Abstract
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.
Highlights
A reliable and accurate identification of fungal plant pathogens is of the utmost importance in disease diagnosis to implement effective management and quarantine strategies [1]
Phylogenetic analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) principle and the coalescent-based species model, Poisson Tree Processes (PTPs), prove that the D. eres complex is a population with evolving lineages, rather than a complex composed of distinct species
The pairwise homoplasy index test and the comparison of morphological and ecological characters highlight the absence of gene flow within the population, given that there is no evidence of reproductive isolation or of geographical barriers
Summary
A reliable and accurate identification of fungal plant pathogens is of the utmost importance in disease diagnosis to implement effective management and quarantine strategies [1]. The Genealogical Concordance Phylogenetic Species Recognition (GCPSR), introduced by Taylor et al [6], relies in the comparison of individual gene genealogies to identify incongruences, and it has been useful to delimit the species boundaries in morphologically conserved fungi [7]. The common approach of concatenating sequence data to delimit species without following the GCPSR principle [6,8] overestimates the true diversity of species, since each clade in combined trees is frequently recognized as a distinct lineage [9,10]. Species boundaries in closely related taxa can be somehow difficult to determine through multilocus sequence data, as some alleles are not expected to be reciprocally monophyletic in the initial stages of speciation, resulting in phylogenetic incongruences [7,11]. The delimitation of species using multi-species coalescent models provides a more comprehensive insight into the speciation events, as it can estimate species boundaries even in the presence of incongruence between individual genealogies [12]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
