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The nuclear genomes of most animal species include segments of the mitogenome, but the count of these NUMTs varies greatly. This study examines the incidence of NUMTs derived from a 658 bp region of the cytochrome c oxidase I (COI) gene as a proxy for other coding regions of the mitochondrial genome. Analysis focuses on the most diverse group of terrestrial organisms, insects, because COI-based identification systems play a key role in clarifying their diversity, an essential antecedent to genome sequencing. Nearly 10,000 COI NUMTs ≥ 100 bp were detected in the genomes of 1,002 insect species with a range from 0–443. NUMT counts were similar among congeners, but differences among genera in a family were often large with genome size explaining 56% of the mitogenome-wide variation in counts. While many of these NUMTs possessed an indel or premature stop codon allowing their exclusion, the others could complicate species diagnosis as they averaged 10.1% divergence from their mitochondrial homologue. The count of NUMTs varies widely among insect lineages, peaking in groups that employ direct development or incomplete metamorphosis. They can raise the apparent species count by up to 22% when the 658 bp barcode region is examined while shorter targets (300 bp, 150 bp) elevate exposure (58–111%) to “ghost” species. As a result, NUMTs represent a particular complication for protocols (e.g., eDNA, metabarcoding) which employ short amplicons for biodiversity assessments.

The use of DNA barcoding has revolutionized 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 maximize sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,888 genera and 202 families. 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 maximize output and minimize 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.

Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

The type of Lasiocampa decolorata (KLUG, 1830), collected in 1820, was successfully barcoded to generate a 658bp COI-fragment after 194 years. The resulting molecular data allowed the description of two closely related species from Morocco: Lasiocampa hannae SPEIDEL, MOOSERWITT sp. n. from the Anti Atlas and Lasiocampa editae SPEIDEL, MOOSERWITT sp. n. from the High Atlas.