Molecular and phenotypic characterization of three phylogenetic species discovered within the Neofusicoccum parvum/N. ribis complex

LITERATURE CITED

• Ahumada R. 2002. Diseases in commercial Eucalyptus plantations in Chile, with special reference to Myco-sphaerella and Botryosphaeria species (Master’s thesis). Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. 151 p.
   Google Scholar
• Alves A, Phillips AJL, Henriques I, Correia A. 2007. Rapid differentiation of species of Botryosphaeriaceae by PCR fingerprinting. Res Microbiol 158:112–121.
   Google Scholar
• Burgess TI, Barber PA, Hardy GESJ. 2005. Botryosphaeria spp. associated with eucalypts in Western Australia including description of Fusicoccum macroclavatum sp. nov. Aust Plant Path 34:557–567.
   Google Scholar
• ———, Sakalidis M, Hardy GESJ. 2006. Gene flow of the canker pathogen Botryosphaeria australis between Eucalyptus globulus plantations and native eucalypt forests in Western Australia. Austral Ecol 31:559–566.
   Google Scholar
• ———, Wingfield MJ. 2002. Quarantine is important in restricting the spread of exotic seed-borne tree pathogens in the southern hemisphere. Int Forest Rev 4:56–65.
   Google Scholar
• Crous PW, Slippers B, Wingfield MJ, Rheeder J, Marasas WFO, Philips AJL, Alves A, Burgess T, Barber P, Groenewald JZ. 2006. Phylogenetic lineages in the Botryosphaeriaceae. Stud Mycol 55:235–253.
   Google Scholar
• Dayrat B. 2005. Toward integrative taxonomy. Biol J Linnean Soc 85:407–415.
   Google Scholar
• Denman S, Crous PW, Taylor JE, Kang JC, Pascoe I, Wingfield MJ. 2000. An overview of the taxonomic history of Botryosphaeria and a re-evaluation of its anamorphs based on morphology and ITS rDNA phylogeny. Stud Mycol 45:129–140.
   Google Scholar
• de Wet J, Burgess T, Slippers B, Preisig O, Wingfield BD, Wingfield MJ. 2003. Multiple gene genealogies and microsatellite markers reflect relationships between morphotypes of Sphaeropsis sapinea and distinguish a new species of Diplodia. Mycol Res 107:557–566.
   Google Scholar
• Felsenstein J. 1985. Confidence intervals on phylogenetics: an approach using bootstrap. Evolution 39:783–791.
   Google Scholar
• Geiser DM, Pitt JI, Taylor JW. 1998. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci USA 95:388–393.
   Google Scholar
• Grünig CR, Duò A, Sieber TN, Holdenrieder O. 2008. Assignment of species rank to six reproductively isolated cryptic species of the Phialocephala fortinii s.l. -Acephala applanata species complex. Mycologia 100:47–67.
   Google Scholar
• Gure A, Slippers B, Stenlid J. 2005. Seed-borne Botryosphaeria spp. from native Prunus and Podocarpus trees in Ethiopia, with a description of the anamorph Diplodia rosulata sp. nov. Mycol Res 109:1005–1014.
   Google Scholar
• Jacobs KA, Rehner SA. 1998. Comparison of cultural and morphological characters and ITS sequences in anamorphs of Botryosphaeria and related taxa. Mycologia 90:601–610.
   Google Scholar
• Jacobs R. 2002. Characterisation of Botryosphaeria species from mango in South Africa [Master’s thesis]. Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. 162 p.
   Google Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066.
   Google Scholar
• Koufopanou V, Burt A, Taylor JW. 1997. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc Natl Acad Sci USA 94:5478–5482.
   Google Scholar
• Mohali SRM. 2005. Taxonomy and ecology of Botryosphaeria species and their anamorphs from Venezuela [Doctoral dissertation]. Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. 206 p.
   Google Scholar
• Nylander JAA. 2004. MrModeltest 2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
   Google Scholar
• O’Donnell K, Kistler HC, Tacke BK, Casper HH. 2000a. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc Natl Acad Sci USA 97:7905–7910.
   Google Scholar
• ———, Nirenberg HI, Aoki T, Cigelnik E. 2000b. A multigene phylogeny of the Gibberella fujikuroi species complex: detection of additional phylogenetically distinct species. Mycoscience 41:61–78.
   Google Scholar
• ———, Ward TJ, Geiser DM, Kistler HC, Aoki T. 2004. 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 41:600–623.
   Google Scholar
• Pavlic D, Slippers B, Coutinho TA, Gryzenhout M, Wingfield MJ. 2004. Lasiodiplodia gonubiensis sp. nov., a new Botryosphaeria anamorph from native Syzygium cordatum in South Africa. Stud Mycol 50:313–322.
   Google Scholar
• ———, ———, ———, Wingfield MJ. 2007. Botryosphaeriaceae occurring on native Syzygium cordatum in South Africa and their potential threat to Eucalyptus. Plant Path 56:624–636.
   Google Scholar
• ———, ———, ———, ———. 2009. Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: A case study on the Neofusicoccum parvum/N. ribis complex. Mol Phylogenet Evol 51:259–268.
   Google Scholar
• ———, Wingfield MJ, Barber P, Slippers B, Hardy GESJ, Burgess TI. 2008. Seven new species of the Botryosphaeriaceae discovered on baobab and other native trees in Western Australia. Mycologia 100:851–866.
   Google Scholar
• Pennycook SR, Samuels GJ. 1985. Botryosphaeria and Fusicoccum species associated with ripe fruit rot of Actinidia deliciosa (Kiwifruit) in New Zealand. Myco-taxon 24:445–458.
   Google Scholar
• Pringle A, Baker DM, Platt JL, Wares JP, Latgé JP, Taylor JW. 2005. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59:1886–1899.
   Google Scholar
• Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311.
   Google Scholar
• Rodas PCA. 2003. Diseases of Eucalyptus in Colombia (Master’s thesis). Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. 224 p.
   Google Scholar
• Roe AD, Sperling FAH. 2007. Population structure and species boundary delimitation of cryptic Dioryctria moths: an integrative approach. Mol Ecol 16:3617–3633.
   Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574.
   Google Scholar
• Slippers B. 2003. Taxonomy, phylogeny- and ecology of botryosphaeriaceous fungi occurring on various woody hosts [Doctoral dissertation]. Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. 279 p.
   Google Scholar
• ———, Crous PW, Denman S, Coutinho TA, Wingfield BD, Wingfield MJ. 2004a. Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea. Mycologia 96:83–101.
   Google Scholar
• ———, Fourie G, Crous PW, Coutinho TA, Wingfield BD, Carnegie AJ, Wingfield MJ. 2004b. Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa. Stud Mycol 50:343–358.
   Google Scholar
• ———, ———, ———, ———, ———, ———. 2004c. Multiple gene sequences delimit Botryosphaeria australis sp. nov. from B. lutea. Mycologia 96:1028–1039.
   Google Scholar
• ———, Summerell BA, Crous PW, Coutinho TA, Wingfield BD, Wingfield MJ. 2005. Preliminary studies on Botryosphaeria species from Wollemia nobilis and related southern hemisphere conifers in Australasia and South Africa. Aust Plant Path 34:213–220.
   Google Scholar
• ———, Wingfield MJ. 2007. Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact. Fungal Biol Rev 21:90–106.
   Google Scholar
• Smith H, Crous PW, Wingfield MJ, Coutinho TA, Wingfield BD. 2001. Botryosphaeria eucalyptorum sp. nov., a new species in the B. dothidea-complex on Eucalyptus in South Africa. Mycologia 93:277–285.
   Google Scholar
• ———, Wingfield MJ, Petrini O. 1996. Botryosphaeria dothidea endophytic in Eucalyptus grandis and Eucalyptus nitens in South Africa. For Ecol Manage 89:189–195.
   Google Scholar
• Steenkamp ET, Wingfield BD, Desjardins AE, Marasas WFO, Wingfield MJ. 2002. Cryptic speciation in Fusarium subglutinans. Mycologia 94:1032–1043.
   Google Scholar
• Swofford DL. 2000. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunder-land, Massachusetts: Sinauer Associates.
   Google Scholar
• Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32.
   Google Scholar
• Zhou S, Stanosz GR. 2001. Relationships among Botryosphaeria species and associated anamorphic fungi inferred from the analyses of ITS and 5.8S rDNA sequences. Mycologia 93:516–527.
   Google Scholar