Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

Molecular Phylogenetics and Evolution

Volumn 64, Issue 3, 2012, Pages 533-544

  Oliveira, Deodoro C S G ^a   Almeida, Francisca C ^b   O'Grady, Patrick M ^c   Armella, Miguel A ^d   DeSalle, Rob ^e   Etges, William J ^f  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d DEPARTAMENTO DE QUÍMICA   (Mexico)

^e DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^f UNIVERSITY OF ARKANSAS   (United States)

Author keywords

Biogeography; Cactus; Drosophila repleta species group; Host plants; Molecular clock; Molecular phylogeny

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; DROSOPHILA; EVOLUTION; GENETICS; OPUNTIA; PHYLOGENY; PHYLOGEOGRAPHY; PHYSIOLOGY; SOUTH AMERICA; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; CELL NUCLEUS; DNA, MITOCHONDRIAL; DROSOPHILA; LIKELIHOOD FUNCTIONS; OPUNTIA; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA;

CACTACEAE; DROSOPHILA REPLETA; MYA; OPUNTIA; OPUNTIOIDEAE; REPLETA GROUP;

EID: 84863106687     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.05.012     Document Type: Article

References (106)

1. Acurio A.E., Rafael V.L. Inventario taxonómico de drosophilidae (Diptera) en el Parque Nacional Yasuni, Amazonia Ecuatoriana. Acta Amazon. 2009, 39:713-718.
2. Acurio A.E., Rafael V.L. Diversity and geographical distribution of Drosophila (Diptera, Drosophilidae) in Ecuador. Dros. Inform. Serv. 2010, 92:20-25.
3. Almeida F.C., DeSalle R. Evidence of adaptive evolution of accessory gland proteins in closely related species of the Drosophila repleta group. Mol. Biol. Evol. 2008, 25:2043-2053.
4. Almeida F., DeSalle R. Orthology, function, and evolution of accessory gland proteins in the Drosophila repleta group. Genetics 2009, 181:235-245.
5. Barker J.S.F., Starmer W.T. Ecological Genetics and Evolution: The Cactus-Yeast-Drosophila Model 1982, Academic Press, New York.
6. Barker J.S.F., Starmer W.T., MacIntyre R.I. Ecological and Evolutionary Genetics of Drosophila 1990, Plenum Press, New York.
7. Beckenbach A.T., Wei W., Liu H. Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences. Mol. Biol. Evol. 1993, 10:619-634.
8. Beckenbach A.T., Heed W.B., Etges W.J. A mitochondrial DNA analysis of vicariant speciation in two lineages in the Drosophila mulleri subgroup. Evol. Ecol. Res. 2008, 10:475-492.
9. Bergsten J. A review of long-branch attraction. Cladistics 2005, 21:163-193.
10. Bonacum J., DeSalle R., O'Grady P., Oliveira D., Wintermute J., Zilversmit M. New nuclear and mitochondrial primers for systematics and comparative genomics in Drosophilidae. Dros. Inform. Serv. 2001, 84:201-204.
11. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 1988, 42:795-803.
12. Brncic D. Las especies Chilenas de Drosophilidae. Colec. Monografias Biol. Univ. Chile 1957, 8:1-136.
13. Bull N.J., Schwarz M.P., Cooper S.J.B. Phylogenetic divergence of the Australian allodapine bees (Hymenoptera, Apidae). Mol. Phylogenet. Evol. 2003, 27:212-222.
14. Cáceres M., Ranz J.M., Barbadilla A., Long M., Ruiz A. Generation of a widespread Drosophila inversion by a transposable element. Science 1999, 285:415-418.
15. Carson, H.L., 1971. The ecology of Drosophila breeding sites. Harold L. Lyon Arboretum Lecture Number Two. University of Hawaii, Honolulu, pp. 1-27.
16. Carson H.L. Danko Brncic and the flower flies. Rev. Chil. Hist. Nat. 2001, 74:33-40.
17. Carson H.L., Wasserman M. A widespread chromosomal polymorphism in a widespread species, Drosophila buzzatii. Am. Nat. 1965, 99:111-115.
18. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
19. Coyne J.A., Orr H.A. " Patterns of speciation in Drosophila" revisited. Evolution 1997, 51:295-303.
20. Diniz N.M., Sene F.M. Chromosomal phylogeny of the Drosophila fasciola species subgroup revisited (Diptera, Drosophilidae). Genet. Mol. Biol. 2004, 27:561-566.
21. Durando C.M., Baker R.H., Etges W.J., Heed W.B., Wasserman M., DeSalle R. Phylogenetic analysis of the repleta species group of the genus Drosophila using multiple sources of characters. Mol. Phylogenet. Evol. 2000, 16:296-307.
22. Edwards E.J., Nyffeler R., Donoghue M.J. Basal cactus phylogeny: implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form. Am. J. Bot. 2005, 92:1177-1188.
23. Etges W.J., Jackson L.L. Epicuticular hydrocarbon variation in Drosophila mojavensis cluster species. J. Chem. Ecol. 2001, 27:2125-2149.
24. Etges W.J., Johnson W.R., Duncan G.A., Huckins G., Heed W.B. Ecological genetics of cactophilic Drosophila. Ecology of Sonoran Desert Plants and Plant Communities 1999, 164-214. University of Arizona Press, Tucson. R. Robichaux (Ed.).
25. Etges W.J., Armella M.A., O'Grady P., Heed W.B. Two new species of Drosophila (Diptera: Drosophilidae) in the repleta group from Mexico. Ann. Entomol. Soc. Am. 2001, 94:16-20.
26. Etges W.J., de Oliveira C.C., Noor M.A.F., Ritchie M.G. Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence and reproductive isolation. Evolution 2010, 64:3549-3569.
27. Fanara J.J., Fontdevila A., Hasson E. Oviposition preference and life history traits in cactophilic Drosophila koepferae and D. buzzatti in association with their natural hosts. Evol. Ecol. 1999, 13:173-190.
28. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Constructing a significance test for incongruence. Syst. Biol. 1995, 44:570-572.
29. Fellows D.P., Heed W.B. Factors affecting host plant selection in desert-adapted cactiphilic Drosophila. Ecology 1972, 53:850-858.
30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
31. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 1988, 22:521-565.
32. Fogleman J.C., Abril J.R. Ecological and evolutionary importance of host plant chemistry. Ecological and Evolutionary Genetics of Drosophila 1990, 121-141. Plenum, New York. J.S.F. Barker, W.T. Starmer, R.J. MacIntyre (Eds.).
33. Fogleman J.C., Danielson P.B. Chemical interactions in the Cactus-Microorganism-Drosophila model system of the Sonoran Desert. Am. Zool. 2001, 41:877-889.
34. Fogleman J., Williams J. Oviposition site preference of cactophilic Drosophila in the eremophila complex. Dros. Inform. Serv. 1987, 66:51-52.
35. Gibbs A.G., Matzkin L.M. Evolution of water balance in the genus Drosophila. J. Exp. Biol. 2001, 204:2331-2338.
36. Gibbs A.G., Perkins M.C., Markow T.A. No place to hide: microclimates of Sonoran Desert Drosophila. J. Therm. Biol. 2003, 28:353-362.
37. Griffith M.P. What did the first cactus look like? An attempt to reconcile the morphological and molecular evidence. Taxon 2004, 53:493-499.
38. Griffith M.P., Porter J.M. Phylogeny of Opuntioideae (Cactaceae). Int. J. Plant Sci. 2009, 170:107-116.
39. Hallstrom B.M., Janke A. Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations. BMC Evol. Biol. 2008, 8:162.
40. Hasson E., Naviera H., Fontdevila A. The breeding sites of the Argentinian species of the Drosophila mulleri complex (subgenus Drosophila repleta group). Rev. Chil. Hist. Nat. 1992, 65:319-326.
41. Heed W.B. Ecology and genetics of Sonoran Desert Drosophila. Ecological Genetics: The Interface 1978, 109-126. Springer-Verlag, New York. P.F. Brussard (Ed.).
42. Heed W.B. The origin of Drosophila in the Sonoran Desert. Ecological Genetics and Evolution: The Cactus-Yeast-Drosophila Model System 1982, 65-80. Academic Press, Sydney. J.S.F. Barker, W.T. Starmer (Eds.).
43. Heed W.B. Origin of Drosophila of the Sonoran Desert revisited: In search of a founder event and the description of a new species in the eremophila complex. Genetics, Speciation and the Founder Principle 1989, 253-278. Oxford Univ. Press. L.V. Giddings, K.Y. Kaneshiro, W.W. Anderson (Eds.).
44. Heed W.B., Grimaldi D.A. Revision of the morphocryptic, Caribbean mayaguana species subcluster in the Drosophila repleta group (Diptera: Drosophilidae). Am. Mus. Novit. 1991, 2999:1-10.
45. Huelsenbeck, J.P., Ronquist, F., 2005. Bayesian analysis of molecular evolution using MrBayes. In: Nielsen, R. (Ed.), Statistical Methods in Molecular, Evolution, pp. 183-232.
46. Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
47. Kelleher E.S., Swanson W.J., Markow T.A. Gene duplication and adaptive evolution of digestive proteases in Drosophila arizonae female reproductive tracts. PLoS Genet. 2007, 3(8):e148.
48. Kircher H.W. Chemical composition of cacti and its relationship to Sonoran Desert Drosophila. Ecological Genetics and Evolution. The Cactus-Yeast-Drosophila Model System 1982, 143-158. Academic Press, Sydney. J.S.F. Barker, W.T. Starmer (Eds.).
49. Kocher T.D. Adaptive evolution and explosive speciation: the cichlid fish model. Nat. Rev. Genet. 2004, 5:288-298.
50. Krebs R.A., Barker J.S.F. Crosses between D. aldrichi from Australia and northwest Mexico suggest that they are different species. Dros. Inform. Serv. 1994, 75:133-134.
51. Maddison, D.R., Maddison, W.P., 2005. MacClade 4: Analysis of Phylogeny and Character Evolution, Ver. 4.08. Sinauer, Sunderland, MA.
52. Maddison, W.P., Maddison, D.R., 2009. Mesquite: A Modular System for Evolutionary Analysis. Version 2.6.
53. Markow T.A., O'Grady P. Drosophila: A Guide to Species Identification and Use 2006, Academic Press, New York.
54. Marshal L.G. Land mammals and the Great American Interchange. Am. Sci. 1988, 76:380-388.
55. Matzkin L.M., Eanes W.F. Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila. Genetics 2003, 163:181-194.
56. Mauseth J.D. Continental drift, climate and the evolution of cacti. Cact. Succ. J. 1990, 62:302-308.
57. Morais P.B., Rosa C.A., Hagler A.N., Mendonca-Hagler L.C. Yeast communities as descriptors of habitat use by the Drosophila fasciola subgroup (repleta group) in Atlantic rain forests. Oecologia 1995, 104:45-51.
58. Moran T., Fontdevila A. On the phylogeny of the Drosophila hydei subgroup: new insights from combined analyses of nuclear and mitochondrial data. Mol. Phylogenet. Evol. 2007, 43:1198-1205.
59. Negre B., Casillas S., Suzanne M., Sánchez-Herrero E., Akam M., Nefedov M., Barbadilla A., de Jong P., Ruiz A. Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res. 2005, 15:692-700.
60. Nyffeler R. Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/matK and trnL-trnF sequences. Am. J. Bot. 2002, 89:312-326.
61. Nyffeler R., Eggli U. A farewell to dated ideas and concepts - molecular phylogenetics and a revised suprageneric classification of the family Cactaceae. Schumannia 2010, 6:109-149.
62. Oliveira D.C.S.G., O'Grady P.M., Etges W.J., Heed W.B., DeSalle R. Molecular systematics and geographical distribution of the Drosophila longicornis species complex (Diptera: Drosophilidae). Zootaxa 2005, 1069:1-32.
63. Oliveira D.C.S.G., Leonidas M., Etges W.J., O'Grady P.M., DeSalle R. Species delimitation in the Drosophila aldrichi subcluster (Diptera: Drosophilidae) using DNA sequences. Zootaxa 2008, 1725:37-47.
64. Patterson J.T. The Drosophilidae of Southwest. Univ. Tex. Publ. 1943, 4314:7-203.
65. Patterson J.T., Stone W.S. Evolution in the Genus Drosophila 1952, MacMillan, New York.
66. Pereira M.A.Q.R., Vilela C.R., Sene F.M. Notes on breeding and feeding sites of some species of the repleta group of the genus Drosophila (Diptera, Drosophilidae). Cienc. Cult. (São Paulo) 1983, 35:1313-1319.
67. Pitnick S., Heed W.B. New species of cactus-breeding Drosophila (Diptera: Drosophilidae) in the nannoptera species group. Ann. Entomol. Soc. Am. 1994, 87:307-310.
68. Powell J.R., DeSalle R. Drosophila molecular phylogenies and their uses. Evol. Biol. 1995, 28:87-138.
69. Rafael V., Arcos G. Subgrupo inca, un nuevo subgrupo del grupo repleta, con descripción de Drosophila huancavilcae n. sp (Diptera, Drosophilidae). Evol. Biol. 1989, 3:233-243.
70. Rafael V., Vela D. Drosophila yangana sp. nov. un nuevo miembro del grupo repleta, subgrupo inca (Diptera: Drosophilidae). Rev. Pontificia Univ. Católica Ecuador 2003, 71:129-139.
71. Rambaut, A., Drummond, A.J., 2003. Tracer: MCMC Trace Analysis Package.
72. Robe L.J., Loreto E.L.S., Valente V.L.S. Radiation of the " Drosophila" subgenus (Drosophilidae, Diptera) in the Neotropics. J. Zool. Syst. Evol. Res. 2010, 48:310-321.
73. Rodriguez-Trelles F., Alarcon L., Fontdevila A. Molecular evolution and phylogeny of the buzzatii complex (Drosophila repleta group): a maximum-likelihood approach. Mol. Biol. Evol. 2000, 17:1112-1122.
74. Rokas A., Kruger D., Carroll S.B. Animal evolution and the molecular signature of radiations compressed in time. Science 2005, 310:1933-1938.
75. Ronquist, F., 1996. DIVA 1.1. Computer Program and Manual Available by Anonymous FTP from Uppsala University (). http://www.ftp.sysbot.uu.se.
76. Ronquist F. Dispersal-Vicariance Analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 1997, 46:195-203.
77. Ruiz A., Heed W.B. Host plant specificity in the cactophilic Drosophila mulleri species complex. J. Anim. Ecol. 1988, 57:237-249.
78. Ruiz A., Heed W.B., Wasserman M. Evolution of the mojavensis cluster of cactophilic Drosophila with descriptions of two new species. J. Hered. 1990, 81:30-42.
79. Ruiz A., Cansian A.M., Kuhn G.C.S., Alves M.A.R., Sene F.M. The Drosophila serido speciation puzzle: putting new pieces together. Genetica 2000, 108:217-227.
80. Russo C.A., Takezaki N., Nei M. Molecular phylogeny and divergence times of Drosophilid species. Mol. Biol. Evol. 1995, 12:391-404.
81. Rutschmann, F., 2004. Bayesian Molecular Dating using PAML/Multidivtime. A Step-by-step Manual. University of Zurich, Zurich.
82. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
83. Silva-Bernardi E.C.C., Morales A.C., Sene F.M., Manfrin M.H. Phylogenetic relationships in the Drosophila fasciola species subgroup (Diptera, Drosophilidae) inferred from partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. Genet. Mol. Biol. 2006, 29:566-571.
84. Sorenson, M.D., 1999. TreeRot, Version 2. Boston University, Boston, MA.
85. Spicer G.S., Bell C.D. Molecular Phylogeny of the Drosophila virilis Species Group (Diptera: Drosophilidae) Inferred from Mitochondrial 12S and 16S Ribosomal RNA Genes. Ann. Entomol. Soc. Am. 2002, 95:156-161.
86. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
87. Stehli F.G., Webb S.D. The Great American Biotic Interchange 1985, Plenum Press, New York.
88. Stensmyr M.C., Stieber R., Hansson B.S. The Cayman crab fly revisited - phylogeny and biology of Drosophila endobranchia. PLoS One 2008, 3:e1942.
89. Sullivan J., Joyce P. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 2005, 36:445-466.
90. Suyo M.P.P., Pilares L. Drosophila novemaristata: descripcion, taxonomia y nuevas localidades peruanas. Rev. Peru. Entomol. 1987, 30:61-64.
91. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and other methods), Version 4.0 beta. Smithsonian Institution, Washington DC.
92. Tamura K., Subramanian S., Kumar S. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 2004, 21:36-44.
93. Tatarenkov A., Ayala F.J. Phylogenetic relationships among species groups of the virilis-repleta radiation of Drosophila. Mol. Phylogenet. Evol. 2001, 21:327-331.
94. Thorne J.L., Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 2002, 51:689-702.
95. Throckmorton L. The phylogeny, ecology, and geography of Drosophila. Handbook of Genetics 1975, 421-469. Plenum, New York. R. King (Ed.).
96. Vela D., Rafael V. Catorce nuevas especies del género Drosophila (Diptera, Drosophilidae) en el Bosque húmedo montano del volcán Pasochoa, Pichincha. Ecuador. Rev. Ecuat. Med. Cienc. Biol. 2005, 27:28-41.
97. Vilela C.R. A revision of the Drosophila repleta species group (Diptera, Drosophilidae). Rev. Bras. Entomol. 1983, 27:1-114.
98. Wagstaff B.J., Begun D.J. Molecular population genetics of accessory gland protein genes and testis-expressed genes in Drosophila mojavensis and D. arizonae. Genetics 2005, 171:1083-1101.
99. Wagstaff B.J., Begun D.J. Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. Genetics 2007, 177:1023-1030.
100. Ward B.L., Starmer W.T., Russell J.S., Heed W.B. The correlation of climate and host plant morphology with a gradient of an inversion polymorphism in Drosophila pachea. Evolution 1975, 28:565-575.
101. Wasserman M. Cytological studies of the repleta group of the genus Drosophila. IV. The hydei subgroup. Univ. Tex. Publ. 1962, 6205:73-84.
102. Wasserman M. Evolution and speciation in selected species groups. Evolution of the repleta group. The Genetics and biology of Drosophila 1982, 61-139. Academic Press, London. M. Ashburner, H.L. Carson, J.N. Thompson (Eds.).
103. Wasserman M. Cytological evolution of the Drosophila repleta species group. Drosophila Inversion Polymorphism 1992, 455-552. CRC Press, Boca Raton, FL. C.B. Krimbas, J.R. Powell (Eds.).
104. Wharton L.T. Interspecific hybridzation in the repleta group. Univ. Tex. Publ. 1944, 4445:175-193.
105. Wilgenbusch, J.C., Warren, D.L., Swofford, D.L., 2004. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. http://ceb.csit.fsu.edu/awty.
106. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.