Life: fossils, molecules and evolutionary timescales. Annals of Botany 2009, 104:789-794.
22. Galbraith D.W., Harkins K.R., Maddox J.M., Ayres N.M., Sharma D.P., Firoozabady E. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 1983, 220:1049-1051.
23. Gaudeul M., Rouhan G., Gardner M.F., Hollingsworth P.M. AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae). American Journal of Botany 2012, 99:68-81.
24. Geeraerts A., Raeymaekers J.A.M., Vinckier S., Pletsers A., Smets E., Huysmans S. Systematic palynology in Ebenaceae with focus on Ebenoideae: morphological diversity and character evolution. Review of Palaeobotany and Palynology 2009, 153:336-353.
25. Gernhard T. The conditioned reconstructed process. Journal of Theoretical Biology 2008, 253:769-788.
26. Givnish T.J., Millam K.C., Berry P.E., Sytsma K.J. Phylogeny, adaptive radiation, and historical biogeography of Bromeliaceae inferred form ndhF sequence data. Aliso 2007, 23:3-26.
27. Givnish T.J., Millam K.C., Mast A.R., Paterson T.B., Theim T.J., Hipp A.L., Henss J.M., Smith J.F., Wood K.R., Sytsma K.J. Origin, adaptive radiation and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae). Proceedings of the Royal Society B 2009, 276. 407-146.
28. Givnish T.J., Barfuss M.H.J., Van Ee B., Riina R., Schulte K., Horres R., Gonsiska P.A., Jabaily R.S., Crayn D.M., Smith J.A.C., Winter K., Brown G.K., Evans T.M., Holst B.K., Luther H., Till W., Zizka G., Berry P.E., Sytsma K.J. Phylogeny, adaptive radiation, and historical biogeography in Bromeliacae: insight from an eight-locus plastid phylogeny. American Journal of Botany 2011, 98:872-895.
29. Grandcolas P., Murienne J., Robillard T., Desutter-Grandcolas L., Jourdan H., Guilbert E., Deharveng L. New Caledonia: a very old Darwinian island?. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 2008, 363:3309-3317.
30. Green A.F., Ramsey T.S., Ramsey J. Phylogeny and biogeography of ivies (Hedera spp., Araliaceae), a polyploid complex of woody vines. Systematic Botnay 2011, 36:1114-1127.
31. Greilhuber J., Ebert I. Genome size variation in Pisum sativum. Genome 1994, 37:646-655.
32. Guindon S., Gascuel O. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 2003, 52:696-704.
33. Guo Y.-P., Wang S.-Z., Vogl C., Ehrendorfer F. Nuclear and plastid haplotypes suggest rapid diploid and polyploid speciation in the N Hemisphere Achillea millefolium complex (Asteraceae). BMC Evolutionary Biology 2012, 12:2.
34. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 1999, 41:95-98.
35. Hasegawa M., Kishino H., Yano T.-A. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 1985, 22:160-174.
36. Hughes C., Eastwood R. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. PNAS 2006, 103:10334-10339.
37. Knope M.L., Morden C.W., Funk V.A., Fukami T. Area and the rapid radiation of Hawaiian Bidens (Asteraceae). Journal of Biogeography 2012, 39:1206-1216.
38. Ladiges P.Y., Cantrill D. New Caledonia-Australian connections: biogeographic patterns and geology. Australian Systematic Botany 2007, 20:383-389.
39. Leitch I.J. Genome size through the ages. Heredity 2007, 99:121-122.
40. Lowry P.P. Diversity, endemism and extinction in the flora of New Caledonia: a review. Rare, Threatened, and Endangered Floras of Asia and the Pacific Rim 1998, 181-206. Institute of Botany, Taipei, Taiwan. C.F. Peng, P.P. Lowry (Eds.).
41. Magallón S. Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. Systematic Biology 2010, 59:384-399.
42. Mathews S., Donoghue M.J. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 1999, 286:947-950.
43. Mathews S., Clements M.D., Beilstein M.A. A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philosophical Transaction of the Royal Society B Biological Sciences 2010, 365:383-395.
44. McLoughlin S. The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Australian Journal of Botany 2001, 49:271-300.
45. Millán-Martínez M. Fossil record and age of the Asteridae. Botanical Reviews 2010, 76:83-135.
46. Miller, M.A., Pfeiffer, W., Schwarz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, Louisiana, 14 November, 2010, pp. 1-8.
47. Mittermeier R.A., Gil P.R., Hoffmann M., Pilgrim J., Brooks T., Mittermeier C.G., Lamoreux J., da Fonseca G.A.B. Hotspots Revisited: Earth's Biologically Richest and Most Endangered Terrestrial Ecoregions 2004, CEMEX, Mexico City.
48. Moody M.L., Rieseberg L.H. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus). Molecular Phylogenetics and Evolution 2012, 64:145-155.
49. Morat P., Jaffré T., Tronchet F., Munzinger J., Pillon Y., Veillon J.-M., Chalopin M. Le référentiel taxonomique Florical et les caractéristiques de la flore vasculaire indigène de la Nouvelle-Calédonie. Adansonia 2012, 34:177-219.
50. Murienne J. Testing biodiversity hypothesis in New Caledonia using phylogenetics. Journal of Biogeography 2009, 36:1433-1434.
51. Murienne J., Grandcolas P., Piulachs M., Bellés X., D'Haese C., Legendre F., Pellens R., Guilbert E. Evolution on a shaky piece of Gondwana: is local endemism recent in New Caledonia?. Cladistics 2005, 21:2-7.
52. Murienne J., Guilbert E., Grandcolas P. Species' diversity in the New Caledonian endemic genera Cephalidiosus and Nobarnus (Insecta: Heteroptera: Tingidae), an approach using phylogeny and species' distribution modelling. Biological Journal of the Linnean Society 2009, 97:177-184.
53. Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., Kent J. Biodiversity hotspots for conservation priorities. Nature 2000, 403:853-858.
54. Nattier R., Robillard T., Desutter-Grandcolas L., Couloux A., Grandcolas P. Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea). Journal of Biogeography 2011, 38:2195-2209.
55. Nie Z.-L., Wen J., Azuma H., Qui Y.-L., Sun H., Meng Y., Sun W.-B., Zimmer E.A. Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets. Molecular Phylogenetics and Evolution 2008, 48:1027-1040.
56. Nixon K.C., Crepet W.L. Late cretaceous fossil flowers with ericalean affinity. American Journal of Botany 1993, 80:616-623.
57. Otto F., Oldiges H., Göhde W., Jain V.K. Flow cytometric measurement of nuclear DNA content variations as a potential in vivo mutagenicity test. Cytometry 1981, 2:189-191.
58. Parisod C., Alix K., Just J., Petit M., Sarilar V., Mhiri C., Ainouche M., Chalhoub B., Grandbastien M.A. Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytologist 2009, 186:37-45.
59. Pelletier B. Geology of the New Caledonia region and its implications for the study of the New Caledonian biodiversity. Compendium of marine species from New Caledonia, Documents Scientifiques et Techniques II4 2006, 17-30. Institut de Recherche pour le Développement Nouméa. C. Payri, B. Richer de Forges (Eds.).
60. Pellicer J., Fay M.F., Leitch I.J. The largest eukaryotic genome of them all?. Botanical Journal of the Linnean Society 2010, 164:10-15.
61. Petrov D.A. Evolution of genome size: new approaches to an old problem. Trends in Genetics 2001, 17:23-28.
62. Pillon Y. Time and tempo of diversification in the flora of New Caledonia. Botanical Journal of the Linnean Society 2012, 170:288-298.
63. Pillon Y., Hopkins H.C., Munzinger J., Amir H., Chase M.W. Cryptic species, gene recombination and hybridization in the genus Spiraeanthemum (Cunoniaceae) from New Caledonia. Botanical Journal of the Linnean Society 2009, 161:137-152.
64. Pillon Y., Munzinger J., Amir H., Hopkins H.C., Chase M.W. Reticulate evolution on a mosaic of soils: diversification of the New Caledonian endemic genus Codia (Cunoniaceae). Molecular Ecology 2009, 18:2263-2275.
65. Pillon Y., Munzinger J., Amir H., Lebrun M. Ultramafic soils and species sorting in the flora of New Caledonia. Journal of Ecology 2010, 98:1108-1116.
66. Pillon Y., Johansen J., Sakishima T., Chamala S., Barbazuk W.B., Roalson E.H., Price D.K., Stacy E.A. Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations. BMC Evolutionary Biology 2013, 13:35.
67. Pirie M.D., Doyle J.A. Dating clades with fossils and molecules: the case of Annoaceae. Botanical Journal of the Linnean Society 2012, 169:84-116.
68. Richardson J.E., Pennington R.T., Pennington T.D., Hollingsworth P.M. Rapid diversification of a species-rich genus of Neotropical rain forest trees. Science 2001, 293:2242-2245.
69. Salard M., Avias J. Contribution à la connaissance de la flore fossile de la Nouvelle-Calédonie. Palaeontographica, Abteilung B, Paläophytologie 1968, 124:1-44.
70. Silvestro D., Schnitzler J., Zizka G. A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology 2011, 11:311-325.
71. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
72. Swenson U., Hill R.S., McLoughlin S. Biogeography of Nothofagus supports the sequence of Gondwana break-up. Taxon 2001, 50:1025-1041.
73. Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
74. Tamura M., Tao R., Yonemori K., Utsunomiya N., Sugiura A. Ploidy level and genome size of several Diospyros species. Journal of the Japanese Horticultural Society 1998, 67:306-312.
75. Tank D.C., Sang T. Phylogenetic utility of the glycerol-3-phosphate acyltransferase gene: evolution and implications in Paeonia (Paeoniaceae). Molecular Phylogenetics and Evolution 2001, 19:421-429.
76. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 1986, 17:57-86.
77. Tel-Zur N., Abbo S., Myslabodsky D., Mizrahi Y. Modified CTAB procedure for DNA isolation from ephiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Molecular Biology Reporter 1999, 17:249-254.
78. Temsch E.M., Greilhuber J., Krisai R. Genome size in liverworts. Preslia 2010, 82:63-80.
79. Weiss-Schneeweiss H., Villaseñor J.L., Stuessy T.F. Chromosome numbers, karyotypes, and evolution in Melampodium (Asteraceae). International Journal of Plant Science 2009, 170:1168-1182.
80. White F. Twenty-two new and little known species of Diospyros (Ebenaceae) from New Caledonia with comments on section Maba. Bulletin du Muséum National d'Histoire naturelle 4ème série - Section B. Adansonia 1992, 2:179-222.
81. White F. Flore de la Nouvelle-Calédonie et Dépendances. 19. Ébénacées 1993, Muséum National d'Histoire Naturelle, Paris.
82. Yockteng R., Nadot S. Phylogenetic relationships among Passiflora species based on the glutamine synthetase nuclear gene expressed in chloroplast (ncpGS). Molecular Phylogenetics and Evolution 2004, 31:379-396.
83. Yule G.U. A mathematical theory of evolution, based on the conclusions of Dr. J.C. Willis, FRS. Philosophical Transactions of the Royal Society of London Series B 1925, 213:21-87.
84. Zimmer E.A., Wen J. Using nuclear gene data for plant phylogenetics: progress and prospects. Molecular Phylogenetics and Evolution 2012, 65:774-785.
85. Zuckerkandl H., Pauling L. Evolutionary divergence and convergence in proteins. Evolving Genes and Proteins 1965, 97-166. Academic Press, New York. G. Bryson, H.J. Vogel (Eds.).