Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.

Aims: The main aim of this study was to fill a gap in barcoding data of the European Chironomidae of the Balkan region, developing and testing the efficiency of a reference DNA barcode library for ancient Lake Skadar basin species (Montenegro/Albania), a region of Europe never before subjected to barcoding studies on Chironomidae. Another aim was to test the efficiency of DNA barcoding for the identification of European Chironomidae, including the estimation of optimal identification thresholds, using >12,000 barcodes.Location: Lake Skadar basin and adjacent area (Montenegro/Albania).Methods: Through this study, 770 individuals of Chironomidae from the Lake Skadar region were barcoded, both at adult and pre‐imaginal stages. Adults were morphologically identified, while larvae were assigned to species by molecular identification, using different methods, of which the efficiency was tested, for a total of 97 different barcoded species.Results: The identification efficiency of the reference dataset developed for the Lake Skadar region was 98.6%, a value in line with that obtained when the identification efficiency for European Chironomidae was evaluated (95.8%), which confirms the accuracy of DNA barcoding for the identification of these insects. Moreover, we found that the optimal threshold for the molecular identification of the family is 1.6% nucleotide distance, though more specific thresholds are suggested for the identification of species belonging to Chironomidae subfamilies, since they are related to lower identification errors than to the use of a general threshold. The analysis of inconsistency between molecular and morphological identification shed light on taxonomic issues within European Chironomidae. Previously postulated species synonyms were confirmed, and also further cases requiring deeper investigation were detected.Main conclusions: Our de novo DNA barcode library was shown to have a high identification efficiency. Taxon‐specific thresholds increase the efficacy of molecular identification. Hypothesized species synonyms could be validated through molecular techniques.

Knowledge and management of aquatic ecosystems (formerly Bulletin Français de la Pèche et de la Pisciculture), an international journal on freshwater ecosystem

Tanytarsus latens sp. nov. is described from Finland (Ostrobothnia borealis, Satakunta). Both morphological and molecular analyses indicate that T. latens belongs to the mendax species group. The adult male hypopygium of the new species resembles that of Tanytarsus occultus Brundin and of T. desertor Giłka et Paasivirta, while the molecular analysis based on the mitochondrial cytochrome oxidase (COI) gene fragment evidences that T. latens is a sister species to most of European Tanytarsus of the mendax group’s core, for which the COI barcodes are known. Notes on biology of T. latens are also provided.