Whole-Genome Phylogenetic Reconstruction of the Evolution of the Cladocera reveals Homoplasy and Ancient Rapid Radiation. Cladocera phylogenomics

The Cladocera (Crustacea: Branchiopoda) constitute an ancient arthropod group with key representatives in freshwater, brackish and marine ecosystems worldwide. Some cladocerans have become important model systems in ecology, evolution and ecotoxicology. Cladocera are remarkably diverse and have colonised a wide range of aquatic niches as predators, deposit- and suspension feeders. We present the first phylogenetic reconstruction of the evolutionary history of the Cladocera using whole genomes. We assembled eight de novo genomes of key taxa which include representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representatives, including previously sequenced taxa and spanning all living branchiopod orders. The cladoceran families in our study cover over 90% of the total species diversity in the group. Our analysis supports monophyly of the Cladocera and reveals a remarkable homoplasy in cladoceran body plans. We found an unanticipated, large genetic distance between lineages with similar ecological specialisations, such as the pelagic predatory orders. In addition, we examined potential relative timings of divergence in major lineages using reliable, fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin for the cladoceran ancestor and ancient rapid radiations around the Perm/Triassic boundary. The current approach raises new questions about the role of homoplasy and rapid radiation in the diversification of the cladocerans and thus helps to examine trait evolution of a functionally well understood arthropod group from a fresh perspective and whole-genome evidence.