Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances

Abstract

A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the existence of the CBC substitution inflated the ITS2 genetic distances to different extents, and the deviation could be 180% higher if the relative ratio of substitution rate in ITS2 secondary structure stems was threefold higher than that in the loops. However, the CBC effect was minor if that ratio was below two, indicating that the DNA model is still applicable in recent lineages in which few CBCs occur. We thus provide a general empirical threshold to take account of CBC before ITS2 phylogenetic analyses.

Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species

“…Although the application of partitioning is theoretically justified, more partitions with more complex models mean more parameters are estimated, causing the concern of over-parameterization [46]. Recent empirical studies have found that using single DNA models for unpartitioned sequences violated ITS2 evolution but was insufficient to mislead phylogenetic inference within closely related lineages, wherein few base pair substitutions are observed in paired regions [27,47]. Taken together, a threshold for the magnitude of model violations should be considered before using the partition method for ITS2 phylogenetic inference.…”

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

“…According to Cao et al [ 22 ] and Zhang et al [ 59 ], the site covariation (CBC)—in combination with phylogenetic comparisons—is increasingly being used as a more effective method for structure prediction. Hence, to corroborate the species delimitation revealed by the phylogeny and consensus model (Type I–IV with a total of four to six domains), a minimum of nine CBCs among individual structural helices and a total of 645 CBCs were identified between the internal and external subclasses of different species, as an additional molecular marker.…”

“…From the secondary-structure alignment, an extra molecular marker named compensatory base changes (CBCs) was considered to delineate the species [22,47]-from which, specific structural features were extracted using the 4SALE tool (http://4sale.bioapps. biozentrum.uni-wuerzburg.de/, accessed on 2 February 2022) [48].…”

“…The ITS2 secondary structure provides features such as the so called compensatory base changes (CBCs, nucleotide substitutional events), suggested as additional evidence for the distinguishing of some closely related species [ 22 , 23 ]. Wolf et al [ 23 ] mentioned that if there is a CBC, then the samples are two different species, at a probability of ~93%; if there is not a CBC, then the samples are the same species, at a probability of ~76%.…”

Después de más de un siglo en el olvido resurge una especie en Dysopsis (Euphorbiaceae)

“…La estructura secundaria del ITS2 en Dysopsis contiene todas las regiones conservadas presentes en las angiospermas (Cao et al 2022) (Fig. S3).…”