Abstract
Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens.
Highlights
Delimiting species boundaries among fungi lays the groundwork for detailing the natural history and ecology of species and defines a robust framework from which further comparative studies can be designed
Individual Gene Trees In order to test the hypothesis that multiple sympatric lineages within the C. gloeosporioides species complex infect cranberry in the field, North American isolates need to be placed in a broader phylogenetic context
Despite the low phylogenetic resolution inferred from nuclear ribosomal internal transcribed spacer (nrITS) data, six nodes within the species complex were supported in more than 75% of the parsimony bootstrapped datasets (Figure S1) and eight nodes in more than 70% of the maximum likelihood bootstrapped datasets (Figure S5)
Summary
Delimiting species boundaries among fungi lays the groundwork for detailing the natural history and ecology of species and defines a robust framework from which further comparative studies can be designed (i.e. population genetics/genomics). This is prerequisite to providing targeted and effective disease control measures and identifying specific pathogens against which plant breeders can focus their efforts in developing and selecting disease resistant cultivars. Within, adjacent to, and beyond agricultural landscapes has the potential to provide a broader view of the natural history of pathogen species and offer insight into the evolution of differential traits among closely related lineages [1]. The recent epitypification of C. gloeosporioides provides a much
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