BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.

Premise: Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.

Methods And Results: BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data.

AI can help humans find common ground in democratic deliberation.

Finding agreement through a free exchange of views is often difficult. Collective deliberation can be slow, difficult to scale, and unequally attentive to different voices. In this study, we trained an artificial intelligence (AI) to mediate human deliberation.

Environmental DNA Isolation, Validation, and Preservation Methods.

Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.

Multiple outgroups can cause random rooting in phylogenomics.

Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods.

An individual differences perspective on pragmatic abilities in the preschool years.

Pragmatic abilities are fundamental to successful language use and learning. Individual differences studies contribute to understanding the psychological processes involved in pragmatic reasoning. Small sample sizes, insufficient measurement tools, and a lack of theoretical precision have hindered progress, however.