title: Species boundaries in plant pathogenic fungi: a Colletotrichum case study.
abstract: BACKGROUND
  Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven.
  
  
  RESULTS
  In this study, multiple approaches were used to test the null hypothesis "C. siamense is a species complex", using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat.
  
  
  CONCLUSIONS
  This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi.
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.|Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.affiliation: Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806, Görlitz, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Damm
authors.affiliation: Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.|CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.|Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
authors.forename: Pedro W
authors.initials: PW
authors.lastname: Crous
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. cail@im.ac.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Cai
mesh_terms: D005075:Biological Evolution; D020231:Colletotrichum / Q000145:classification* / Q000166:cytology / Q000235:genetics* / Q000502:physiology; D017753:Ecosystem; D051456:Gene Flow; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology
keywords: Coalescent; GCPSR; Mating test; Phylogeny; Species delimitation