Molecular phylogeny of Macaranga, Mallotus, and related genera (Euphorbiaceae s.s.): Insights from plastid and nuclear DNA sequence data

American Journal of Botany

Volumn 94, Issue 10, 2007, Pages 1726-1743

  Kulju, Kristo K M ^a   Sierra, Soraya E C ^a   Draisma, Stefano G A ^a   Samuel, Rosabelle ^b   Van Welzen, Peter C ^a  

^a UNIVERSITEIT LEIDEN BRANCH   (Netherlands)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

Afro Asian distribution; Biogeography; Cordemoya; Euphorbiaceae; Macaranga; Mallotus; Molecular phylogenetics; Rottlerinae

Indexed keywords

BIOGEOGRAPHY; DICOTYLEDON; DISPERSAL; DNA; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; PLASTID;

AFRICA; ASIA; EURASIA; INDIAN OCEAN; INDIAN OCEAN ISLANDS; MADAGASCAR;

CORDEMOYA; EUPHORBIA; EUPHORBIACEAE; MACARANGA; MALLOTUS (PLANT); TREWIA;

EID: 35348934281     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.94.10.1726     Document Type: Article

References (100)

1. AIRY SHAW, H. K. 1963. Notes on Malaysian and other Asiatic Euphorbiaceae. Kew Bulletin 16: 341-372.
2. AIRY SHAW, H. K. 1965. Notes on Malaysian and other Asiatic Euphorbiaceae. Kew Bulletin 19: 299-328.
3. AIRY SHAW, H. K. 1968. Malesian and other Asiatic Euphorbiaceae. Kew Bulletin 21: 379-400.
4. AIRY SHAW, H. K. 1969. Notes on Malesian and other Asiatic Euphorbiaceae. Kew Bulletin 23: 1-131.
5. AIRY SHAW, H. K. 1971. Notes on Malesian and other Asiatic Euphorbiaceae. Kew Bulletin 25: 473-553.
6. AKHMETIEV, M. A., AND S. V. VIKULIN. 1995. Peltate leaves Macaranga Thouin (Euphorbiaceae) in the Cenozoic of Eastern Sikhote-Alin' [in Russian]. Paleontological Journal 1995(2): 151-156.
7. ALEJANDRO, G. D., S. G. RAZAFIMANDIMBISON, AND S. LIEDE-SCHUMANN. 2005. Polyphyly of Mussaenda inferred from ITS and trnT-F data and its implications for generic limits in Mussaendeae (Rubiaceae). American Journal of Botany 92: 544-557.
8. ALFARO, M. E., S. ZOLLER, AND F. LUTZONI. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20: 255-266.
9. AUSTIN, J. J., E. N. ARNOLD, AND C. G. JONES. 2004. Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene Islands. Molecular Phylogenetics and Evolution 31: 109-122.
10. BÄNFER, G., B. FIALA, AND K. WEISING. 2004. AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies. Plant Systematics and Evolution 249: 213-231.
11. BÄNFER, G., U. MOOG, B. FIALA, M. MOHAMED, K. WEISING, AND F. R. BLATTNER. 2006. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridisation, vicariance and long-distance dispersal. Molecular Ecology 15: 4409-4424.
12. BERRY, P. E., A. L. HIPP, K. J. WURDACK, B. VAN EE, AND R. RIINA. 2005. Molecular phylogenetics of the giant genus Croton and tribe Crotoneae (Euphorbiaceae sensu stricto) using ITS and trnL-trnF DNA sequence data. American Journal of Botany 92: 1520-1534.
13. BLATTNER, F. R., K. WEISING, G. BÄNFER, U. MASCHWITZ, AND B. FIALA. 2001. Molecular analysis of phylogenetic relationships among myrmecophytic Macaranga species (Euphorbiaceae). Molecular Phylogenetics and Evolution 19: 331-344.
14. BOLLENDORFF, S. M., P. C. VAN WELZEN, AND J. W. F. SLIK. 2000. A taxonomic revision of Mallotus section Polyadenii (Euphorbiaceae). Blumea 45: 319-340.
15. DARLU, P., AND G. LECOINTRE. 2002. When does the incongruence length difference test fail? Molecular Biology and Evolution 19: 432-437.
16. DAVIES, S. J. 2001. Systematics of Macaranga sects. Pachystemon and Pruinosae (Euphorbiaceae). Harvard Papers in Botany 6: 371-448.
17. DAVIES, S. J., S. K. Y. LUM, R. CHAN, AND L. K. WANG. 2001. Evolution of myrmecophytism in western Malesian Macaranga (Euphorbiaceae). Evolution 55: 1542-1559.
18. DAVIS, C. C., O. W. CAMPBELL, K. J. WURDACK, C. A. JARAMILLO, AND M. J. DONOGHUE. 2005. Explosive radiation of Malphigiales supports a Mid-Cretaceous origin of modern tropical rain forests. American Naturalist 165: E36-E65.
19. DAYANANDAN, S., P. S. ASHTON, S. M. WILLIAMS, AND R. B. PRIMACK. 1999. Phylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast rbcL gene. American Journal of Botany 86: 1182-1190.
20. DINERSTEIN, E., AND C. M. WEMMER. 1988. Fruits rhinoceros eat: dispersal of Trewia nudiflora (Euphorbiaceae) in lowland Nepal. Ecology 69: 1768-1774.
21. DOLPHIN, K., R. BELSHAW, C. D. L. ORME, AND D. L. J. QUICKE. 2000. Noise and incongruence: interpreting results of the incongruence length difference test. Molecular Phylogenetics and Evolution 17: 401-406.
22. DOUADY, C. J., F. DELSUC, Y. BOUCHER, W. F. DOOLITTLE, AND E. J. P. DOUZERY. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution 20: 248-254.
23. EMSHWILLER, E., AND J. J. DOYLE. 1999. Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Molecular Phylogenetics and Evolution 12: 310-319.
24. EMSHWILLER, E., AND J. J. DOYLE. 2002. Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthetase data. American Journal of Botany 89: 1042-1056.
25. ESSER, H.-J. 2003. Fruit characters in Malesian Euphorbiaceae. Telopea 10: 169-177.
26. FARRIS, J. S., V. A. ALBERT, M. KALLERSJÖ , D. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
27. FARRIS, J. S., M. KALLERSJÖ, A. G. KLUGE, AND C. BULT. 1994. Testing significance of incongruence. Cladistics 10: 315-319.
28. FELSENSTEIN, J. 1985. Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39: 783-791.
29. FLYNN, J. J., AND M. A. NEDBAL. 1998. Phylogeny of the Carnivora (Mammalia): congruence vs. incompatibility among multiple data sets. Molecular Phylogenetics and Evolution 9: 414-426.
30. FREUDENSTEIN, J. V., C. VAN DEN BERG, D. H. GOLDMAN, P. J. KORES, M. MOLVRAY, AND M. W. CHASE. 2004. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. American Journal of Botany 91: 149-157.
31. GUINDON, S., AND O. GASCUEL. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
32. HALL, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
33. HILLIS, D. M., AND J. J. BULL. 1993. An empirical-test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192.
34. HIPP, A. L., J. C. HALL, AND K. J. SYTSMA. 2004. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Systematic Biology 53: 81-89.
35. HOLLAND, B., AND V. MOULTON. 2003. Consensus networks: a method for visualising incompatibilities in collections of trees. In G. Benson and R. Page [eds.], Algorithms in bioinformatics, WABI 2003. Springer-Verlag, Berlin, Germany.
36. HOLLAND, B. R., F. DELSUC, AND V. MOULTON. 2005. Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Systematic Biology 54: 66-76.
37. HORIUCHI, J., AND H. TAKIMOTO. 2001. Plant mega-fossils from the Late Early to Early Middle Miocene Asakawa formation at Inuboe Pass, Ibaraki Prefecture, Kanto District, Japan. Bulletin of Ibaraki Nature Museum 4: 1-32.
38. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
39. HUSON, D. H., AND D. BRYANT. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
40. JANSA, S. A., S. M. GOODMAN, AND P. K. TUCKER. 1999. Molecular phylogeny and biogeography of the native rodents of Madagascar (Muridae: Nesomyinae): a test of the single-origin hypothesis. Cladistics 15: 253-270.
41. KATHRIARACHCHI, H., R. SAMUEL, P. HOFFMANN, J. MLINAREC, K. J. WURDACK, H. RALIMANANA, T. F. STUESSY, AND M. W. CHASE. 2006. Phylogenetics of tribe Phyllantheae (Phyllanthaceae; Euphorbiaceae sensu lato) based on nrITS and plastid matK DNA sequence data. American Journal of Botany 93: 637-655.
42. KELCHNER, S. A. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 482-498.
43. KULJU, K. K. M., S. E. C. SIERRA, AND P. C. VAN WELZEN. 2007. Re-shaping Mallotus [part 2]: inclusion of Neotrewia, Octospermum and Trewia in Mallotus s.s. (Euphorbiaceae s.s.). Blumea 52: 115-136.
44. MADDISON, D. R., AND W. P. MADDISON. 2001. MacClade 4: analysis of phylogeny and character evolution, version 4.06. Sinauer, Sunderland, Massachusetts, USA.
45. MCLOUGHLIN, S. 2001. The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Australian Journal of Botany 49: 271-300.
46. MCPHERSON, G. 1995. On Mallotus and Deuteromallotus (Euphorbiaceae) in Madagascar. Bulletin Du Museum National D'Histoire Naturelle B, Adansonia 17: 169-173.
47. MÜLLER, J. 1865. Euphorbiaceae. Linnaea 34: 184-197.
48. MÜLLER, J. 1866. Euphorbiaceae tribus Acalypheae. In A. de Candolle [ed.], Prodromus systematis naturalis regni vegetabilis, vol. 15, 2, 956-1015. Masson & Fils, Paris, France.
49. MÜLLER, K. 2004. PRAP-computation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 31: 780-782.
50. MÜLLER, K. 2005a. SeqState: primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 4: 65-69.
51. MÜLLER, K. 2005b. The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support. BMC Evolutionary Biology 5.
52. MÜLLER, K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667-676.
53. NIXON, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
54. NYLANDER, J. A. A. 2004. MrModel test, version 2. Program distributed by the author. Evolutionary Biology Center, Uppsala University.
55. PAX, F., AND K. HOFFMANN. 1914. Euphorbiaceae-Acalypheae-Mercurialinae. In A. Engler [ed.], Das Pflanzenreich, vol. IV.147.vii. Engelmann, Leipzig, Germany.
56. PAX, F., AND K. HOFFMANN. 1919. Euphorbiaceae-Additamentum VI. In A. Engler [ed.], Das Pflanzenreich, vol. IV.147.xiv. Engelmann, Leipzig, Germany.
57. PAX, F., AND K. HOFFMANN. 1931. Euphorbiaceae. In A. Engler and K. Prantl [eds.], Die Natürlichen Pflanzenfamilien, vol. 19c, 11-233. Engelmann, Leipzig, Germany.
58. POSADA, D., AND T. R. BUCKLEY. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808.
59. QUANDT, D., K. MÜLLER, AND S. HUTTUNEN. 2003. Characterisation of the chloroplast DNA psbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions. Plant Biology 5: 400-410.
60. RADCLIFFE-SMITH, A. 2001. Genera Euphorbiacearum. Royal Botanic Gardens, Kew, UK.
61. RANNALA, B., AND Z. H. YANG. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43: 304-311.
62. RAVEN, P. H., AND D. I. AXELROD. 1974. Angiosperm biogeography and past continental movements. Annals of the Missouri Botanical Garden 61: 539-673.
63. RAXWORTHY, C. J., M. R. J. FORSTNER, AND R. A. NUSSBAUM. 2002. Chameleon radiation by oceanic dispersal. Nature 415: 784-787.
64. RENNER, S. S. 2004. Multiple Miocene Melastomataceae dispersal between Madagascar, Africa and India. Philosophical Transactions of the Royal Society, B, Biological Sciences 359: 1485-1494.
65. RIDLEY, H. N. 1910. Symbiosis of ants and plants. Annals of Botany 24: 457-483.
66. RONQUIST, F., AND J. P. HUELSENBECK. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
67. SAMUEL, R., W. GUTERMANN, T. F. STUESSY, C. F. RUAS, H. W. LACK, K. TREMETSBERGER, S. TALAVERA, B. HERMANOWSKI, AND F. EHRENDORFER. 2006. Molecular phylogenetics reveals Leontodon (Asteraceae, Lactuceae) to be diphyletic. American Journal of Botany 93: 1193-1205.
68. SAMUEL, R., H. KATHRIARACHCHI, P. HOFFMANN, M. H. J. BARFUSS, K. J. WURDACK, C. C. DAVIS, AND M. W. CHASE. 2005. Molecular phylogenetics of Phyllanthaceae: evidence from plastid MatK and nuclear phyC sequences. American Journal of Botany 92: 132-141.
69. SANG, T., D. J. CRAWFORD, AND T. F. STUESSY. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution. Proceedings of the National Academy of Sciences, USA 92: 6813-6817.
70. SCHATZ, G. E. 1996. Malagasy/Indo-Australo-Malesian phytogeographic connections. In W. R. Lourenco [ed.], Biogeography of Madagascar, 73-83. Editions de l'ORSTOM, Paris, France.
71. SIERRA, S. E. C., M. APARICIO, M. J. H. GEBRAAD, K. K. M. KULJU, AND P. C. VAN WELZEN. 2007. The morphological range in Mallotus and a taxonomic revision of its section Rottleropsis (including Axenfeldia) in Malesia, Thailand and Africa. Blumea 52: 21-113.
72. SIERRA, S. E. C., M. APARICIO, K. K. M. KULJU, Ž. FIŠER, P. C. VAN WELZEN, AND R. W. J. M. VAN DER HAM. 2006. Re-shaping Mallotus [part 1]: expanded circumscription and revision of the genus Cordemoya (Euphorbiaceae). Blumea 51: 519-540.
73. SIERRA, S. E. C., AND P. C. VAN WELZEN. 2005. A taxonomic revision of Mallotus section Mallotus (Euphorbiaceae) in Malesia. Blumea 50: 249-274.
74. SIERRA, S. E. C., P. C. VAN WELZEN, AND J. W. F. SLIK. 2005. A taxonomic revision of Mallotus section Philippinenses (former section Rottlera-Euphorbiaceae) in Malesia and Thailand. Blumea 50: 221-248.
75. SIMMONS, M. P., AND H. OCHOTERENA. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
76. SIMMONS, M. P., K. M. PICKETT, AND M. MIYA. 2004. How meaningful are Bayesian support values? Molecular Biology and Evolution 21: 188-199.
77. SLIK, J. W. F., P. J. A. KEßLER, AND P. C. VAN WELZEN. 2003. Macaranga and Mallotus species (Euphorbiaceae) as indicators for disturbance in the mixed lowland dipterocarp forest of East Kalimantan (Indonesia). Ecological Indicators 2: 311-324.
78. SLIK, J. W. F., AND P. C. VAN WELZEN. 2001a. A phylogeny of Mallotus (Euphorbiaceae) based on morphology: indications for a pioneer origin of Macaranga. Systematic Botany 26: 786-796.
79. SLIK, J. W. F., AND P. C. VAN WELZEN. 2001b. A taxonomic revision of Mallotus sections Hancea and Stylanthus (Euphorbiaceae). Blumea 46: 3-66.
80. SULLIVAN, J. 1996. Combining data with different distributions of among-site rate variation. Systematic Biology 45: 375-380.
81. SUZUKI, Y., G. V. GLAZKO, AND M. NEI. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences, USA 99: 16138-16143.
82. SWOFFORD, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA.
83. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. Mable [eds.], Molecular systematics, 407-514. Sinauer, Sunderland, Massachusetts, USA.
84. TABERLET, P., L. GIELLY, G. PAUTOU, AND J. BOUVET. 1991. Universal primers for amplification of 3 noncoding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
85. THOMPSON, J. D., D. G. HIGGINS, AND T. J. GIBSON. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
86. VAN WELZEN, P. C., AND S. E. C. SIERRA. 2006. The Mallotus wrayi complex (Euphorbiaceae). Blumea 51: 373-388.
87. VAN WELZEN, P. C., S. E. C. SIERRA, M. J. H. GEBRAAD, AND K. K. M. KULJU. 2006. The distinction of five Mallotus species formerly in section Hancea (Euphorbiaceae). Blumea 51: 367-372.
88. WEBSTER, G. L. 1994. Synopsis of the genera and suprageneric taxa of Euphorbiaceae. Annals of the Missouri Botanical Garden 81: 33-144.
89. WHITE, T. J., T. BRUNS, S. LEE, AND J. TAYLOR. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White [eds.], PCR protocols. A guide to methods and applications, 315-322. Academic Press, San Diego, California, USA.
90. WHITMORE, T. C. 1965. Studies in Macaranga, an easy genus of Malayan wayside trees. Malayan Nature Journal 20: 89-99.
91. WHITMORE, T. C. 1969. Studies in Macaranga, III. First thoughts on species evolution in Malayan Macaranga. Biological Journal of the Linnean Society 1: 223-231.
92. WHITMORE, T. C. 1980. Studies in Macaranga, VIII. Macaranga in New Guinea and the Bismarck Archipelago. Kew Bulletin 34: 599-606.
93. WHITMORE, T. C. In press. Prodromus of Macaranga (Euphorbiaceae). M. J. E. Coode and P. Hoffmann [eds.]. Royal Botanic Gardens, Kew, UK.
94. WIENS, J. J. 1998. Combining data sets with different phylogenetic histories. Systematic Biology 47: 568-581.
95. WURDACK, K. J., P. HOFFMANN, AND M. W. CHASE. 2005. Molecular phylogenetic analysis of uniovulate Euphorbiaceae (Euphorbiaceae sensu stricto) using plastid rbcL and trnL-F DNA sequences. American Journal of Botany 92: 1397-1420.
96. WURDACK, K. J., P. HOFFMANN, R. SAMUEL, A. DE BRUIJN, M. VAN DER BANK, AND M. W. CHASE. 2004. Molecular phylogenetic analysis of Phyllanthaceae (Phyllanthoideae pro parte, Euphorbiaceae sensu lato) using plastid RbcL DNA sequences. American Journal of Botany 91: 1882-1900.
97. YODER, A. D., J. A. IRWIN, AND B. A. PAYSEUR. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology 50: 408-424.
98. YUAN, Y.-M., S. WOHLHAUSER, M. MÖLLER, J. KLACKENBERG, M. W. CALLMANDER, AND P. KÜPFER. 2005. Phylogeny and biogeography of Exacum (Gentianaceae): a disjunctive distribution in the Indian Ocean basin resulted from long-distance dispersal and extentive radiation. Systematic Biology 54: 21-34.
99. ZOHARY, M. 1973. Geobotanical foundations of the Middle East. Gustav Fischer-Verlag, Stuttgart, Germany.
100. ZOLLINGER, H. 1856. Über die Rottlera-Arten. Linnaea 28: 299-332.