Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae).

ABSTRACT:

Background and aims

Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.

Methods

We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired a

SUBMITTER: Li M 

PROVIDER: S-EPMC6758584 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature