Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming

Adephaga is the second largest suborder of Coleoptera and contains aquatic terrestrial groups that are sometimes classified as Hydradephaga Geadephaga, respectively. The phylogenetic relationships have been studied intensively, but major subgroups Geadephaga placement Hygrobiidae within Dytiscoidea remain obscure. Here, we infer new DNA-hybridization baits for exon-capture phylogenomics combine hybrid-capture sequence data with transcriptomes to generate phylogenomic taxon sampling presented date. Our analyses show suitable capture target loci across different lineages Adephaga. Phylogenetic moderately trimmed supermatrices confirm hypothesis paraphyletic ‘Hydradephaga’, Gyrinidae placed sister all other families in morphology-based phylogenies, even though quartet-concordance did not support this result. All conducted site-heterogeneous models suggest Trachypachidae a clade Carabidae + Cicindelidae congruence results from morphological studies. Haliplidae inferred Dytiscoidea, while Noteridae (+ most likely Meruidae) remaining Dytiscoidea. A strongly supported (Amphizoidae monophyletic Aspidytidae) when model used. In general, find stringent trimming reduced deviation assumptions also reduction information. We C60 provide greater stability amino-acid than site-homogeneous models. Thus, can potentially reduce incongruence phylogenomics. Lastly, gene-tree errors prominent data, after sub-sampling genes these errors, subsampling based on likelihood mapping criterion summary coalescent higher topological concatenation-based tree. Overall, our demonstrate moderate alignment strategies, application mitigation should be routinely included pipeline order more accurately phylogeny species.