@article {Cai2021.09.22.461358, author = {Chenyang Cai and Erik Tihelka and Mattia Giacomelli and John F. Lawrence and Adam {\'S}lipi{\'n}ski and Robin Kundrata and Sh{\^u}hei Yamamoto and Margaret K. Thayer and Alfred F. Newton and Richard A. B. Leschen and Matthew L. Gimmel and Liang L{\"u} and Michael S. Engel and Diying Huang and Davide Pisani and Philip C.J. Donoghue}, title = {Integrated phylogenomics and fossil data illuminate the evolution of beetles}, elocation-id = {2021.09.22.461358}, year = {2021}, doi = {10.1101/2021.09.22.461358}, publisher = {Cold Spring Harbor Laboratory}, abstract = {With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein coding genes sampling 129 out of the 194 recognized extant families as well as the first comprehensive set of fully-justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov., and Staphyliniformia sensu nov., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic origin of all modern beetle suborders, and a Triassic{\textendash}Jurassic origin of most extant families. While fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.Competing Interest StatementThe authors have declared no competing interest.}, URL = {https://www.biorxiv.org/content/early/2021/09/24/2021.09.22.461358}, eprint = {https://www.biorxiv.org/content/early/2021/09/24/2021.09.22.461358.full.pdf}, journal = {bioRxiv} }