A new species of Docosia Winnertz from Central Europe, with DNA barcoding based on four gene markers (Diptera, Mycetophilidae)

Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library

Simple Summary

DNA barcoding is a method by which a specific region of the mitochondrial genome is used to quantify genetic distances within and between animal species. Most DNA barcodes of the world are assembled on the Barcode of Life online database BoldSystems (BOLD). There, machine-generated barcode index numbers (BINs) are automatically assigned to clusters of specimens thought to represent species. I review the current state of DNA barcoding of the superfamily Sciaroidea, a diverse insect group consisting of close to 16,000 described fly species in eight families. To date, over 1.2 million specimens of Sciaroidea have been barcoded and the 56,648 assigned BINs on BOLD already represent 3.5 times the number of described species. Still, 95% of the BINs have currently no associated scientific name and very little effort has been put into building a quality-checked reference library where named species are linked to the BINs on BOLD. In the Nordic region, however, substantial progress is made towards building a complete reference library. While DNA barcoding has tremendous potential for advancing the knowledge for many diverse groups of insects, its potential will never be fully reached absent more engagement of trained taxonomists to build voucher collections, curate the reference libraries, and describe new species.

Abstract

DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.

Every Single Specimen Counts: A New Docosia Winnertz (Diptera: Mycetophilidae) Species Described from a Singleton

Simple Summary

A new fungus gnat species has been described from a single specimen collected from Georgia (Sakartvelo). The new species, named after its occurrence in Caucasia as Docosia caucasica sp. n., is distinguished from congeners by the characters in male terminalia and a unique COI sequence. As a substantial proportion of species in ecological communities tend to be rare, about 20–30% of new insect taxa have been described from a singleton so far. Therefore, following high-quality standards when describing new species, particularly when dealing with minimalistic material, is crucial. As much as possible, using multiple sets of characters, like morphology and DNA sequencing, is encouraged.

Abstract

A new species—Docosia caucasica sp. n.—has been described from material collected from the Lesser Caucasus Mountains in Georgia (Sakartvelo). The new species belongs to a group of Palaearctic species characterized by distinct posterolateral processes of gonocoxites and apically modified setae at the posteroventral margin of the gonocoxites medially. Within the group, D. caucasica sp. n. is most similar to D. landrocki Laštovka and Ševčík, 2006 in having a similar outline of the medial process of posteroventral margin of the gonocoxites and the gonostylus. There is also a marked difference within the partial cytochrome c oxidase subunit 1 gene (COI) sequence of D. caucasica sp. n. and other Docosia spp. available in public databases. As the new species is described from a single male specimen only, the adequacy and code compliance of that are discussed.

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.

New and poorly known Palaearctic fungus gnats (Diptera, Sciaroidea)

Background

Fungus gnats (Sciaroidea) are a globally species rich group of lower Diptera. In Europe, Fennoscandian peninsula in particular holds a notable diversity, ca. 1000 species, of which 10 % are still unnamed. Fungus gnats are predominantly terrestrial insects, but some species dwell in wetland habitats.

New information

Eight new fungus gnat species, belonging to the families Keroplatidae (Orfeliaboreoalpina Salmela sp.n.) and Mycetophilidae (Sciophilaholopaineni Salmela sp.n., S.curvata Salmela sp.n., Boletinasasakawai Salmela & Kolcsár sp.n., B.norokorpii Salmela & Kolcsár sp.n., Phroniasompio Salmela sp.n., P.reducta Salmela sp.n., P.prolongata Salmela sp.n.), are described. Four of the species are known from Fennoscandia only whilst two are supposed to have boreo-alpine disjunct ranges, i.e. having populations in Fennoscandia and the Central European Alps. One of the species probably has a boreal range (Finnish Lapland and Central Siberia). Type material of Boletinacurta Sasakawa & Kimura from Japan was found to consist of two species, and a further species close to these taxa is described from Finland. Phroniaelegantula Hackman is redescribed and reported for the first time from Norway. DNA barcodes are provided for the first time for five species.