TreeBASE Search-Matrices for study 26680

@ARTICLE{TreeBASE2Ref31059, author = {Sandra Hil?rio and Liliana Santos and Artur Alves}, title = {Diaporthe amygdali, a species complex or a complex species?}, year = {2021}, keywords = {Coalescent, GMYC, Phylogeny, PTP, Species delimitation, Systematics}, doi = {10.1016/j.funbio.2021.01.006}, url = {http://www.sciencedirect.com/science/article/pii/S1878614621000131?via%3Dihub}, pmid = {}, journal = {Fungal Biology}, volume = {}, number = {}, pages = {}, abstract = {Diaporthe represents a cosmopolitan group of fungi comprised of plant pathogens causing serious diseases on many economically important plant hosts. Therefore, an accurate identification of these pathogens is an essential step to establish adequate control measures. Nowadays, the concatenation of multilocus DNA sequences has revealed an important tool to infer phylogenetic relationships and to identify species boundaries in Diaporthe. However, the discordance between individual gene trees and the combined multilocus analysis seems to occur in the genus Diaporthe, but somehow overlooked. In this study, we noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, denominated as D. amygdali complex, occupy a monophyletic clade whose phylogenetic limits remain unclear. Therefore, to assess the boundaries of this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and the coalescent models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). Results based on these models do not support the recognition of lineages as distinct species and showed incongruent results for the concatenated gene tree. Moreover, we also showed that there are no reproductive isolation and geographical barriers to gene flow in this complex, thus, evidencing that D. amygdali complex constitutes a single species. At our knowledge, this is the first time that coalescent-based methods are implemented in the genus Diaporthe. This study provides crucial background information about the importance of coalescent methods to infer the evolutionary histories of species, and to delimitate the boundaries in the genus Diaporthe.} }