A genome-guided phylogenomic analysis of Platygastroidea (Hymenoptera: Proctotrupomorpha)

Phylogenetic analyses performed using genome-scale datasets are becoming the norm in modern systematic research. It is not uncommon for phylogenies to be built using thousands of genetic markers. The means by which these markers are selected is crucial to accurate phylogenetic inference. In this research, we display how loci can be selected and showcase a protocol that utilizes sequence data (DNA or AA) from one species to assemble orthologous loci in taxa of interest using whole-genome sequencing reads. Single-copy protein-coding gene sequences were harvested from the genome of Trissolcus basalis (Scelionidae) and used to assemble orthologs in 60 genera of platygastroid wasps. Several datasets that vary in taxon occupancy, composition, and degree of missing data were constructed and evaluated under partitioned and posterior mean site frequency profiles in a maximum likelihood framework. These concatenated supermatrix approaches were contrasted with a coalescent-based supertree approach to generate the most well-informed, robust analysis of platygastroid relationships to date.