Exploring Phylogenetic Relationships and Divergence Times of Bioluminescent Species Using Genomic and Transcriptomic Data

Next-generation sequencing (NGS) has dominated the scene of genomics and evolutionary biology as a great amount of genomic data have been accumulated for a diverse set of species. At the same time, phylogenetic approaches and programs are in development to allow better use of such large-size datasets. Phylogenomics appears as a promising field to accommodate and explore all the information of NGS data in phylogenetic methods, being an important approach to investigate the evolution of bioluminescence in different organisms. To guarantee accurate results in phylogenomic studies, it is mandatory to correctly identify orthologous genes in phylogenetic reconstruction. Here, we show a simplified step-by-step framework to perform phylogenetic analysis along with divergence time estimation, beginning with an orthologous search. As empirical data, we exemplify transcriptome sequences of six species of the Elateroidea superfamily (Coleoptera). We introduce several bioinformatics tools for handling genomic data, especially those available in the software OrthoFinder, IQTREE, BEAST2, and TreePL.