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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. Jane E Stewart1,5*, Lavern W Timmer2, Christopher B Lawrence3, Barry M Pryor4 and Tobin L Peever1
* Correspondence: of Plant Pathology, Washington State University, Pullman, WA, USAĥCurrent address: Department of Plant Pathology, University of Georgia, Athens, Georgiaįulllist of author information is available at the end of the article Keywords: Coalescent, Species delimitation, Species tree, Gene tree Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained. Two phylogenetic species of Alternarla were identified as causing citrus brown spot worldwide. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable.
Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. Little support was found for most of these morphospecies using quantitative species recognition approaches. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.Ĭonclusions: The number of Alternarla species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. A consensus of species tree estimation methods supported two species of Alternarla causing citrus brown spot worldwide. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. Results: Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common. Using a worldwide sample of Alternarla alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogenīackground: Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters.
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