Phylogenomics and microRNAs congruently resolve the ecdysozoan phylogeny

Ecdysozoa, the group including Nematoda (roundorms) and the Arthropoda (e.g. spiders, centipedes, insects andcrustaceans), include the largest majority of Earth biodiversity and biomass. The monophyly of thisassemblage of phyla as long been debated and has only recently been confirmed by the analyses of completeanimal genomes. However, the relationships within this group remain uncertain. We assembled large-scalephylogenomic data sets, and identified the nearly complete microRNA repertoire (also sequencing small RNAlibraries) for a representative sample of ecdysozoan species. These independent genomic-scale data sets wereanalysed and the relationships among the Ecdysoza resolved by means of congruence. We were able to show thatof the two generally accepted ecdysozoan clades (the Panarthropoda and the Cycloneuralians) only the first, whichincludes the Arthropoda, the Tardigrada (water bears) and the Onychophora (velvet worms), is monophyletic. Thesecond, Cycloneuralia, most likely represents a paraphyletic assemblage of phyla. In addition, we were able toshow that within Panarthropoda, the velvet worms represent the sister group of the Arthropoda with the water bearsrepresenting the sister group of the Arthropoda plus Onychophora. Our results substantially clarify the relationshipsamong the Ecdysozoa and provide an invaluable framework to understand evolutionary patterns (both genomic and morphological) within this group.