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A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci.
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.Ĭoalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Using a worldwide sample of Alternaria 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. 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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