Multi-gene phylogeny of the pantropical subfamily Chrysophylloideae (Sapotaceae): Evidence of generic polyphyly and extensive morphological homoplasy

Cladistics

Volumn 24, Issue 6, 2008, Pages 1006-1031

  Swenson, Ulf ^a   Richardson, James E ^b   Bartish, Igor V ^c  

^a SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^b ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^c UNIVERSITÉ DE RENNES 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; CHLOROPLAST; CLADISTICS; DICOTYLEDON; DNA; GEOGRAPHICAL DISTRIBUTION; HYBRIDIZATION; MORPHOLOGY; PARSIMONY ANALYSIS; PHYLOGENY; RECONSTRUCTION; TAXONOMY;

AFRICA; SOUTH AMERICA;

ANINGERIA; CHRYSOPHYLLUM; COTYLEDON (GENUS); DONELLA; GAMBEYA; MALACANTHA; POUTERIA; PRADOSIA; SAPOTACEAE;

EID: 56649108105     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2008.00235.x     Document Type: Article

References (66)

1. Akaike, H., 1974. A new look at the statistical model identification. IEEE Trans. Automat. Contr. 19, 716 723.
2. Anderberg, A.A., Swenson, U., 2003. Evolutionary lineages in Sapotaceae (Ericales): a cladistic analysis based on ndhF sequence data. Int. J. Plant Sci. 164, 763 773.
3. Antonelli, A., 2008. Higher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: molecular signal overshadows morphology. Mol. Phylogenet. Evol. 46, 1 18.
4. Aubréville, A., 1964. Les Sapotacées: taxonomie et phytogéographie. Adansonia Mém. 1, 1 157.
5. Aubréville, A., 1974. Flore de Madagascar et des Comores: 164e famille - Sapotacées. Muséum National d'Histoire Naturelle, Paris.
6. Aubréville, A., Pellegrin, F., 1935. De quelques Sapotacées de la Cote d'Ivoire. Bull. Soc. Bot. France 81, 792 800.
7. Baehni, C., 1965. Mémoire sur les Sapotacées 3. Inventaire des genres. Boissiera 11, 1 262.
8. Baillon, H., 1891. Histoire des Plantes. Librairie Hachette, Paris, Vol. 11, pp. 255 304.
9. Bartish, I.V., Swenson, U., Munzinger, J., Anderberg, A.A., 2005. Phylogenetic relationships among New Caledonian Sapotaceae (Ericales): molecular evidence for generic polyphyly and repeated dispersal. Am. J. Bot. 92, 667 673.
10. Bartish, I.V., Kadereit, J.W., Comes, H.P., 2006. Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (ChsI) sequences and chloroplast DNA variation. Mol. Ecol. 15, 4065 4083.
11. Bentham, G., Hooker, J.D., 1876. Genera Plantarum 2. Reeve & Co., London.
12. Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795 803.
13. Burnham, R.J., Johnson, K.R., 2004. South American paleobotany and the origins of Neotropical rainforests. Philos. Trans. R. Soc. Lond. Ser. B 359, 1595 1610.
14. Coddington, J.A., 1988. Cladistic tests of adaptational hypotheses. Cladistics 4, 3 22.
15. Cronn, R., Small, R.L., Haselkorn, T., Wendel, J.F., 2003. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57, 2475 2489.
16. Doyle, J.J., 1995. The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Syst. Bot. 20, 574 588.
17. Ewango, C.E.N., Breteler, F.J., 2001. Présence du genre Pradosia (Sapotaceae) en Afrique: description d'une nouvelle espèce, P. spinosa. Adansonia 23, 147 150.
18. Farris, J.S., 1989. The retention index and the rescaled consistency index. Cladistics 5, 417 419.
19. Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C., 1995. Testing significance of incongruence. Cladistics 10, 315 319.
20. Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D., Kluge, A.G., 1996. Parsimony jackknifing outperforms neighbour-joining. Cladistics 12, 99 124.
21. Gaubert, P., Wozencraft, W.C., Cordeiro-Estrela, P., Veron, G., 2005. Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Syst. Biol. 54, 865 894.
22. Govaerts, R., Frodin, D.G., Pennington, T.D., 2001. World Checklist and Bibliography of Sapotaceae. Royal Botanic Gardens, Kew.
23. Hall, T., 2004. BioEdit, ver. 7.0.0. http://www.mbio.ncsu.edu/BioEdit/ bioedit.html (accessed 21 October 2008).
24. Hamilton, M.B., 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8, 521 523.
25. Harley, M.M., 1991. The pollen morphology of the Sapotaceae. Kew. Bull. 46, 379 491.
26. Huelsenbeck, J.P., Ronquist, F.R., 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754 755.
27. Kadereit, G., Mucina, L., Freitag, H., 2006. Phylogeny of Salicornioideae (Chenopodiaceae): diversification, biogeography, and evolutionary trends in leaf and flower morphology. Taxon 55, 617 642.
28. Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidea, Serpentes). Syst. Zool. 38, 7 25.
29. Kluge, A.G., Farris, J.S., 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1 32.
30. Kluge, A.G., Wolf, A.J., 1993. Cladistics: what's in a word? Cladistics 9, 183 199.
31. Lam, H.J., 1939. On the system of the Sapotaceae, with some remarks on taxonomical methods. Recueil Trav. Bot. Neerl. 36, 509 525.
32. Lecointre, G., Deleporte, P., 2005. Total evidence requires exclusion of phylogenetically misleading data. Zool. Scr. 34, 101 117.
33. Lewis, P.O., 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913 925.
34. Maddison, D.R., Maddison, W.P., 2000. MacClade 4: Analysis of Phylogeny and Character Evolution, ver. 4.0. Sinauer, Sunderland, MA.
35. Mummenhoff, K., Linder, P., Friesen, N., Bowman, J.L., Lee, J.-Y., Franzke, A., 2004. Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand. Am. J. Bot. 91, 254 261.
36. Olmstead, R.G., Scotland, R.W., 2005. Molecular and morphological datasets. Taxon 54, 7 8.
37. Pennington, T.D., 1990. Flora Neotropica Monograph 52: Sapotaceae. New York Botanical Garden, New York.
38. Pennington, T.D., 1991. The Genera of Sapotaceae. Royal Botanic Gardens, Kew.
39. Pierre, J.B.L., 1891. Notes Botaniques Sapotacées, Paris.
40. Posada, D., Crandall, K.A., 1998. ModelTest: testing the model of DNA substitution. Bioinformatics 14, 817 818.
41. Rannala, B., Yang, Z., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304 311.
42. Ronquist, F., Huelsenbeck, J.P., 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572 1574.
43. van Royen, P., 1957. Revision of the Sapotaceae of the Malaysian area in a wider sense. VII. Planchonella Pierre. Blumea 8, 235 445.
44. Rydin, C., Pedersen, K.R., Friis, E.M., 2004. On the evolutionary history of Ephedra: Cretaceous fossils and extant molecules. Proc. Natl. Acad. Sci. U.S.A. 101, 16571 16576.
45. Savolainen, V., Manen, J.F., Douzery, E., Spichiger, R., 1994. Molecular phylogeny of families related to Celastrales based on rbcL 5′ flanking sequences. Mol. Phylogenet. Evol. 3, 27 37.
46. Scotland, R.W., Olmstead, R.G., Bennett, J.R., 2003. Phylogeny reconstruction: the role of morphology. Syst. Biol. 52, 539 548.
47. Sereno, P.C., 2007. Logical basis for morphological characters in phylogenetics. Cladistics 23, 565 587.
48. Simmons, M.P., 2004. Independence of alignment and tree search. Mol. Phylogenet. Evol. 31, 874 879.
49. Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 369 381.
50. Smedmark, J.E.E., Anderberg, A.A., 2007. Boreotropical migration explains hybridization between geographically distant lineages in the pantropical clade Sideroxyleae (Sapotaceae). Am. J. Bot. 94, 1491 1505.
51. Smedmark, J.E.E., Swenson, U., Anderberg, A.A., 2006. Accounting for variation of substitution rates through time in Bayesian phylogeny reconstruction of Sapotoideae (Sapotaceae). Mol. Phylogenet. Evol. 39, 706 721.
52. Staden, R., Beal, K., Bonfield, J.K., 1998. The Staden package. In : Misener, S., Krawets, S.A. (Eds Computer Methods in Molecular Biology 132, Bioinformatics Methods and Protocols. Humana Press, Totowa, pp. 115 130.
53. Strand, A.E., Leebens-Mack, J., Milligan, B.G., 1997. Nuclear DNA-based markers for plant evolutionary biology. Mol. Ecol. 6, 113 118.
54. Swenson, U., Anderberg, A.A., 2005. Phylogeny, character evolution, and classification of Sapotaceae (Ericales). Cladistics 21, 101 130.
55. Swenson, U., Bartish, I.V., Munzinger, J., 2007a. Phylogeny, diagnostic characters, and generic limitation of Australasian Chrysophylloideae (Sapotaceae, Ericales): evidence from ITS sequence data and morphology. Cladistics 23, 201 228.
56. Swenson, U., Munzinger, J., Bartish, I.V., 2007b. Molecular phylogeny of Planchonella (Sapotaceae) and eight new species from New Caledonia. Taxon 56, 329 354.
57. Swenson, U., Lowry, P.P. II., Munzinger, J., Rydin, C., Bartish, I.V., 2008. Phylogeny and generic limits in the Niemeyera complex of New Caledonian Sapotaceae: evidence of multiple origins of the amisomerous flower. Mol. Phylogenet. Evol. doi :.
58. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Version 4.0b10. Sinauer, Sunderland.
59. Taberlet, P., Gielly, L., Pautou, G., Bouvet, J., 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17, 1105 1109.
60. Thomson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876 4882.
61. Triono, T., Brown, A.H.D., West, J.G., Crisp, M.D., 2007. A phylogeny of Pouteria (Sapotaceae) from Malesia and Australasia. Aust. Syst. Bot. 20, 107 118.
62. Wenzel, J.W., 1997. When is a phylogenetic test good enough? Mem. Mus. Natl. Hist. Nat. 173, 31 45.
63. Wiens, J.J., 2004. The role of morphological data in phylogenetic reconstruction. Syst. Biol. 53, 653 661.
64. Wilkinson, M., 1992. Ordered versus unordered characters. Cladistics 8, 375 385.
65. Wilkinson, M., 1995. A comparison of two methods of character construction. Cladistics 11, 297 308.
66. Yang, Z., Rannala, B., 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14, 717 724.