2.2.2. Six-Marker Phylogeny

Six genetic markers (EF3, mtLSU, ITS, nuLSU, nuSSU, and RPB2) were utilized to infer a species (coalescent) tree in ASTRAL (Accurate Species TRee ALgorithm) III [60] that encompassed a total of 147 terminals representing 83 species (File S2). Each of these loci had the following number of samples and alignment length: EF3 (33 taxa, 421 bp); mtLSU (62 taxa, 649 bp); ITS (147 taxa, 816 bp); nuLSU (139 taxa, 1471 bp); nuSSU (69 taxa, 1268 bp); and RPB2 (11 taxa, 1033 bp). The ITS alignment was separately subjected to ML analysis as described above for the full dataset (File S3).

To compare the resulting ITS-based ML tree with the six-marker ASTRAL tree, generalized Robinson–Foulds distances were calculated between the ASTRAL and the ITS tree in R Studio with the TreeDist package [61,62], following the tutorial by Smith (https: //ms609.github.io/TreeDist/articles/Generalized-RF.html accessed on 1 July 2021).
