The phylogeny of crickets, katydids, and allies (Orthoptera: Ensifera): Design and performance of the first Orthoptera-specific target enrichment probe set

We aim to use next-generation sequencing data to infer a robust phylogeny of Ensifera (Orthoptera) to better understand the evolution of auditory communication, however, the orders of Polyneoptera are lagging behind other insect groups in the development of phylogenomic resources. With help from Arbor Biosciences, we used 92 orthopteran transcriptomes to design an Orthoptera-specific target enrichment probe set, which targets 1,825 single-copy protein-coding genes. We are using a bioinformatics pipeline developed for transcriptome sequences to process the read data and interpret sequencing success. Preliminary datasets have been filtered and analyzed in a number of ways to determine an optimal amount of missing data, parsimony informative sites, and overall runtime. Thus far, analyses produce consistent and highly-supported trees and seem largely unaffected by high amounts of missing data (80–90%). Alternative bioinformatics strategies have been tested but encountered difficulties being implemented with this dataset.