The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa

ABSTRACTDeveloping a comprehensive and reliable taxonomy for the Colletotrichumgloeosporioides species complexwill require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogeneticinference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichumspecies associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogeneticallyinformative sites. Similarly, the choice of phylogeneticmarker affects the delimitation of species boundaries, particularly if low phylogeneticsignal is confounded with strong discordance, and inference of the species tree from multiple-gene trees. According to both phylogeneticinformativeness profiling and Bayesian concordance analyses, the most informative loci are DNA lyase(APN2), intergenic spacer (IGS) between DNA lyaseand the mating-typelocus MAT...