Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

In a flipped classroom model, learning of basic content is shifted before class while in-class time is used for concept application. Empirical and controlled research studies are lacking on the best strategies to provide the necessary pre-class content instruction. In this study, we tested three methods of pre-class content learning—interactive online tutorials, video lectures, and textbook-style readings—while holding the content and the in-class application activities constant. Identical introductory, non-majors biology classes were manipulated at both a public, open-enrollment institution and a private, highly selective institution. We found that video lectures offer a small advantage to overall student learning over interactive tutorials or textbook-style readings. Although our two populations differed in their ability to effectively learn from pre-class activities, through a student-centered flipped classroom approach, students at both institutions demonstrated equal learning gains by the final assessment. Potential reasons for some observed differences are suggested.