Pancrustacea Phylogeny

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals onearth, containing over 80% of animal species. It has been the subject of several recent phylogenomicanalyses, but despite analyzing hundreds of genes, relationships within Pancrustacea show a notable lackof stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly ofmalacostracans, using a precise tree-based approach to infer orthology. Our results show that smallchanges in taxon sampling have a large impact on phylogenetic estimation. By analyzing only sharedorthologs between two slightly different taxon sets, we show that the differences in the resultingtopologies are due to the effects of taxon sampling on the phylogenetic reconstruction method, not onortholog identification. We compare trees resulting from our phylogenomic analyses with those from theliterature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statisticaltopology tests reject the previously published trees in favor of the ML trees produced here. Our resultsreject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Werecover a novel relationship between decapods, euphausiids, and syncarids that we refer to as theSyneucarida. With denser taxon sampling, we find Stomatopoda sister to this clade, which we nameStomatocaridea, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocaridea. Anew Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results inthe context of other pancrustacean phylogenetic hypotheses and highlight the key taxa to sample in futurestudies.