Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

Segment 9 of male Raphidioptera, comprising tergite, sternite, gonocoxites, gonostyli and gonapophyses, is a benchmark for homologies in the male and female terminalia of the three Neuropterida orders Raphidioptera, Megaloptera and Neuroptera. The segments relating to genitalia are 9, 10 and 11 in males and 7, 8 and 9 in females. Results from holomorphological and recent molecular cladistic analyses of Neuropterida agree in supporting the sister‐group relationships between: (1) the Raphidioptera and the clade Megaloptera + Neuroptera, and (2) the suborder Nevrorthiformia and all other Neuroptera. The main discrepancy between the results of these studies is the nonmonophyly of the suborder Hemerobiiformia in the molecular analysis. The monophyly of the Megaloptera (which has been repeatedly questioned) is further corroborated by a hitherto overlooked ground pattern autapomorphy: the presence of eversible sacs within the complex of the fused gonocoxites 11 in Corydalidae and Sialidae. The recently discovered paired complex of gonocoxites 10 (parameres) in Nipponeurorthus (Nevrorthidae) indicates that the curious apex of sternite 9 of Nevrorthus and Austroneurorthus is the amalgamation of the sclerites of gonocoxites 10 with sternite 9, interpreted as synapomorphic. In the molecular study, the Nevrorthidae, Sisyridae and Osmylidae branch off in consecutive splitting events, a result that is supported by the analysis of male genital sclerites reported here. Extraordinary parallel apomorphies (e.g. excessive enlargement and modification of gonocoxites 10 ending in a thread‐like ‘penisfilum’) in derived representatives of Coniopterygidae, Berothidae, Rhachiberothidae and Mantispidae corroborate the dilarid clade of the morphological analysis and leads us to hypothesize a sister‐group relationship of the Coniopterygidae with the dilarid clade. A re‐interpretation of the tignum of Chrysopidae as gonocoxites 11 means that the structure previously called the gonarcus represents the fused gonocoxites 9. In Hemerobiidae, the corresponding sclerite is consequently also homologized as fused gonocoxites 9. The enlargement of the lateral wings of the gonocoxites in both families is interpreted as a synapomorphy. Excessive enlargement of gonostyli 11 in the Polystoechotid clade and Myrmeleontiformia supports a sister‐group relationship of these two clades. The occurrence of certain serial homologues of female genitalia structures (gonocoxites and gonapophyses), such as the digitiform processus together with the flat appendices in segment 8 of certain Myrmeleontidae, or the wart‐like processus together with the flat circular sclerites in segment 7 of certain Berothidae, as well as the presence of gonocoxites 8 as pseudosternites in certain Nemopteridae and Coniopterygidae, are probably character reversals. The digitiform processus of tergite 9 (pseudogonocoxites) in Rhachiberothidae and Austroberothella (Berothidae) are either independently developed acquisitions with a function in oviposition, or are homologous sclerites...

Neuroptera (lacewings) and allied orders Megaloptera (dobsonflies, alderflies) and Raphidioptera (snakeflies) are predatory insects and together make up the clade Neuropterida. The higher‐level relationships within Neuropterida have historically been widely disputed with multiple competing hypotheses. Moreover, the evolution of important biological innovations among various Neuropterida families, such as the origin, timing and direction of transitions between aquatic and terrestrial habitats of larvae, remains poorly understood. To investigate the origin and diversification of lacewings and their allies, we undertook phylogenetic analyses of mitochondrial genomes of all families of Neuropterida using Bayesian inference, maximum likelihood and maximum parsimony methods. We present a robust, fully resolved phylogeny and divergence time estimation for Neuropterida with strong statistical support for almost all nodes. Mitochondrial sequence data are typified by significant compositional heterogeneity across lineages, and parsimony and models assuming homogeneous rates did not recover Neuroptera as monophyletic. Only a model accounting for compositional heterogeneity (i.e. CAT‐GTR) recovered all orders of Neuropterida as monophyletic. Significant findings of the mitogenomic phylogeny include recovering Raphidioptera as sister to Megaloptera plus Neuroptera. The sister family of all other lacewings are the dusty‐wings (Coniopterygidae), rather than Nevrorthidae. Nevrorthidae are instead returned to their traditional position as the sister group of the spongilla‐flies (Sisyridae) and closely related to Osmylidae. Our divergence time analysis indicates that the Mesozoic was indeed a ‘golden age’ for lacewings, with most families of Neuropterida diverging during the Triassic and Jurassic and all extant families present by the Early Cretaceous. Based on ancestral character state reconstructions of larval habitat we evaluate competing hypotheses regarding the life style of early neuropteridan larvae as either aquatic or terrestrial.

External and internal head structures of larvae of Nevrorthidae were described in detail. The results were compared to conditions found in other representatives of Neuroptera and the other two neuropterid orders. The cladistic analysis supported the monophyly of Neuroptera, Neuroptera exclusive of Nevrorthidae, Hemerobiiformia, and Myrmeleontiformia. Neuroptera exclusive of Nevrorthidae are supported by the formation of an undivided postmentum and the presence of cryptonephric Malpighian tubules. The highly specialized articulation of the neck (Rollengelenk) and the absence of a salivary duct are autapomorphies of Nevrorthidae. Ithonidae and Polystoechotidae form a clade and are the sister group of the remaining Hemerobiiformia, which are characterized by the complete lack of a gula and a terminal filament of the antenna. Within this lineage, a clade comprising Mantispidae, Dilaridae, Berothidae, and Rhachiberothidae is well supported. Larvae of Myrmeleontiformia are characterized by a complex transformation of head structures, with a hypostomal bridge, a small triangular gula, largely reduced maxillary grooves, and anteriorly shifted posterior tentorial grooves. The slender finger-like mid-dorsal apodeme is another autapomorphy of the group. Psychopsidae are placed as the sister group of the remaining Myrmeleontiformia, which are characterized by a conspicuous, protruding ocular region (often less distinct or even absent in Nemopteridae). Ascalaphidae are the sister group of Myrmeleontidae. Larvae of both families share the fusion of the tibia and tarsus in the hind leg. The larval characters analysed were not sufficient for full resolution of the myrmeleontiform and hemerobiiform lineages. The position of several families such as Osmylidae, Sisyridae, and Coniopterygidae remains uncertain. The results are in agreement with an aquatic ancestor of Neuroptera and secondarily acquired terrestrial habits within the lineage (Neuroptera exclusive of Nevrorthidae), and another invasion of the aquatic environment by Sisyridae.