The holometabolous insect order Trichoptera (caddisflies) includes more known species than all of the other primarily aquatic orders of insects combined. They are distributed unevenly; with the greatest number and density occurring in the Oriental Biogeographic Region and the smallest in the East Palearctic. Ecosystem services provided by Trichoptera are also very diverse and include their essential roles in food webs, in biological monitoring of water quality, as food for fish and other predators (many of which are of human concern), and as engineers that stabilize gravel bed sediment. They are especially important in capturing and using a wide variety of nutrients in many forms, transforming them for use by other organisms in freshwaters and surrounding riparian areas. The general pattern of evolution for trichopteran families is becoming clearer as more genes from more taxa are sequenced and as morphological characters are becoming understood in greater detail. This increasingly credible phylogeny provides a foundation for interpreting and hypothesizing the functional traits of this diverse order of freshwater organisms and for understanding the richness of the ecological services corresponding with those traits. Our research also is gaining insight into the timing of evolutionary diversification in the order. Correlations for the use of angiosperm plant material as food and case construction material by the earliest ancestors of infraorder Plenitentoria-by at least 175 Ma-may provide insight into the timing of the origin of angiosperms.

The Trichoptera, or caddisflies, are traditionally split into two taxonomic subdivisions: the 'retreat-making' Annulipalpia and the 'case-making' Integripalpia (sensu Ross). The monophyly of these groups is well documented; however, the establishment of a third subdivision, 'Spicipalpia', and the positions of the five 'spicipalpian' families is much debated. In contrast to previous molecular studies using nuclear ribosomal RNA, a recent trichopteran study (using nuclear protein-coding genes) placed one of these 'spicipalpian' families, the free-living predatory Rhyacophilidae, as the sister taxon to the rest of Trichoptera, a result that has significant implications for both the understanding of trichopteran evolution and its timing. This paper sets out to investigate the relationships of Trichoptera using several newly sequenced genes, together with previously published gene sequences. This dataset is the largest trichopteran dataset to date, covering six independent genes and > 10 000 nucleotides, and containing 185 species representing 49 families. With all data included, likelihood and Bayesian analyses support a monophyletic Annulipalpia and a monophyletic Integripalpia, which includes the 'spicipalpians' as a paraphyletic grade at the base of this clade. However, an analysis of the protein-coding data alone using similar analytical methods recovers Rhyacophilidae as the most basal taxon in Trichoptera, with low support. A reanalysis correcting for nucleotide composition bias provides support for the placement of the 'spicipalpian' taxa as sister to the Integripalpia, consistent with the total data analysis, suggesting that the basal position of Rhyacophilidae in the uncorrected analysis could be (or is probably) an artefact of base composition. We find it likely that ancestral trichopterans made incipient cases and retreats, and these had independent origins as precocious pupal chambers. Molecular dating analysis in beast, using the birth-death model of speciation, with a relaxed-clock model of sequence evolution informed by 37 fossil constraints, suggests that the most recent common ancestor of Trichoptera appeared in the Permian (c. 275 Ma) in line with the first appearance of Trichoptera in the fossil record, and that vicariance explains the distribution of most trichopteran taxa. A new infraordinal name, Phryganides, is introduced for the tube-case-making families of Integripalpia.

Earwigs are one of the comparatively species-poor insect orders. Although various aspects of the phylogeny of this lineage are poorly understood, before the present study, there was a general consensus that Dermaptera comprises two major lineages: the paraphyletic Protodermaptera or 'lower earwigs' and the monophyletic Epidermaptera or 'higher earwigs', which are nested within the former. Our phylogenomic study based on the analysis of 3247 nuclear single-copy genes reverses these relationships by placing monophyletic Protodermaptera within paraphyletic Epidermaptera. This phylogenetic reversal among the major earwig lineages is not contradicted by morphological arguments but results in far-reaching reinterpretations of the dermapteran ground plan. Within Dermaptera, Apachyidae form the sister group to the remaining earwigs which might imply that social behaviour is not part of the earwig ground plan. Our results corroborate the monophyly of Eudermaptera within Epidermaptera and the paraphyly of several traditional families. The monophyly of Protodermaptera is supported by molecular and morphological evidence, although the exact position of Karschiellidae which were not included in the molecular dataset cannot be determined.

We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.

Background: Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (> 16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group. Findings: We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled. Conclusions: We report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.

Caddisfly (Trichoptera) larvae assemble a variety of underwater structures using bioadhesive silk. The order is divided into two primary sub-orders distinguished by how the larvae deploy their silk. Foraging Integripalpia larvae construct portable tube cases. Annulipalpia larvae construct stationary retreats, some with suspended nets to capture food. To identify silk molecular adaptations that may have contributed to caddisfly diversification, we report initial characterization of silk from a net-spinner genus, Parapsyche, for comparison with the silk of a tube case-maker genus, Hesperophylax. Overall, general features of silk structure and processing are conserved across the sub-orders despite approximately 200 Ma of divergence: the H-fibroin proteins comprise repeating phosphoserine-rich motifs, naturally spun silk fibres contain approximately 1 : 1 molar ratios of divalent metal ions to phosphate, silk fibre precursors are stored as complex fluids of at least two types of complexes, and silk gland proteins contain only traces of divalent metal ions, suggesting metal ions that solidify the fibres are absorbed from the aqueous environment after silk extrusion. However, the number and arrangement of the repeating phosphoserine blocks differ between genera, suggesting molecular adaptation of H-fibroin through duplication and shuffling of conserved structural modules may correspond with the radiation of caddisflies into diverse environments. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.