Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History.

The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.

A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections.

Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes.

Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly Eubasilissa regina. Both genomes were highly contiguous (N50  = 9.7 Mbp/32.4 Mbp, L50  = 13/11) and complete (BUSCO complete  = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.

First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing.

We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.

Entomological Collections in the Age of Big Data.

With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.

Taxonomic revision of Plyomydas Wilcox & Papavero, 1971 with the description of two new species and its transfer to Mydinae (Insecta: Diptera: Mydidae)

ABSTRACT The monotypic Neotropical Mydidae genus Plyomydas Wilcox & Papavero, 1971, to date confined to coastal Peru, is reviewed. Two new species, Plyomydas adelphe sp. nov. and Plyomydas phalaros sp. nov., are described from mid-elevational western Argentina, which extends the distribution of the genus considerably. Distribution, occurrence in biodiversity hotspots sensu Conservation International, and seasonal incidence are discussed. Descriptions/re-descriptions, photographs, illustrations, and identification keys are provided and made openly accessible in data depositories to support future studies of the included taxa. Plyomydas is transferred from the Leptomydinae to the Mydinae: Messiasiini based on the absence of acanthophorite spines on abdominal tergite 10 in females and the presence of vein M3 + M4 terminating in the costal vein C. Leptomydinae is therefore restricted to the Northern Hemisphere with the exception of Hessemydas Kondratieff, Carr & Irwin, 2005 known from Madagascar. Messiasia notospila (Wiedemann, 1828) is compared to Plyomydas species.

Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes.

A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.

Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae).

A cybercatalog to the Apioceridae (apiocerid flies) of the Afrotropical Region is provided. Each taxon entry includes links to open-access, online repositories such as ZooBank, BHL/BioStor/BLR, Plazi, GBIF, Morphbank, EoL, and a research web-site to access taxonomic information, digitized literature, morphological descriptions, specimen occurrence data, and images. Cybercatalogs as the one presented here will need to become the future of taxonomic catalogs taking advantage of the growing number of online repositories, linked data, and be easily updatable. Comments on the deposition of the holotype of Apiocera braunsi Melander, 1907 are made.

Review of Anasillomos Londt, 1983 with the description of a new species (Insecta: Diptera: Asilidae).

The southern African assassin-fly genus Anasillomos Londt, 1983 is reviewed. A new species, Anasillomosjuergeni sp. n., is described from the Namib desert and represents the second species in the genus. Descriptions/re-descriptions, photographs, and identification keys are provided to aid in the identification. Distribution, occurrence in biodiversity hotspots sensu Conservation International, and seasonal incidence are discussed.

Review of the genus Namadytes Hesse, 1969 (Insecta: Diptera: Mydidae: Syllegomydinae).

The Mydidae genus Namadytes Hesse, 1969 is reviewed. It is known from five species, primarily occurring in Namibia. The study of newly available material from both Namibia and South Africa deposited in several natural history collections results in the recognition of three species and new synonymy of two, i.e., Namadytespallidus Hesse, 1972 is a new junior synonym of Namadytesmaculiventris (Hesse, 1969) and Namadytesprozeskyi Hesse, 1969: 282 is a new junior synonym of Namadytesvansoni Hesse, 1969: 280. All three species are re-described and comments on sexual dimorphism and intraspecific variation are made, a dichotomous key for their identification is presented, and illustrations and photographs are provided to support the descriptions and facilitate future identification. Distribution, occurrence in biodiversity hotspots sensu Conservation International, and seasonal incidence with associated weather and climatic data are discussed for all species. A morphological structure ventral to the halter and posterior to the metathoracic spiracle, the infra-halter sclerite, is here newly termed.

New species and new records of Mydidae from the Afrotropical and Oriental regions (Insecta, Diptera, Asiloidea).

New Mydidae species are described from the Afrotropical and Oriental regions including the first records of this family from several countries in eastern Africa (Kenya, Tanzania, and Uganda) and Mauritania in western Africa as well as Nepal and Thailand in Asia. The new species are, Leptomydinae: Leptomydas notossp. n. (south-western India), Leptomydas raptisp. n. (south-central Nepal), Leptomydas tigrissp. n. (north-central Thailand); Syllegomydinae: Mydaselpidini: Mydaselpis ngurumanisp. n. (south-eastern Kenya, north-eastern Tanzania), Vespiodes phaiossp. n. (south-eastern Kenya); Syllegomydinae: Syllegomydini: Syllegomydas (Notobates) astrictussp. n. (Kenya), Syllegomydas (Notobates) heothinossp. n. (Kenya and Uganda), Syllegomydas (Syllegomydas) elachyssp. n. (northern Zimbabwe). Syllegomydas (Syllegomydas) proximus Séguy, 1928 is recorded from western Mauritania and re-described. Syllegomydas (Notobates) dispar (Loew, 1852), which was previously listed as incertae sedis in the Afrotropical Diptera catalogue, is re-described and illustrated based on examination of the type specimens and several additional specimens from Mozambique. Cephalocera annulata Brunetti, 1912 and Syllegomydas bucciferus Séguy, 1928, described from north-eastern India and previously unplaced in the Oriental Diptera catalogue, are newly combined with Leptomydas Gerstaecker, 1868 and together with Leptomydas indianus Brunetti, 1912, also from north-eastern India, placed in Leptomydinae. Comments on the possible synonymy of the genera of Mydaselpidini are made. Illustrations and photographs are provided to support the descriptions and future identification. A provisional dichotomous key to Mydidae genera occurring in eastern Africa (Kenya, Malawi, Mozambique, Somalia, Tanzania, Uganda) and the Oriental Region is provided. Distribution, occurrence in biodiversity hotspots and high-biodiversity wilderness areas, and seasonal incidence are discussed for all species.

Taxonomic revision of Ectyphus Gerstaecker, 1868 and Parectyphus Hesse, 1972 with a key to world Ectyphinae (Insecta, Diptera, Mydidae).

The Afrotropical Mydidae genera Ectyphus Gerstaecker, 1868 and Parectyphus Hesse, 1972 are revised. Six species of Ectyphus are recognised (Ectyphus abdominalis Bezzi, 1924, Ectyphus armipes Bezzi, 1924, Ectyphus capillatus Hesse, 1969, Ectyphus pinguis Gerstaecker, 1868, and Ectyphus pretoriensis Bezzi, 1924), of which one is newly described from Kenya, Ectyphus amboselisp. n. Two species, Ectyphus bitaeniatus Hesse, 1969 and Ectyphus flavidorsalis Hesse, 1969, are newly synonymised with Ectyphus pinguis. The monotypic genus Parectyphus Hesse, 1972 and the male of its type species Parectyphus namibiensis Hesse, 1972 are re-described while the female is described for the first time. Comments on the distribution of all species within biodiversity hotspots are given. A dichotomous identification key to the genera and species of world Ectyphinae is provided and illustrated keys to the world Ectyphinae are made available online in both dichotomous and multi-access, matrix-based formats.