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. 2022 Mar 23;9(3):211771.
doi: 10.1098/rsos.211771. eCollection 2022 Mar.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Chenyang Cai  1   2 , Erik Tihelka  1   2 , Mattia Giacomelli  3 , John F Lawrence  4 , Adam Ślipiński  4 , Robin Kundrata  5 , Shûhei Yamamoto  6 , Margaret K Thayer  7 , Alfred F Newton  7 , Richard A B Leschen  8 , Matthew L Gimmel  9 , Liang Lü  10 , Michael S Engel  11   12 , Patrice Bouchard  11 , Diying Huang  1 , Davide Pisani  2   3 , Philip C J Donoghue  2
Affiliations

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Chenyang Cai et al. R Soc Open Sci. .

Abstract

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. 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 (NPC) genes sampling 129 out of the 193 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., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

Keywords: CAT-GTR; Coleoptera; classification; diversification; phylogenomics; substitution modelling.

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Conflict of interest statement

We declare we have no competing interests.

Figures

Figure 1.
Figure 1.
A full phylogeny of beetles displaying the systematic position of all sampled taxa analysed under the site-heterogeneous CAT-GTR + G4 model. Branch lengths have been omitted for clarity. Newly proposed taxonomic changes are followed. Support values are shown as BPP. Black numbered nodes indicate calibrations, see electronic supplementary material for full list of calibrations.
Figure 2.
Figure 2.
Timescale of beetle evolution displayed as a family-level tree adapted from figure 1. Ages were estimated based on 57 calibrated nodes, integrating the results of analyses using IR and AC molecular clock models in MCMCtree. Newly proposed taxonomic changes are followed. Abbreviations: Arch., Archostemata; Bostrichif., Bostrichiformia; Carbonif., Carboniferous; Clambif., Clambiformia ser. nov.; Laem., Laemophloeidae; Myxo., Myxophaga; Neo., Neogene; Nosodendrif., Nosodendriformia ser. nov., Rhinorhipif., Rhinorhipiformia ser. nov.; Trogoss. + Thym., Trogossitidae + Thymalidae; Q., Quaternary.
Figure 3.
Figure 3.
Proposed classification of Coleoptera showing the relationships of the suborders, series and superfamilies of beetles. Asterisks denote well-supported nodes with BPP ≥ 0.95.
Figure 4.
Figure 4.
95% CIs for the divergence of selected major beetle clades in the present and previous studies.
See this image and copyright information in PMC

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