Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in (Basidiomycota).

BACKGROUND

The delimitation of species of has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as .

OBJECTIVES

The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in .

METHODOLOGY

Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale.

RESULTS AND CONCLUSIONS

The phylogenetic tree results showed delimited monophyletic clades in spp., where all 142 sequences were divided into two main clades A and B and assigned to seven species (, , , , ), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, belongs to type I; , , and belong to type II; and , , , and spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.