Diversification of true water bugs revealed by transcriptome‐based phylogenomics

True water bugs (Hemiptera: Heteroptera: Nepomorpha) are among the most common insects of freshwater ecosystems, comprising approximately 2300 extant species spread over five recognized superfamilies, including Corixoidea, Nepoidea, Ochteroidea, Notonectoidea and Naucoroidea. They exhibit striking morphological and behavioural adaptations to various freshwater environments, including oar‐like swimming legs, breathing siphons or plastron respiration. The phylogeny of Nepomorpha remains contentious, particularly for the early‐diverging lineage, which has hindered the understanding of the evolution of morphology and respiratory behaviour within the clade. In the present study, we assembled a large‐scale phylogenomic dataset, including 2018 single‐copy, protein‐coding gene sequences from 85 representative species of heteropterans (44 nepomorphans) to investigate the phylogeny of Nepomorpha and the corresponding implications for character evolution. Our inferences suggest that Corixoidea is the sister group of the remaining Nepomorpha, then Nepoidea and Ochteroidea; these clades successively branched in the Triassic, following the end‐Permian extinction event about 251 million years ago. The five superfamilies radiated in the Jurassic, when geological reconfigurations and drastic climate changes occurred. An ancestral state reconstruction demonstrated that the ancestral respiration type in true water bugs is likely a simple air‐bubble type, which was widely utilized in true water bugs. Subsequently, different clades have evolved variously specialized adaptations to improve its efficiency. We propose that the crawling legs of Nepidae are secondary or symplesiomorphic characters, which cannot serve as the evidence for the sister group role of Nepoidea to the remaining nepomorphans. Phylogenomic analyses suggest that Corixoidea is the sister group of the remaining Nepomorpha. Divergence time estimates show that the five superfamilies successively diverged between the middle Triassic and the earliest of the Middle Jurassic. Ancestral state reconstructions reveal that the ancestral respiration type in true water bugs is likely an air‐bubble type, with various specialized adaptations in different clades.