Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences
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[1] T. White. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics , 1990 .
[2] A. Miller,et al. Using phylogenetic species recognition to delimit species boundaries within Lasiosphaeria , 2004, Mycologia.
[3] J. Burnett. Fungal Populations and Species , 2003 .
[4] M. Nei,et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.
[5] A. Arnold,et al. Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. , 2008, Mycological research.
[6] B. Crespi,et al. Ecological divergence promotes the evolution of cryptic reproductive isolation , 2006, Proceedings of the Royal Society B: Biological Sciences.
[7] M. Tejesvi,et al. Phylogenetic analysis of endophytic Pestalotiopsis species from ethnopharmaceutically important medicinal trees , 2009 .
[8] K. Hyde,et al. Molecular identification of white morphotype strains of endophytic fungi from Pinus tabulaeformis. , 2003, Mycological research.
[9] J. L. Gittleman,et al. The Impact of Species Concept on Biodiversity Studies , 2004, The Quarterly Review of Biology.
[10] A. J. Shaw,et al. Biogeographic and phylogenetic patterns in diversity of liverwort-associated endophytes. , 2008, American journal of botany.
[11] Jw Taylor,et al. THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification. , 1999, Annual review of phytopathology.
[12] A. Magurran,et al. Measuring Biological Diversity , 2004 .
[13] D. Swofford. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .
[14] M. Berbee,et al. Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences , 1999 .
[15] M. Berbee,et al. Pleospora species with Stemphylium anamorphs: a four locus phylogeny resolves new lineages yet does not distinguish among species in the Pleospora herbarum clade , 2009, Mycologia.
[16] R. Vilgalys,et al. Endophytic Xylaria (Xylariaceae) among liverworts and angiosperms: phylogenetics, distribution, and symbiosis. , 2003, American journal of botany.
[17] C. A. Machado,et al. The causes of phylogenetic conflict in a classic Drosophila species group , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[18] J. Handelsman,et al. Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness , 2005, Applied and Environmental Microbiology.
[19] D. Hibbett,et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. , 2004, American journal of botany.
[20] K. O’Donnell,et al. Molecular systematics and phylogeography of Gibberella fujikuroi species complex , 1998 .
[21] W. L. Araújo,et al. Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease , 2005, International journal of biological sciences.
[22] Noah A Rosenberg,et al. The probability of topological concordance of gene trees and species trees. , 2002, Theoretical population biology.
[23] Rytas Vilgalys,et al. Taxonomic misidentification in public DNA databases. , 2003, The New phytologist.
[24] R. Henrik Nilsson,et al. Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification , 2008, Evolutionary bioinformatics online.
[25] D. Posada. jModelTest: phylogenetic model averaging. , 2008, Molecular biology and evolution.
[26] K. Hyde,et al. Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic? , 1999, Biodiversity & Conservation.
[27] Bryan C Carstens,et al. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. , 2007, Systematic biology.
[28] K. Hyde,et al. An evaluation of the fungal 'morphotype' concept based on ribosomal DNA sequences , 2003 .
[29] P. Coley,et al. Are tropical fungal endophytes hyperdiverse , 2000 .
[30] Ignazio Carbone,et al. A method for designing primer sets for speciation studies in filamentous ascomycetes , 1999 .
[31] M. P. Cummings,et al. A Genealogical Approach to Quantifying Lineage Divergence , 2008, Evolution; international journal of organic evolution.
[32] S. Rehner,et al. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs , 2005, Mycologia.
[33] John P. Huelsenbeck,et al. MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..
[34] T. S. Suryanarayanan,et al. Endophytic Phomopsis species: host range and implications for diversity estimates. , 2006, Canadian journal of microbiology.
[35] D. Maddison,et al. Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .
[36] E. Holmes,et al. Phylogenetic evidence for recombination in dengue virus. , 1999, Molecular biology and evolution.
[37] Brian C. O'Meara,et al. New Heuristic Methods for Joint Species Delimitation and Species Tree Inference , 2009, Systematic biology.
[38] M. Wingfield,et al. Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: a case study on the Neofusicoccum parvum/N. ribis complex. , 2009, Molecular phylogenetics and evolution.
[39] F. Lutzoni,et al. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. , 2007, Molecular phylogenetics and evolution.
[40] D. Huson,et al. Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.
[41] F. Lutzoni,et al. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? , 2007, Ecology.
[42] K. Katoh,et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.
[43] M. P. Cummings. PHYLIP (Phylogeny Inference Package) , 2004 .
[44] Bryan C. Carstens,et al. Delimiting species without monophyletic gene trees. , 2007, Systematic biology.
[45] T. White,et al. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis , 2002, Mycologia.
[46] S. Lumyong,et al. A Phylogenetic Evaluation of Whether Endophytes Become Saprotrophs at Host Senescence , 2007, Microbial Ecology.
[47] G. A. Horridge,et al. Animal species and evolution. , 1964 .
[48] J. Rougemont,et al. A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.
[49] M. Wingfield,et al. Leptographium wingfieldii introduced into North America and found associated with exotic Tomicus piniperda and native bark beetles. , 2004, Mycological research.
[50] Michael P. Cummings,et al. PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .
[51] K. Hyde,et al. Phylogenetic evaluation of species nomenclature of Pestalotiopsis in relation to host association , 2004 .
[52] James B. Anderson,et al. Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora , 2008, BMC Evolutionary Biology.
[53] R. Gazis,et al. Trichoderma amazonicum, a new endophytic species on Hevea brasiliensis and H. guianensis from the Amazon basin , 2011, Mycologia.
[54] D. Geiser,et al. Multilocus phylogenetic structure within the Trichoderma harzianum/Hypocrea lixii complex. , 2003, Molecular phylogenetics and evolution.
[55] Elena Blume,et al. Variabilidade genética na região its do rDNA de isolados de trichoderma spp. (Biocontrolador) e Fusarium oxysporum f. sp. Chrysanthemi , 2010 .
[56] D. Hawksworth. The magnitude of fungal diversity: the 1.5 million species estimate revisited * * Paper presented at , 2001 .
[57] John Alroy,et al. Principles of genealogical concordance in species concepts and biological taxonomy , 1990 .
[58] J. Moncalvo,et al. Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa. , 2004, Microbiology.
[59] Robert K. Colwell,et al. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness , 2001 .
[60] K. M. Sefc,et al. Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini. , 2010, Molecular phylogenetics and evolution.
[61] Amy K Stockman,et al. An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring. , 2008, Systematic biology.
[62] D. Shtienberg,et al. Ecological Genetic Divergence of the Fungal Pathogen Didymella rabiei on Sympatric Wild and Domesticated Cicer spp. (Chickpea) , 2009, Applied and Environmental Microbiology.
[63] P. Cannon,et al. Diversity and molecular relationships of endophytic Colletotrichum isolates from the Iwokrama Forest Reserve, Guyana. , 2004, Mycological research.
[64] M. Polihronakis. Hierarchical comparative analysis of genetic and genitalic geographical structure: testing patterns of male and female genital evolution in the scarab beetle Phyllophaga hirticula (Coleoptera: Scarabaeidae) , 2008 .
[65] D. Hibbett,et al. Phylogenetic species recognition and species concepts in fungi. , 2000, Fungal genetics and biology : FG & B.
[66] H. Evans,et al. Molecular characterisation of fungal endophytic morphospecies associated with the indigenous forest tree, Theobroma gileri, in Ecuador. , 2008, Mycological research.
[67] H. Evans,et al. Endophytes and mycoparasites associated with an indigenous forest tree, Theobroma gileri, in Ecuador and a preliminary assessment of their potential as biocontrol agents of cocoa diseases , 2003, Mycological Progress.
[68] Irina S Druzhinina,et al. The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages , 2010, BMC Evolutionary Biology.
[69] Liang-Dong Guo,et al. A comparative study of endophytic fungi in needles, bark, and xylem of Pinus tabulaeformis , 2007 .
[70] Yaping Zhang,et al. Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panamá: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes , 2010, Mycologia.
[71] D. Morrison,et al. Using data-display networks for exploratory data analysis in phylogenetic studies. , 2010, Molecular biology and evolution.
[72] R. Gazis,et al. Diversity of fungal endophytes in leaves and stems of wild rubber trees (Hevea brasiliensis) in Peru , 2010 .
[73] Joel Cracraft,et al. Species Concepts and Speciation Analysis , 1983 .
[74] Rachel E Gallery,et al. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples. , 2009, Mycological research.
[75] A. Solow,et al. Measuring biological diversity , 2006, Environmental and Ecological Statistics.
[76] E. Kellogg,et al. Testing for Phylogenetic Conflict Among Molecular Data Sets in the Tribe Triticeae (Gramineae) , 1996 .
[77] Markus E. Lautenbacher,et al. TRACER version 1.1: A mathematica package for γ-algebra in arbitrary dimensions , 1993 .
[78] D. Hillis,et al. Taxon sampling and the accuracy of phylogenetic analyses , 2008 .