Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.

Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Worldwide revision of synanthropic silverfish (Insecta: Zygentoma: Lepismatidae) combining morphological and molecular data.

Synanthropic silverfish are the best-known and most widely distributed insects of the order Zygentoma. However, there is a great gap in the knowledge and confusion about the geographic distribution and the diagnostic characteristics that allow their identification. In this work, we provide an exhaustive and deep analysis of the most common 9 synanthropic silverfish of the world, combining previously published and newly derived morphological and molecular data. Updated descriptions of Ctenolepisma calvum (Ritter, 1910) and Ctenolepisma (Sceletolepisma) villosum (Fabricius, 1775) are included, and morphological remarks, illustrations, and photographs of the remaining synanthropic species are provided to clarify their diagnosis and differentiation among them and from other free-living species. In addition, Ctenolepisma targionii (Grassi and Rovelli, 1889) is synonymized with C. villosum. A molecular phylogeny is presented based on the COI sequences of all the synanthropic species deposited in BOLD and GenBank, with 15 new sequences provided by this study. This has allowed us to detect and correct a series of identification errors based on the lack of morphological knowledge of several species. Moreover, 2 different lineages of Ctenolepisma longicaudatumEscherich, 1905 have also been detected. To help future studies, we also provide a taxonomic interpretation guide for the most important diagnostic characters of the order Zygentoma, as well as an identification key for all the Synanthropic studied species. Finally, an approximation of the global distribution of synanthropic silverfish is discussed. Several new records indicate that the expansion of these species, generally associated with the transport of goods and people, is still far from over.

DNA Barcoding and Metabarcoding Protocols for Species Identification.

The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.

Disproportionate declines of formerly abundant species underlie insect loss.

Studies have reported widespread declines in terrestrial insect abundances in recent years1-4, but trends in other biodiversity metrics are less clear-cut5-7. Here we examined long-term trends in 923 terrestrial insect assemblages monitored in 106 studies, and found concomitant declines in abundance and species richness. For studies that were resolved to species level (551 sites in 57 studies), we observed a decline in the number of initially abundant species through time, but not in the number of very rare species. At the population level, we found that species that were most abundant at the start of the time series showed the strongest average declines (corrected for regression-to-the-mean effects). Rarer species were, on average, also declining, but these were offset by increases of other species. Our results suggest that the observed decreases in total insect abundance2 can mostly be explained by widespread declines of formerly abundant species. This counters the common narrative that biodiversity loss is mostly characterized by declines of rare species8,9. Although our results suggest that fundamental changes are occurring in insect assemblages, it is important to recognize that they represent only trends from those locations for which sufficient long-term data are available. Nevertheless, given the importance of abundant species in ecosystems10, their general declines are likely to have broad repercussions for food webs and ecosystem functioning.

Bridging two insect flight modes in evolution, physiology and robophysics.

Since taking flight, insects have undergone repeated evolutionary transitions between two seemingly distinct flight modes1-3. Some insects neurally activate their muscles synchronously with each wingstroke. However, many insects have achieved wingbeat frequencies beyond the speed limit of typical neuromuscular systems by evolving flight muscles that are asynchronous with neural activation and activate in response to mechanical stretch2-8. These modes reflect the two fundamental ways of generating rhythmic movement: time-periodic forcing versus emergent oscillations from self-excitation8-10. How repeated evolutionary transitions have occurred and what governs the switching between these distinct modes remain unknown. Here we find that, despite widespread asynchronous actuation in insects across the phylogeny3,6, asynchrony probably evolved only once at the order level, with many reversions to the ancestral, synchronous mode. A synchronous moth species, evolved from an asynchronous ancestor, still preserves the stretch-activated muscle physiology. Numerical and robophysical analyses of a unified biophysical framework reveal that rather than a dichotomy, these two modes are two regimes of the same dynamics. Insects can transition between flight modes across a bridge in physiological parameter space. Finally, we integrate these two actuation modes into an insect-scale robot11-13 that enables transitions between modes and unlocks a new self-excited wingstroke strategy for engineered flight. Together, this framework accounts for repeated transitions in insect flight evolution and shows how flight modes can flip with changes in physiological parameters.

Comparison of different traps and attractants in 3 food processing facilities in Greece on the capture of stored product insects.

Certain lures are marketed toward particular pests or classes of pests, while others might be multi-species lures. Investigative aims for this study included both which trap was most sensitive and whether different combinations of traps and attractants were delivering novel information about the stored product insect community. Comparisons were made for all combinations of 3 commercial traps and 4 different attractants plus an untreated control on the capture of stored-product insects for 2 consecutive years in 3 food processing facilities in Central Greece. The traps used in the experiments were Dome Trap (Trécé Inc., USA), Wall Trap (Trécé) and Box Trap (Insects Limited, Ltd., USA). The attractants that were evaluated were 0.13 g of (i) PantryPatrol gel (Insects Limited), (ii) Storgard kairomone food attractant oil (Trécé), (iii) wheat germ (Honeyville, USA), and (iv) Dermestid tablet attractant (Insects Limited). The traps were inspected approximately every 15 days and rotated. A total of 34,000+ individuals were captured belonging to 26 families and at least 48 species. The results indicated that Indian meal moth, Plodia interpunctella (Hübner), red flour beetle, Tribolium castaneum (Herbst), and cigarette beetle, Lasioderma serricorne (F.) were the most abundant. Although there were noticeable differences among the different traps and attractants for specific species, all combinations provided similar information on population dynamics. Generally, Dome traps baited with either the oil or the gel, were found to be the most sensitive. The results of the present study demonstrate the importance of long-term trapping protocols, as a keystone in IPM-based control strategies in food processing facilities.

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics.

BACKGROUND: Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata. RESULTS: HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size. CONCLUSIONS: Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.

An annotated checklist of earwigs (Dermaptera) of South India with two new records from India.

The checklist of earwigs occurring in South India,viz., Andhra Pradesh, Karnataka, Kerala, Tamil Nadu and Telangana, was compiled from published literature and augmented by collecting efforts between 2020 and 2022. A total of 102 species belonging to 45 genera and eight families are listed herein from South India. Specimens representing 29 species were collected from the South Indian states during 20202022 surveys, of whichDendroiketes corticinusandChaetospania anderssonirepresent two new records for India. The highest number of species was recorded from Tamil Nadu (79 species), followed by Karnataka (39 species) and Kerala (26 species), while the least number were from Telangana (6) and Andhra Pradesh (4 species). The records indicated that the South Indian states, which cover a significant portion of the Western Ghats of India (Karnataka, Kerala and Tamil Nadu), are more diverse than previously indicated.

Morphology and phylogenetic significance of the thoracic muscles in Psocodea (Insecta: Paraneoptera).

The thoracic musculature of the insect order Psocodea has been examined in only a few species of a single suborder to date. In the present study, we examined the thoracic musculature of species selected from all three suborders of Psocodea to elucidate the ground plan of the order and to examine the phylogenetic utility of the character system. The sister-group relationship between the suborders Troctomorpha and Psocomorpha received support from two novel nonhomoplasious synapomorphies, although the support from other morphological characters for this relationship is ambiguous. The sister-group relationship between the infraorders Epipsocetae and Psocetae also received support from one nonhomoplasious synapomorphy, although no other morphological characters supporting this relationship have been identified to date. The present examination revealed the potential of thoracic muscle characters for estimating deep phylogeny, possibly including interordinal relationships.

Competition for pollinators destabilizes plant coexistence.

Mounting concern over the global decline of pollinators has fuelled calls for investigating their role in maintaining plant diversity1,2. Theory predicts that competition for pollinators can stabilize interactions between plant species by providing opportunities for niche differentiation3, while at the same time can drive competitive imbalances that favour exclusion4. Here we empirically tested these contrasting effects by manipulating competition for pollinators in a way that predicts its long-term implications for plant coexistence. We subjected annual plant individuals situated across experimentally imposed gradients in neighbour density to either ambient insect pollination or a pollen supplementation treatment alleviating competition for pollinators. The vital rates of these individuals informed plant population dynamic models predicting the key theoretical metrics of species coexistence. Competition for pollinators generally destabilized the interactions between plant species, reducing the proportion of pairs expected to coexist. Interactions with pollinators also influenced the competitive imbalances between plant species, effects that are expected to strengthen with pollinator decline, potentially disrupting plant coexistence. Indeed, results from an experiment simulating pollinator decline showed that plant species experiencing greater reductions in floral visitation also suffered greater declines in population growth rate. Our results reveal that competition for pollinators may weaken plant coexistence by destabilizing interactions and contributing to competitive imbalances, information critical for interpreting the impacts of pollinator decline.

Vertical stratification of insect abundance and species richness in an Amazonian tropical forest.

Tropical forests are among the most biodiverse biomes on the planet. Nevertheless, quantifying the abundance and species richness within megadiverse groups is a significant challenge. We designed a study to address this challenge by documenting the variability of the insect fauna across a vertical canopy gradient in a Central Amazonian tropical forest. Insects were sampled over two weeks using 6-m Gressitt-style Malaise traps set at five heights (0 m-32 m-8 m intervals) on a metal tower in a tropical forest north of Manaus, Brazil. The traps contained 37,778 specimens of 18 orders of insects. Using simulation approaches and nonparametric analyses, we interpreted the abundance and richness of insects along this gradient. Diptera, Hymenoptera, and Coleoptera had their greatest abundance at the ground level, whereas Lepidoptera and Hemiptera were more abundant in the upper levels of the canopy. We identified species of 38 of the 56 families of Diptera, finding that 527 out of 856 species (61.6%) were not sampled at the ground level. Mycetophilidae, Tipulidae, and Phoridae were significantly more diverse and/or abundant at the ground level, while Tachinidae, Dolichopodidae, and Lauxaniidae were more diverse or abundant at upper levels. Our study suggests the need for a careful discussion of strategies of tropical forest conservation based on a much more complete understanding of the three-dimensional distribution of its insect diversity.

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

InsectBase 2.0: a comprehensive gene resource for insects.

Insects are the largest group of animals on the planet and have a huge impact on human life by providing resources, transmitting diseases, and damaging agricultural crop production. Recently, a large amount of insect genome and gene data has been generated. A comprehensive database is highly desirable for managing, sharing, and mining these resources. Here, we present an updated database, InsectBase 2.0 (http://v2.insect-genome.com/), covering 815 insect genomes, 25 805 transcriptomes and >16 million genes, including 15 045 111 coding sequences, 3 436 022 3'UTRs, 4 345 664 5'UTRs, 112 162 miRNAs and 1 293 430 lncRNAs. In addition, we used an in-house standard pipeline to annotate 1 434 653 genes belonging to 164 gene families; 215 986 potential horizontally transferred genes; and 419 KEGG pathways. Web services such as BLAST, JBrowse2 and Synteny Viewer are provided for searching and visualization. InsectBase 2.0 serves as a valuable platform for entomologists and researchers in the related communities of animal evolution and invertebrate comparative genomics.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

Three new species of Euplocania Enderlein (Psocodea, 'Psocoptera', Ptiloneuridae), for the state of Roraima, Brazil

The three new species of Brazilian Euplocania are described and illustrated, two species belong in the amabilis species group (Euplocania maraca sp. nov. and Euplocania ufrr sp. nov.) and one species belong in the marginata species group (Euplocania macuxi sp. nov.). Information on species groups, species subgroups and distribution by Brazilian states is included for known species of Euplocania.(AU)

Review of the inquilinous fauna associated with insect galls in Brazilian restingas / Revisão da fauna inquilina associada a galhas de insetos em restingas brasileiras

Several records of associated fauna, including parasitoids, inquilines, predators, and successors, have been reported by insect gall inventories in Brazilian restingas. Although most guilds are well established, inquilines have frequently been misinterpreted. In this paper, the inquilinous fauna of insect galls is revised based on five criteria: food habit; coexistence with the inducer; modification of gall tissues or production of new tissues; phylogenetic relationship with the inducer; and mobility. Gall inventories dated from 1988 to 2019 were examined, totaling 16 publications, eight of them with inquiline records. This guild was reported in 53 gall morphotypes in 44 plant species and four morphospecies distributed among 36 genera of 24 host families for a total of 65 records. Most inquilines were repositioned into the cecidophage guild and others into the kleptoparasite guild, resulting in a large reduction in the frequency of inquilines (from 65 to five records), and in first reports of cecidophages and kleptoparasites, with 46 and 13 records, respectively. Cecidophage was the most diverse guild with insects of five orders (Diptera, Coleoptera, Lepidoptera, Hemiptera, and Thysanoptera) while kleptoparasites were represented only by two orders (Diptera and Hymenoptera) and inquiline solely by Hymenoptera. Other results indicate that Leptothorax sp. (Formicidae) could be a successor and not an inquiline.

Vários registros de fauna associada, incluindo parasitoides, inquilinos, predadores e sucessores são encontrados em inventários de galhas de insetos em restingas brasileiras. Embora a maioria das guildas esteja bem estabelecida, os inquilinos são frequentemente interpretados de forma equivocada. Nesse trabalho, a fauna inquilina de galhas de insetos é revisada com base em cinco critérios: hábito alimentar, coexistência com o indutor, modificação dos tecidos da galha ou produção de novos tecidos, relação filogenética com o indutor e mobilidade. Inventários de galhas publicados entre 1988 e 2019 foram examinados, totalizando 16 artigos, oito deles com registro de inquilinos. Essa guilda foi assinalada em 53 morfotipos de galhas em 44 espécies de plantas e quatro morfoespécies distribuídas em 36 gêneros de 24 famílias vegetais, totalizando 65 registros. A maioria dos inquilinos foi reposicionada na guilda dos cecidófagos e outros na guilda dos cleptoparasitas, resultando em uma grande redução da frequência dos inquilinos (de 65 para cinco registros), e na primeira ocorrência de cecidófagos e cleptoparasitas, com 46 e 13 registros, respectivamente. A guilda dos cecidófagos foi a mais diversa, com insetos de cinco ordens (Diptera, Coleoptera, Lepidoptera, Hemiptera e Thysanoptera), enquanto que os cleptoparasitas foram representados por apenas duas ordens (Diptera e Hymenoptera) e os inquilinos somente por Hymenoptera. Outros resultados indicam que Leptothorax sp. (Formicidae) pode ser um sucessor e não um inquilino.

Mitochondrial Genomes of the Genus Claassenia (Plecoptera: Perlidae) and Phylogenetic Assignment to Subfamily Perlinae.

Mitochondrial genomes of three stoneflies, e.g., Claassenia magna Wu, 1948, Claassenia sp. 2 and Claassenia xucheni Chen, 2019 were sequenced in this study with 15,774, 15,777 and 15,746 bp in length, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Although the dihydrouridine arm was absent in trnSer, the remaining 21 tRNAs displayed the characteristic cloverleaf secondary structure. Stem-loop structures were identified in the CRs of all three mitogenomes, but tandem repeats were only apparent in Claassenia xucheni. The mitogenomes of three Claassenia species were analyzed and compared with mitogenomes in 21 other stoneflies from the Perlidae and three Euholognatha species (Rhopalopsole bulbifera, Capnia zijinshana and Amphinemura longispina) as outgroups. Phylogenetic analyses using maximum likelihood and Bayesian inference. Phylogenetic analysis supported that Claassenia was recovered as the sister group of other Perlinae and Claassenia+Perlinae emerged from the paraphyletic Acroneuriinae. The final results supported that Claassenia was classified into subfamily Perlinae and proposed Claassenia represent a transitional group of the subfamilies Acroneuriinae and Perlinae. This study provided new molecular evidence for exploring the debatable taxonomic position of the genus Claassenia in Perlidae.

DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians.

The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.

Relationship of insect biomass and richness with land use along a climate gradient.

Recently reported insect declines have raised both political and social concern. Although the declines have been attributed to land use and climate change, supporting evidence suffers from low taxonomic resolution, short time series, a focus on local scales, and the collinearity of the identified drivers. In this study, we conducted a systematic assessment of insect populations in southern Germany, which showed that differences in insect biomass and richness are highly context dependent. We found the largest difference in biomass between semi-natural and urban environments (-42%), whereas differences in total richness (-29%) and the richness of threatened species (-56%) were largest from semi-natural to agricultural environments. These results point to urbanization and agriculture as major drivers of decline. We also found that richness and biomass increase monotonously with increasing temperature, independent of habitat. The contrasting patterns of insect biomass and richness question the use of these indicators as mutual surrogates. Our study provides support for the implementation of more comprehensive measures aimed at habitat restoration in order to halt insect declines.