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

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 and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. Key Results Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. Conclusions Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.

Comparing the Use of Two Different Model Approaches on Students’ Understanding of DNA Models

As effective methods to foster students’ understanding of scientific models in science education are needed, increased reflection on thinking about models is regarded as a relevant competence associated with scientific literacy. Our study focuses on the influence of model-based approaches (modeling vs. model viewing) in an out-of-school laboratory module on the students’ understanding of scientific models. A mixed method design examines three subsections of the construct: (1) students’ reasoning about multiple models in science, (2) students’ understanding of models as exact replicas, and (3) students’ understanding of the changing nature of models. There were 293 ninth graders from Bavarian grammar schools that participated in our hands-on module using creative model-based tasks. An open-ended test item evaluated the students’ understanding of “multiple models” (MM). We defined five categories with a majority of students arguing that the individuality of DNA structure leads to various DNA models (modelers = 36.3%, model viewers = 41.1%). Additionally, when applying two subscales of the quantitative instrument Students’ Understanding of Models in Science (SUMS) at three testing points (before, after, and delayed-after participation), a short- and mid-term decrease for the subscale “models as exact replicas” (ER) appeared, while mean scores increased short- and mid-term for the subscale “the changing nature of models” (CNM). Despite the lack of differences between the two approaches, a positive impact of model-based learning on students’ understanding of scientific models was observed.