Speciation of a tropical fungal species pair following transoceanic dispersal

Molecular Phylogenetics and Evolution

Volumn 51, Issue 3, 2009, Pages 413-426

  Liu, Miao ^a   Milgroom, Michael G ^a   Chaverri, Priscila ^a   Hodge, Kathie T ^a  

^a Department of Molecular Biology and Genetics   (United States)

Author keywords

Biogeography; Coalescence; Fungi; Hypocreales; Migration; Moelleriella libera; Moelleriella raciborskii; Neotropics; Paleotropics; Phylogenetics

Indexed keywords

ELONGATION FACTOR 1; FUNGAL DNA; RNA POLYMERASE II; TUBULIN;

ARTICLE; ASCOMYCETES; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; FUNGAL GENE; GENE FLOW; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION;

ASCOMYCOTA; DNA, FUNGAL; EVOLUTION, MOLECULAR; GENE FLOW; GENES, FUNGAL; GENETIC SPECIATION; GENETICS, POPULATION; MODELS, GENETIC; PEPTIDE ELONGATION FACTOR 1; PHYLOGENY; RNA POLYMERASE II; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TUBULIN;

ASCOMYCOTA; CLAVICIPITACEAE; FUNGI; HYPOCREALES;

EID: 67349106680     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.03.014     Document Type: Article

References (86)

1. Argov Y., Rassler Y., Voet H., and Rosen D. The biology and phenology of the citrus whitefly, Dialeurodes citri, on citrus in the Coastal Plain of Israel. Entomol. Exp. Appl. 93 (1999) 21-27
2. Aylor D., and Carbone I. SNAP Combine and Map (2003), Department of Plant Pathology, North Carolina State University, Raleigh, NC
3. Bahlo M., and Griffiths R.C. Inference from gene trees in a subdivided population. Theor. Popul. Biol. 57 (2000) 79-95
4. Beerli P., and Felsenstein J. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152 (1999) 763-773
5. Beerli P., and Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98 (2001) 4563-4568
6. Berbee M.L., and Taylor J.W. Dating the evolutionary radiations of the true fungi. Canadian Journal of Botany 71 (1993) 1114-1127
7. Byrne D.N. Migration and dispersal by the sweet potato whitefly, Bemisia tabaci. Agric. For. Meteorol. 97 (1999) 309-316
8. Byrne D.N., and Bellows T.S.J. Whitefly biology. Annu. Rev. Entomol. 36 (1991) 431-457
9. Carbone I., and Kohn L. Inferring process from pattern in fungal population genetics. In: Arora D.K., and Khachatourians G.G. (Eds). Fungal Genomics, Applied Mycology and Biotechnology Series (2004), Elsevier Science 29-58
10. Carbone I., Liu Y.C., Hillman B.I., and Milgroom M.G. Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics 166 (2004) 1611-1629
11. Chaverri P., Liu M., and Hodge K.T. A monograph of the entomopathogenic genera Hypocrella, Moelleriella and Samuelsia gen nov. (Ascomycota, Hypocreales, Clavicipitaceae), and their anamorphs in the Neotropics. Stud. Mycol. 60 (2008) 1-66
12. Clement M., Posada D., and Randall K. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
13. Couch B.C., Fudal I., Lebrun M.-H., Tharreau D., Valent B., van Kim P., Notteghem J.-L., and Kohn L.M. Origins of host-specific populations of the blast pathogen Magnaporthe oryzae in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice. Genetics 170 (2005) 613-630
14. Davis J.I., and Nixon K.C. Populations, genetic variation, and the delimitation of phylogenetic species. Syst. Biol. 41 (1992) 421-435
15. De Barro P.J., Driver F., Trueman J.W.H., and Curran J. Phylogenetic relationships of world populations of Bemisia tabaci (Gennadius) using ribosomal ITS1. Mol. Phylogenet. Evol. 16 (2000) 29-36
16. de Queiroz A.d. The resurrection of oceanic dispersal in historical biogeography. Trends Ecol. Evol. 20 (2005) 68-73
17. de Queiroz A., and Good D.A. Phenetic clustering in biology: a critique. Q. Rev. Biol. 72 (1997) 3-30
18. den Bakker H.C., Zuccarello G.C., Kuyper T.W., and Noordeloos M.E. Evolution and host specificity in the ectomycorrhizal genus Leccinum. New Phytol. 163 (2004) 201-215
19. Dettman J.R., Jacobson D.J., and Taylor J.W. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57 (2003) 2703-2720
20. Doyle J.J. The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Syst. Bot. 20 (1995) 574-588
21. Evans H.C., and Hywel-Jones N. Aspects of the genera Hypocrella and Aschersonia as pathogens of coccids and whiteflies. In: Cooper D.J., Drummond J., and Pinnock D.E. (Eds). Proceedings of the 5th International Colloquium on Invertebrate Pathology and Microbial Control (1990), Adelaide, Australia 111-115
22. Fang G., Hammar S., and Grumet R. A quick and inexpensive method for removing polysaccharides from plant genomic DNA. BioTechniques 13 (1992) 52-56
23. Fu Y.X. Statistical test of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
24. Fu Y.X., and Li W.H. Statistical tests of neutrality of mutations. Genetics 133 (1993) 693-709
25. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 34 (2003) 397-423
26. Griffiths R.C., and Tavare S. Ancestral inference in population genetics. Stat. Sci. 9 (1994) 307-319
27. Griffiths R.C., and Tavare S. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math. Biosci. 127 (1995) 77-98
28. Harrington T.C., and Rizzo D.M. Defining species in the fungi. In: Worrall J.J. (Ed). Structure and Dynamics of Fungal Populations (1999), Kluwer Press, Dordrecht, Netherlands 43-71
29. Harrington T.C., and Wingfield M.J. The Ceratocystis species on conifers. Can. J. Bot. 76 (1998) 1446-1457
30. Harrison R.G. Link evolutionary pattern and process: the relevance of species concepts for the study of speciation. In: Howard D.J., and Berlocher S.H. (Eds). Endless Forms: Species and Speciation (1998), Oxford University Press, New York
31. Hey J., and Wakeley J. A coalescent estimator of the population recombination rate. Genetics 145 (1997) 833-864
32. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
33. Hibbett D.S. Shiitake mushrooms and molecular clocks: historical biogeography of Lentinula. J. Biogeogr. 28 (2001) 231-241
34. Highton R. Biochemical evolution in the slimy salamander of the Plethodon glutinossu complex in the eastern United States. Part I. Geographic protein variation. Univ. Ill. Biol. Monogr. 57 (1989) 1-78
35. Highton R. Is Ensatina escholtzii a ring-species?. Herpetologica 54 (1998) 254-278
36. Hudson R.R., Boos D.D., and Kaplan N.L. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9 (1992) 138-151
37. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
38. Humphries C.J., and Parenti L.R. Cladistic biogeography: interpreting patterns of plant and animal distributions. second ed. (1999), Oxford University Press, New York
39. Kingman J. The coalescent. Stoch. Process. Appl. 13 (1982) 235-248
40. Kingman J. On the genealogy of large populations. In: Gani J., and Hannan E. (Eds). Essays in Statistical Science (1982), Applied Probability Trust, London 27-43
41. Knapp M., Stöckler K., Havell D., Delsuc F., Sebastiani F., and Lockhart P.J. Relaxed molecular clock provides evidence for long-distance despersal of Nothofagus (Southern Beech). Pub. Libr. Sci. 3 (2005) 38-42
42. Kohn L.M. Mechanisms of fungal speciation. Annu. Rev. Phytopathol. 43 (2005) 279-308
43. Lavin M., and Luckow M. Origins and relationships of tropical North America in the context of the boreotropics hypothesis. Am. J. Bot. 80 (1993) 1-14
44. Lee S.B., Milgroom M.G., and Taylor J.W. A rapid, high-yield mini-prep method for isolation of total genomic DNA from fungi. Fungal Genet. Newsl. 35 (1988) 23-24
45. Liu M., Chaverri P., and Hodge K.T. A taxonomic revision of the insect biocontrol fungus Aschersonia aleyrodis, its allies with white stromata and their Hypocrella sexual states. Mycol. Res. 110 (2006) 537-554
46. Liu M., and Hodge K. Hypocrella zhongdongii sp. Nov., the teleomorph of Aschersonia incrassata. Mycol. Res. 109 (2005) 818-824
47. Liu M., Rombach M.C., Humber R.A., and Hodge K.T. What's in a name? Aschersonia insperata: a new pleoanamorphic fungus with characteristics of Aschersonia and Hirsutella. Mycologia 97 (2005) 249-256
48. Liu Y.J., Whelen S., and Hall B.D. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit. Mol. Biol. Evol. 16 (1999) 1799-1808
49. Mains E.B. North American species of Aschersonia parasitic on Aleyrodidae. J. Insect Pathol. 1 (1959) 43-47
50. Mains E.B. Species of Aschersonia (Sphaeropsidales). Lloydia 22 (1959) 215-221
51. Mains E.B. Species of Hypocrella. Mycopathol. Mycol. Appl. 11 (1959) 311-326
52. Markwordt, J.D., Doshi, R. Carbone, I., 2004. SNAP Clade and Matrix. Distributed over the Internet. Department of Plant Pathology, North Carolina University. Available from: .
53. Mason-Gamer R.J., and Kellogg E.A. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst. Biol. 45 (1996) 524-545
54. Meekes E.T.M., Fransen J.J., and van-Lenteren J.C. Pathogenicity of Aschersonia spp. against whiteflies Bemisia argentifolii and Trialeurodes vaporariorum. J. Invert. Pathol. 81 (2002) 1-11
55. Nielsen R., and Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158 (2001) 885-896
56. Nikoh N., and Fukatsu T. Interkingdom host jumping underground: phylogenetic analysis of entomoparasitic fungi of the genus Cordyceps. Mol. Biol. Evol. 17 (2000) 629-638
57. Nilsson R.H., Hallenberg N., Norden B., Maekawa N., and Wu S.H. Phylogeography of Hyphoderma setigerum (Basidiomycota) in the northern hemisphere. Mycol. Res. 107 (2003) 645-652
58. O'Donnell K., and Cigelnik E. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol. Phylogenet. Evol. 7 (1997) 103-116
59. O'Donnell K., Kistler H.C., Cigelnik E., and Ploetz R.C. Multiple evolutionary origins of the fungus causing Panama disease of banana: concordant evidence from nuclear, mitochondrial gene genealogies. Proc. Natl. Acad. Sci. USA 95 (1998) 2044-2049
60. Patterson C. Methods of paleobiogeography. In: Nelson G., and Rosen D.E. (Eds). Vicariance Biogeography: A Critique (1981), Columbia University Press 446-489
61. Sikes D.S., and Lewis P.O. Beta software, Version 1. PAUPRat: PAUP* Implementation of the Parsimony Ratchet (2001), Distributed by the Authors. Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, USA
62. Perring T.M. The Bemisia tabaci species complex. Crop Prot. 20 (2001) 725-737
63. Petch T. Studies in entomogenous fungi. II. The genera of Hypocrella and Aschersonia. Ann. Roy. Bot. Gard. Peradeniya 7 (1921) 167-278
64. Petch T. Additions to Ceylon fungi. III. Ann. Roy. Bot. Gard. Peradeniya 9 (1925) 313-328
65. Porter A.H. Testing nominal species boundaries using gene flow statistics: the taxonomy of two hybridizing admiral butterflies (Limenitis: Nymphalidae). Syst. Zool. 39 (1990) 148-161
66. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
67. Price E.W., and Carbone I. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21 (2005) 402-404
68. Rosen D.E. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27 (1978) 159-188
69. Rosenberg N.-A., and Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3 (2002) 380-390
70. Rozas J., and Rozas R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15 (1999) 174-175
71. Rua P.D.L., Simon B., Cifuentes D., Martinez-Mora C., and Cenis J.L. New insights into the mitochondrial phylogeny of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in the Mediterranean basin. JZS 44 (2006) 25-33
72. Sorenson M.D., and Franzosa E.A. TreeRot, Version 3 (2007), Boston University, Boston, MA
73. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Version 4 (Computer Program) (1998), Sinauer Associates, Sunderland, Massachusetts
74. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
75. Taylor D.W. Paleobiogeographic relationships of angiosperms from Cretaceous and early Tertiary of the North American area. Bot. Rev. 56 (1990) 279-379
76. Taylor J.W., Jacobson D.J., Kroken S., Kasuga T., Geiser D.M., Hibbett D.S., and Fisher M.C. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31 (2000) 21-32
77. Templeton A.R. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol. Ecol. 7 (1998) 381-397
78. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-809
79. Templeton A.R., Boerwinkle E., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117 (1987) 343-351
80. Thompson J.D., Higgins D.G., and Gibson T.J. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
81. Tiffney B.H. The Eocene North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the northern hemisphere. J. Arnold Arboretum 66 (1985) 243-273
82. Vilgalys R., and Sun B.L. Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc. Natl. Acad. Sci. USA 91 (1994) 4599-4603
83. Watterson G.A. The homozygosity test of neutrality. Genetics 88 (1978) 405-417
84. Wiens J.J. Polymorphism in systematics and comparative biology. Annu. Rev. Ecol. Syst. 30 (1999) 327-362
85. Wolfe J.A. Some aspects of plant geography of the northern hemisphere during the late Cretaceous and Tertiary. Ann. Mo. Bot. Gard. 62 (1975) 264-279
86. Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. Dissertation. The University of Texas at Austin.