Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

Abstract The clade Pancrustacea, comprising crustaceans and hexapods, is
the most diverse group of animals on earth, containing over 80% of animal
species and half of animal biomass. It has been the subject of several
recent phylogenomic analyses, yet relationships within Pancrustacea show a
notable lack of stability. Here, the phylogeny is estimated with expanded
taxon sampling, particularly of malacostracans. We show small changes in
taxon sampling have large impacts on phylogenetic estimation. By analyzing
identical orthologs between two slightly different taxon sets, we show
that the differences in the resulting topologies are due primarily to the
effects of taxon sampling on the phylogenetic reconstruction method. We
compare trees resulting from our phylogenomic analyses with those from the
literature to explore the large tree space of pancrustacean phylogenetic
hypotheses and find that statistical topology tests reject the previously
published trees in favor of the maximum likelihood trees produced here.
Our results reject several clades including Caridoida, Eucarida,
Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda
nested within Allotriocarida with high support and recover a novel
relationship between decapods, euphausiids, and syncarids that we refer to
as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister
to this latter clade, which we collectively name Stomatocarida, dividing
Malacostraca into three clades: Leptostraca, Peracarida, and
Stomatocarida. A new Bayesian divergence time estimation is conducted
using 13 vetted fossils. We review our results in the context of other
pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample
in future studies.