Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.