Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications. Li et al. quantify how CBCs affect selection of substitution models and values for species delimitation in a more recent Corydalis lineage by using both DNA- and RNA-specific models.
They demonstrate that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within such closely related lineages, wherein few CBCs are observed. Neither of the CBCs occurred within any given species, which is consistent with application of the CBC species concept.
Li, M., Zhao, H., Zhao, F., Jiang, L., Peng, H., Zhang, W., & Simmons, M. P. (2019). Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). Annals of Botany, 124(2), 233–243. https://doi.org/10.1093/aob/mcz062