The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on</p><p>earth, containing over 80% of animal species. It has been the subject of several recent phylogenomic</p><p>analyses, but despite analyzing hundreds of genes, relationships within Pancrustacea show a notable lack</p><p>of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of</p><p>malacostracans, using a precise tree-based approach to infer orthology. Our results show that small</p><p>changes in taxon sampling have a large impact on phylogenetic estimation. By analyzing only shared</p><p>orthologs between two slightly different taxon sets, we show that the differences in the resulting</p><p>topologies are due to the effects of taxon sampling on the phylogenetic reconstruction method, not on</p><p>ortholog identification. We compare trees resulting from our phylogenomic analyses with those from the</p><p>literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical</p><p>topology tests reject the previously published trees in favor of the ML trees produced here. Our results</p><p>reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. We</p><p>recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the</p><p>Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this clade, which we name</p><p>Stomatocaridea, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocaridea. A</p><p>new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in</p><p>the context of other pancrustacean phylogenetic hypotheses and highlight the key taxa to sample in future</p><p>studies.
