Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: A case study on the Neofusicoccum parvum/N. ribis complex

Molecular Phylogenetics and Evolution

Volumn 51, Issue 2, 2009, Pages 259-268

  Pavlic, Draginja ^a   Slippers, Bernard ^a   Coutinho, Teresa A ^a   Wingfield, Michael J ^a  

^a Forestry and Agricultural Biotechnology Institute (FABI)   (South Africa)

Author keywords

Botryosphaeriaceae; Cryptic species; Fixed single nucleotide polymorphisms; GCPSR; Multiple gene genealogies; Syzygium cordatum

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

ARTICLE; ASCOMYCETES; CLASSIFICATION; DNA SEQUENCE; FUNGAL GENE; GENE FLOW; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AFRICA; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION;

ASCOMYCOTA; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GENE FLOW; GENES, FUNGAL; GENETIC SPECIATION; GEOGRAPHY; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA; SPECIES SPECIFICITY;

ASCOMYCOTA; BOTRYOSPHAERIACEAE; FUNGI; SYZYGIUM CORDATUM;

EID: 67349212619     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.12.017     Document Type: Article

References (62)

1. Bickford D., Lohman D.J., Sodhi N.S., Ng P.K.L., Meier R., Winker K., Ingram K.K., and Das I. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22 (2006) 148-155
2. Burgess T.I., Barber P.A., Hardy G.E., and St J. Botryosphaeria spp. associated with eucalypts in Western Australia including description of Fusicoccum macroclavatum sp. nov. Aust. Plant Path. 34 (2005) 557-567
3. Burgess T.I., Barber P.A., Mohali S., Pegg G., De Beer Z.W., and Wingfield M.J. Three new Lasiodiplodia spp. from the tropics, recognised based on DNA sequence comparisons and morphology. Mycologia 98 (2006) 423-435
4. Chaverri P., Castlebury L.A., Samuels G.J., and Geiser D.M. Multilocus phylogenetic structure within the Trichoderma harzianum/Hypocrea lixii complex. Mol. Phylogenet. Evol. 27 (2003) 302-313
5. Crous P.W., Slippers B., Wingfield M.J., Rheeder J., Marasas W.F.O., Philips A.J.L., Alves A., Burgess T., Barber P., and Groenewald J.Z. Phylogenetic lineages in the Botryosphaeriaceae. Stud. Mycol. 55 (2006) 235-253
6. Cunningham C.W. Can three incongruence tests predict when data should be combined?. Mol. Biol. Evol. 14 (1997) 733-740
7. Cunnington J.H., Priest M.J., Powney R.A., and Cother N.J. Diversity of Botryosphaeria species on horticultural plants in Victoria and New South Wales. Aust. Plant Path. 36 (2007) 157-159
8. Denman S., Crous P.W., Taylor J.E., Kang J.C., Pascoe I., and Wingfield M.J. An overview of the taxonomic history of Botryosphaeria and a re-evaluation of its anamorphs based on morphology and ITS rDNA phylogeny. Stud. Mycol. 45 (2000) 129-140
9. Dettman J.R., Harbinski F.M., and Taylor J.W. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora. Fungal Genet. Evol. 34 (2001) 49-61
10. 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
11. De Wet J., Burgess T., Slippers B., Preisig O., Wingfield B.D., and Wingfield M.J. Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes of Sphaeropsis sapinea and distinguish a new species of Diplodia. Mycol. Res. 107 (2003) 557-566
12. Farr D.F., Elliott M., Rossman A.Y., and Edmonds R.L. Fusicoccum arbuti sp. nov. causing cankers on Pacific madrone in western North America with notes on Fusicoccum dimidiatum, the correct name for Scytalidium dimidiatum and Nattrassia mangiferae. Mycologia 97 (2005) 730-741
13. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1995) 315-319
14. Felsenstein J. Confidence intervals on phylogenetics: an approach using bootstrap. Evolution 39 (1985) 783-791
15. Geiser D.M., Pitt J.I., and Taylor J.W. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc. Natl. Acad. Sci. USA 95 (1998) 388-393
16. Glass N.L., and Donaldson G.C. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl. Environ. Microbiol. 61 (1995) 1323-1330
17. Grossenbacher J.G., and Duggar B.M. A contribution to the life history, parasitism and biology of Botryosphaeria ribis. NY State AES Tech. Bull. 18 (1911) 113-190
18. Hajibabaei M., Singer G.A.C., Hebert P.D.N., and Hickey D.A. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23 (2007) 167-172
19. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
20. Hofstetter V., Miadlikowska J., Kauff F., and Lutzoni F. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol. Phylogenet. Evol. 44 (2007) 412-426
21. Huelsenbeck J.P., Bull J.J., and Cunningham C.V. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11 (1996) 152-158
22. Katoh K., Misawa K., Kuma K., and Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 (2002) 3059-3066
23. Koufopanou V., Burt A., and Taylor J.W. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. USA 94 (1997) 5478-5482
24. Le Gac M., Hood M.E., Fournier E., and Giraud T. Phylogenetic evidence of host-specific cryptic species in the anther smut fungus. Evolution 61 (2007) 15-26
25. Le Gac M., and Giraud T. Existence of a pattern of reproductive character displacement in Homobasidiomycota but not in Ascomycota. J. Evol. Biol. 21 (2008) 761-772
26. 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
27. Luque J., Martos S., and Phillips A.J.L. Botryosphaeria viticola sp. nov. on grapevines: a new species with a Dothiorella anamorph. Mycologia 97 (2005) 1111-1121
28. Mohali R.S., Slippers B., and Wingfield M.J. Identification of Botryosphaeriaceae from Eucalyptus, Acacia and Pinus in Venezuela. Fungal Divers 25 (2007) 103-125
29. Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.-H., and Ko{combining double acute accent}ljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS ONE 1: e59 (2006) 10.1371/journal.pone.0000059
30. Nylander J.A.A. MrModeltest v2. Program Distributed by the Author (2004), Evolutionary Biology Centre, Uppsala University
31. O'Donnell K., Kistler H.C., Tacke B.K., and Casper H.H. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc. Natl. Acad. Sci. USA 97 (2000) 7905-7910
32. O'Donnell K., Nirenberg H.I., Aoki T., and Cigelnik E. A multigene phylogeny of the Gibberella fujikuroi species complex: detection of additional phylogenetically distinct species. Mycoscience 41 (2000) 61-78
33. O'Donnell K., Ward T.J., Geiser D.M., Kistler H.C., and Aoki T. Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade. Fungal Genet. Biol. 41 (2004) 600-623
34. Pavlic, D., 2004. Botryosphaeria species on native South African Syzygium cordatum and their potential threat to Eucalyptus. M.Sc. thesis. Department of Microbiology and Plant Pathology, University of Pretoria, South Africa.
35. Pavlic D., Slippers B., Coutinho T.A., and Wingfield M.J. Botryosphaeriaceae occurring on native Syzygium cordatum in South Africa and their potential threat to Eucalyptus. Plant Path. 56 (2007) 624-636
36. Pennycook S.R., and Samuels G.J. Botryosphaeria and Fusicoccum species associated with ripe fruit rot of Actinidia deliciosa (Kiwifruit) in New Zealand. Mycotaxon 24 (1985) 445-458
37. Phillips A.J.L., Alves A., Correia A., and Luque J. Two new species of Botryosphaeria with brown, 1-septate ascospores and Dothiorella anamorphs. Mycologia 97 (2005) 513-529
38. Pringle A., Baker D.M., Platt J.L., Wares J.P., Latgé J.P., and Taylor J.W. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59 (2005) 1886-1899
39. Punithalingam, E., Holliday, P., 1973. Botryosphaeria ribis. CMI Descriptions of Pathogenic Fungi and Bacteria, 395.
40. Rannala B., and Yang Z. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43 (1996) 304-311
41. Rodríguez F., Oliver J.L., Marín A., and Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485-501
42. Ronquist F., and Huelsenback J.P. MrBayes: bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
43. Rozas J., Sánchez-DelBarrio J.C., Messegyer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
44. Sakalidis, M., 2004. Resolving the Botryosphaeria ribis - B. parva species complex; a molecular and phenotypic investigation. Honors thesis. School of Biological Sciences and Biotechnology, Murdoch University, Western Australia.
45. Schoch C.L., Shoemaker R.A., Seifert K.A., Hambleton S., Spatafore J.W., and Crous P.W. A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98 (2006) 1041-1052
46. Slippers, B., 2003. Taxonomy, phylogeny- and ecology of botryosphaeriaceous fungi occurring on various woody hosts. Ph.D. dissertation. Department of Microbiology and Plant Pathology, University of Pretoria, South Africa.
47. Slippers B., Burgess T., Crous P.W., Coutinho T.A., Wingfield B.D., and Wingfield M.J. Development of SSR markers for Botryosphaeria spp. with Fusicoccum anamorphs. Mol. Ecol. Notes 4 (2004) 675-677
48. Slippers B., Crous P.W., Denman S., Coutinho T.A., Wingfield B.D., and Wingfield M.J. Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea. Mycologia 96 (2004) 83-101
49. Slippers B., Fourie G., Crous P.W., Coutinho T.A., Wingfield B.D., Carnegie A.J., and Wingfield M.J. Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa. Stud. Mycol. 50 (2004) 343-358
50. Slippers B., Fourie G., Crous P.W., Coutinho T.A., Wingfield B.D., Carnegie A.J., and Wingfield M.J. Multiple gene sequences delimit Botryosphaeria australis sp. nov. from B. lutea. Mycologia 96 (2004) 1028-1039
51. Slippers B., Summerell B.A., Crous P.W., Coutinho T.A., Wingfield B.D., and Wingfield M.J. Preliminary studies on Botryosphaeria species from Wollemia nobilis and related southern hemisphere conifers in Australasia and South Africa. Aust. Plant Path. 34 (2005) 213-220
52. Smith H., Crous P.W., Wingfield M.J., Coutinho T.A., and Wingfield B.D. Botryosphaeria eucalyptorum sp. nov., a new species in the B. dothidea-complex on Eucalyptus in South Africa. Mycologia 93 (2001) 277-285
53. Steenkamp E.T., Wingfield B.D., Desjardins A.E., Marasas W.F.O., and Wingfield M.J. Cryptic speciation in Fusarium subglutinans. Mycologia 94 (2002) 1032-1043
54. Swofford, D.L., 2000. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Sinauer Associates, Massachusetts.
55. Tang A.M.C., Jeewon R., and Hyde K.D. Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi). Antonie de Leeuwenhoek 91 (2007) 327-349
56. 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
57. Taylor J.W., Turner E., Pringle A., Dettman J., and Johannesson H. Fungal species: thoughts on their recognition, maintenance and selection. In: Gadd G.M., Watkinson S.C., and Dyer P.S. (Eds). Fungi in the Environment (2006), Camridge University Press 313-339
58. Trewick S.A. DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 23 (2007) 1-15
59. White T.J., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Snisky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, San Diego 315-322
60. Will K.W., and Rubinoff D. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20 (2004) 47-55
61. Xu J., Vilgalys R., and Mitchell T.G. Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Mol. Ecol. 9 (2000) 1471-1481
62. Zhou S., and Stanosz G.R. Relationships among Botryosphaeria species and associated anamorphic fungi inferred from the analyses of ITS and 5.8S rDNA sequences. Mycologia 93 (2001) 516-527