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

Image-based recognition of parasitoid wasps using advanced neural networks

Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

New faunistic data on Diptera (Hexapoda, Insecta) from the Ziarat Juniperus forest ecosystem (Pakistan)

Background

This study presents the first faunistic record and DNA barcoding for some Diptera species recorded from the Juniperus forest ecosystem of Balochistan, Pakistan. DNA barcoding was used to explore species diversity of Dipterans and collections carried out using a Malaise trap between December 2018 to December 2019. This process involved sequencing the 658 bp Cytochrome Oxidase I (COI) gene.

New information

Amongst the collected Diptera specimens, nine families were identified, representing 13 genera. These species include Atherigonasoccata (Rondani, 1871), Atherigonavaria (Schiner, 1868), Chironomusdorsalis (Meigen, 1818), Eupeodescorollae (Linnaeus, 1758), Eristalistenax (Linnaeus,1758), Goniaornata (Meigen, 1826), Luciliasericata (Meigen, 1826), Paragusquadrifasciatus (Linnaeus, 1758), Polleniarudis (Fabricius, 1794), Raviniapernix (Thompson, 1869), Sarcophagadux (Thompson, 1869), Trupaneaamoena (Schiner, 1868) and Wohlfahrtiabella (Linnaeus, 1758). The families Syrphidae and Sarcophagidae exhibited the highest representation, each comprising three genera and three species. They were followed by the family Muscidae, which had a single genus and two species. Anthomyiidae, Chironomidae, Calliphoridae, Polleniidae, Tachinidae and Tephritidae were represented by only one genus and one species. A nique Barcode Index Number (BIN) was allotted to Tachinidae (specie i.e Goniaornata). The results indicated that barcoding through cytochrome oxidase I is an effective approach for the accurate identification and genetic studies of Diptera species. This discovery highlights the significant diversity of this insect order in study region. Furthermore, a comprehensive list of other Diptera species remains elusive because of difficulties in distinguishing them, based on morphology and a lack of professional entomological knowledge.

A comprehensive DNA barcoding reference database for Plecoptera of Switzerland

DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.

Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing

DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.

Principles for Constructing DNA Barcode Reference Libraries

All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests

Tropical forest recovery is fundamental to addressing the intertwined climate and biodiversity loss crises. While regenerating trees sequester carbon relatively quickly, the pace of biodiversity recovery remains contentious. Here, we use bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. We show that the community composition, and not species richness, of vocalizing vertebrates identified by experts reflects the restoration gradient. Two automated measures - an acoustic index model and a bird community composition derived from an independently developed Convolutional Neural Network - correlated well with restoration (adj-R² = 0.62 and 0.69, respectively). Importantly, both measures reflected composition of non-vocalizing nocturnal insects identified via metabarcoding. We show that such automated monitoring tools, based on new technologies, can effectively monitor the success of forest recovery, using robust and reproducible data.

Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps

Background

Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method.

Methods

We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies.

Results

Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H2O-MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera.

Composition and diversity of bacterial communities associated with honey bee foragers from two contrasting environments

The honey bee is associated with a diverse community of microbes (viruses, bacteria, fungi, and protists), commonly known as the microbiome. Here, we present data on honey bee microbiota from two localities having different surrounding landscapes - mountain (the Rhodope Mountains) and lowland (the Danube plain). The bacterial communities of abdomen of adult bees were studied using amplicon sequencing of the 16S rRNA gene. The composition and dominance structure and their variability within and between localities, alpha and beta diversity, and core and differential taxa were compared at different hierarchical levels (operational taxonomic units to phylum). Seven genera (Lactobacillus, Gilliamella, Bifidobacterium, Commensalibacter, Bartonella, Snodgrassella, and Frischella), known to include core gut-associated phylotypes or species clusters, dominated (92-100%) the bacterial assemblages. Significant variations were found in taxa distribution across both geographical regions and within each apiary. Lactobacillus (Firmicutes) prevailed significantly in the mountain locality followed by Gilliamella and Bartonella (Proteobacteria). Bacteria of four genera, core (Bartonella and Lactobacillus) and non-core (Pseudomonas and Morganella), dominated the bee-associated assemblages of the Danube plain locality. Several ubiquitous bacterial genera (e.g., Klebsiella, Serratia, and Providencia), some species known also as potential and opportunistic bee pathogens, had been found in the lowland locality. Beta diversity analyses confirmed the observed differences in the bacterial communities from both localities. The occurrence of non-core taxa contributes substantially to higher microbial richness and diversity in bees from the Danube plain locality. We assume that the observed differences in the microbiota of honey bees from both apiaries are due to a combination of factors specific for each region. The surrounding landscape features of both localities and related vegetation, anthropogenic impact and land use intensity, the beekeeping management practices, and bee health status might all contribute to observed differences in bee microbiota traits.

Abundant, diverse, unknown: Extreme species richness and turnover despite drastic undersampling in two closely placed tropical Malaise traps

Arthropods account for a large proportion of animal biomass and diversity in terrestrial systems, making them crucial organisms in our environments. However, still too little is known about the highly abundant and megadiverse groups that often make up the bulk of collected samples, especially in the tropics. With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. In our study, which was conducted within the Global Malaise trap Program (GMP) framework, we operated two closely placed Malaise traps in Padang, Sumatra, for three months. We analyzed the samples by DNA barcoding and sequenced a total of more than 70,000 insect specimens. For sequence clustering, we applied three different delimitation techniques, namely RESL, ASAP, and SpeciesIdentifier, which gave similar results. Despite our (very) limited sampling in time and space, our efforts recovered more than 10,000 BINs, of which the majority are associated with "dark taxa". Further analysis indicates a drastic undersampling of both sampling sites, meaning that the true arthropod diversity at our sampling sites is even higher. Regardless of the close proximity of both Malaise traps (< 360 m), we discovered significantly distinct communities.

Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach

Background

Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant.

Methods

Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods.

Results

Our results suggest that using our subsampling approach, identifying less than 10% of a sample's contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.

Phylogenetic Triage and Risk Assessment: How to Predict Emerging Phytoplasma Diseases

Phytoplasma diseases pose a substantial threat to diverse crops of agricultural importance. Management measures are usually implemented only after the disease has already occurred. Early detection of such phytopathogens, prior to disease outbreak, has rarely been attempted, but would be highly beneficial for phytosanitary risk assessment, disease prevention and mitigation. In this study, we present the implementation of a recently proposed proactive disease management protocol (DAMA: Document, Assess, Monitor, Act) for a group of vector-borne phytopathogens. We used insect samples collected during a recent biomonitoring program in southern Germany to screen for the presence of phytoplasmas. Insects were collected with malaise traps in different agricultural settings. DNA was extracted from these mass trap samples and subjected to PCR-based phytoplasma detection and mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding. Phytoplasma DNA was detected in two out of the 152 insect samples analyzed. Phytoplasma identification was performed using iPhyClassifier based on 16S rRNA gene sequence and the detected phytoplasmas were assigned to 'Candidatus Phytoplasma asteris'-related strains. Insect species in the sample were identified by DNA metabarcoding. By using established databases, checklists, and archives, we documented historical associations and records of phytoplasmas and its hosts in the study region. For the assessment in the DAMA protocol, phylogenetic triage was performed in order to determine the risk for tri-trophic interactions (plant-insect-phytoplasma) and associated disease outbreaks in the study region. A phylogenetic heat map constitutes the basis for risk assessment and was used here to identify a minimum number of seven leafhopper species suggested to be monitored by stakeholders in this region. A proactive stance in monitoring changing patterns of association between hosts and pathogens can be a cornerstone in capabilities to prevent future phytoplasma disease outbreaks. To the best of our knowledge, this is the first time that the DAMA protocol has been applied in the field of phytopathology and vector-borne plant diseases.

Mediterranean vineyards and olive groves in Croatia harbour some rare and endemic invertebrates

The Mediterranean is characterised by high biodiversity and numerous endemic species. These species are not only present in natural habitats, but also inhabit areas under human influence, such as agricultural lands. In the biodiversity assessment of Mediterranean vineyards and olive orchards within Zadar County, in Croatia, we identified eight endemic species with Mediterranean distribution, six with a Balkan Peninsula distribution, four with Dinaric Alps distribution and three species rare and endangered in Europe. Alongside these species, we have recorded five new species for Croatian fauna, many of those identified by combining morphological characteristics and the DNA barcoding tool. Araneae and Coleoptera contributed the highest number of endemic species and groups with new record were the following: Coleoptera, Diptera and Araneae. Compared to other sites, an olive orchard with ecological pest management (EPM), surrounded by natural ecosystems, had the highest ratio of endemic and rare species. Our findings emphasise that agricultural lands in the Mediterranean can be habitats for endemic and rare species and that future biodiversity research of these habitats is highly important, to monitor potential biodiversity changes and motivate future species and ecosystem conservation.

Echolocating bats prefer a high risk-high gain foraging strategy to increase prey profitability

Predators that target multiple prey types are predicted to switch foraging modes according to prey profitability to increase energy returns in dynamic environments. Here, we use bat-borne tags and DNA metabarcoding of feces to test the hypothesis that greater mouse-eared bats make immediate foraging decisions based on prey profitability and changes in the environment. We show that these bats use two foraging strategies with similar average nightly captures of 25 small, aerial insects and 29 large, ground-dwelling insects per bat, but with much higher capture success in the air (76%) vs ground (30%). However, owing to the 3-20 times larger ground prey, 85% of the nightly food acquisition comes from ground prey despite the 2.5 times higher failure rates. We find that most bats use the same foraging strategy on a given night suggesting that bats adapt their hunting behavior to weather and ground conditions. We conclude that these bats use high risk-high gain gleaning of ground prey as a primary foraging tactic, but switch to aerial hunting when environmental changes reduce the profitability of ground prey, showing that prey switching matched to environmental dynamics plays a key role in covering the energy intake even in specialized predators.

Species-level dataset is required for setting biodiversity conservation priorities for freshwater macroinvertebrates in Melbourne streams

Family-level identification of freshwater macroinvertebrates is often used to monitor the health of streams due to the lower cost and higher accuracy of identification compared to identifying species. While data on the presence of families from stream monitoring programs can also be used for biodiversity conservation planning, the ability of family-level datasets to accurately reflect regional biodiversity patterns for freshwater macroinvertebrates in Australia remains untested. This study compares family-level and species-level datasets for freshwater insects identified using morphological features and collected over 16 years from 140 sites in Greater Melbourne, Australia. Similar to the results of other studies, our results show a strong positive relationship between family- and species-level taxon richness. However, using the planning software Marxan to compare conservation priorities in our study region, we found that a data analysis of the family-level dataset underestimated the minimum sampling effort required to accurately reflect species diversity. It also identified sub-optimal conservation priority sites and overlooked regionally rare species. We recommend that aquatic macroinvertebrate monitoring programs aimed at understanding regional biodiversity patterns and conservation priorities should routinely include species-level identification, which is now becoming feasible with advances in molecular methods.

Karyotypes and COI Gene Sequences of Chironomus sp. Le1 (Kiknadze and Salova, 1996), Ch. laetus (Belyanina and Filinkova, 1996) and Their Hybrid from the Yamal Peninsula, Arctic Zone of Russia

The study of the biological diversity of the Arctic zone yields intriguing results. Initial research on the lakes of the Yamal Peninsula resulted in the identification of Chironomus laetus and the hybrid Ch. laetus × Ch. sp. Le1. To avoid misidentification, we used morphological, cytogenetic, and molecular genetic approaches. By cytogenetics, in Ch. sp. Le1, seven banding sequences were found: Le1A1, Le1B1, Le1C1, Le1D1, Le1E1, Le1F1, and Le1G1. The karyotype of Ch. laetus was mapped for the first time; it is the first species with the arm combinations AE BC DF G. We propose the name of a new cytocomplex-"laetus". DNA-barcoding of the COI gene was carried out for Ch. laetus and Ch. laetus × Ch. sp. Le1 for the first time. The estimated genetic distance between the sequences of Ch. laetus and Ch. riihimakiensis is 2.3-2.5%. The high similarity in morphology, banding sequences, and the possibility of hybridization indicate a close relationship between Ch. laetus and Ch. sp. Le1, which is assumed to be the northern variant of Ch. riihimakiensis. Molecular genetic data suggests the presence of a subgroup with Ch. laetus.

A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as “Guang Dilong”

For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 Amynthas samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines. Besides Amynthas aspergillum as the authentic source, 8 other Molecular Operational Taxonomic Units (MOTUs) were elucidated. Significantly, even the subgroups within A. aspergillum revealed here differ significantly on chemical compositions and biological activity. Fortunately, this biodiversity could be controlled when the collection was limited to designated areas, as proved by 2796 "decoction pieces" samples. This batch biological identification method should be introduced as a novel concept regarding natural medicine quality control, and to offer guidelines for in-situ conservation and breeding bases construction of wild natural medicine.

Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region, Russia, and the difficulties with its identification using GenBank and BOLD systems

Karyotype and COI gene sequences of Chironomusmelanotus Keyl, 1961 from the Yaroslavl region (Russia) were analyzed. A low level of chromosomal polymorphism has been confirmed, eventually eight banding sequences were found: melA1, melB1, melC1, melD1, melE1, melF1, and melG1; only melD2 was found in two larvae from the Sunoga river. Analysis of phylogenetic tree and estimated genetic distances has shown not all COI gene sequences of Ch.melanotus in GenBank and BOLD to belong to this species. The lower distance of 0.4% was observed between two sequences from the Yaroslavl region and Finland, apparently these are true Ch.melanotus sequences. The distances between true Ch.melanotus and other sequences from Finland were 9.5% and 12.4%, and from Sweden it was 11%. The average genetic distance between studied sequences of 9.1% is out of the range of the 3% threshold previously determined for chironomids. According to our estimates, there are two sequences with a distance of 2.9% that may belong to Ch.annularius Meigen, 1818, and one sequence with a genetic distance of 2.1%, may belonging to Ch.cingulatus Meigen, 1830, which has been confirmed karyologically. Another two sequences form a separate cluster. We suggest that they either belong to a known species, but are not present in the databases, or belong to a distinct, undescribed species.

Net-Winged Midge Genus Blepharicera Macquart (Diptera: Blephariceridae) in China: The First DNA Barcode Database with Descriptions of Four New Species and Notes on Distribution

Mitochondrial (mt) cytochrome c oxidase 1 (COI) gene is more and more widely used for DNA barcoding, which provides a rapid and timely identification as this technique is not limited by polymorphism, sex, and life stages and fundamentally complements traditional evolutionary taxonomy. The present study generated 33 mt COI sequences of seven Chinese Blepharicera Macquart, 1843 species with an average of 594 bp, which represent the first DNA barcode database for Chinese Blepharicera. Genetic distance analysis reveals that intraspecific distances in the genus are generally less than 1.7%, and interspecific distances range from 5.4% to 20.3%. Phylogenetic analysis shows that each species recovered in our analyses is separated from all neighboring species. Based on molecular and morphological data, four Blepharicera species from China, B. beishanica sp. nov., B. dushanzica sp. nov., B. nigra sp. nov. and B. xinjiangica sp. nov., are described and illustrated as new to science. Identification keys for adults and larvae of Chinese Blepharicera are also presented. Geographical analysis shows that Southwest China is the species’ richest region. Our results will be useful in tackling taxonomic problems, understanding species distribution, and resolving nomenclature conflicts associated with Blepharicera species.

Emerging technologies revolutionise insect ecology and monitoring

Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.

Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort

Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.

Exploring Large-Scale Patterns of Genetic Variation in the COI Gene among Insecta: Implications for DNA Barcoding and Threshold-Based Species Delimitation Studies

The genetic variation in the COI gene has had a great effect on the final results of species delimitation studies. However, little research has comprehensively investigated the genetic divergence in COI among Insecta. The fast-growing COI data in BOLD provide an opportunity for the comprehensive appraisal of the genetic variation in COI among Insecta. We calculated the K2P distance of 64,414 insect species downloaded from BOLD. The match ratios of the clustering analysis, based on different thresholds, were also compared among 4288 genera (35,068 species). The results indicate that approximately one-quarter of the species of Insecta showed high intraspecific genetic variation (>3%), and a conservative estimate of this proportion ranges from 12.05% to 22.58%. The application of empirical thresholds (e.g., 2% and 3%) in the clustering analysis may result in the overestimation of the species diversity. If the minimum interspecific genetic distance of the congeneric species is greater than or equal to 2%, it is possible to avoid overestimating the species diversity on the basis of the empirical thresholds. In comparison to the fixed thresholds, the “threshOpt” and “localMinima” algorithms are recommended for the provision of a reference threshold for threshold-based species delimitation studies.

Arthropod dark taxa provide new insights into diversity responses to bark beetle infestations

Natural disturbances are increasing around the globe, also impacting protected areas. Although previous studies have indicated that natural disturbances result in mainly positive effects on biodiversity, these analyses mostly focused on a few well established taxonomic groups, and thus uncertainty remains regarding the comprehensive impact of natural disturbances on biodiversity. Using Malaise traps and meta-barcoding, we studied a broad range of arthropod taxa, including dark and cryptic taxa, along a gradient of bark beetle disturbance severities in five European national parks. We identified order-level community thresholds of disturbance severity and classified barcode index numbers (BINs; a cluster system for DNA sequences, where each cluster corresponds to a species) as negative or positive disturbance indicators. Negative indicator BINs decreased above thresholds of low to medium disturbance severity (20%-30% of trees killed), whereas positive indicator BINs benefited from high disturbance severity (76%-98%). BINs allocated to a species name contained nearly as many positive as negative disturbance indicators, but dark and cryptic taxa, particularly Diptera and Hymenoptera in our data, contained higher numbers of negative disturbance indicator BINs. Analyses of changes in the richness of BINs showed variable responses of arthropods to disturbance severity at lower taxonomic levels, whereas no significant signal was detected at the order level due to the compensatory responses of the underlying taxa. We conclude that the analyses of dark taxa can offer new insights into biodiversity responses to disturbances. Our results suggest considerable potential for forest management to foster arthropod diversity, for example by maintaining both closed-canopy forests (>70% cover) and open forests (<30% cover) on the landscape.

DNA barcoding of the horsefly fauna (Diptera, Tabanidae) of Croatia with notes on the morphology and taxonomy of selected species from Chrysopsinae and Tabaninae

In the Croatian fauna, horseflies (Tabanidae) are represented by 78 species belonging to two subfamilies, five tribes, and 10 genera. Identification of these species is based on morphological characteristics. In this study, 43 species of horseflies were analyzed. The highest number of species (19) belongs to the genus Tabanus, followed by the genera Hybomitra with seven species, Haematopota with six species, Chrysops with four species, Atylotus and Philipomyia with two species each, and the genera Silvius, Dasyrhamphis, and Heptatoma with one species each. The standard DNA barcoding region of the mitochondrial cytochrome c oxidase gene, subunit I (COI), was sequenced and compared to the Barcode of Life Database (BOLD). Our analyses confirmed our morphological identifications and added 16 new Barcode Index Numbers (BINs) for Tabanidae to BOLD. Potential problems in the systematics and taxonomy of this family are highlighted.

Sizing the Knowledge Gap in Taxonomy: The Last Dozen Years of Aphidiinae Research

Simple Summary

Taxonomy is a biological discipline with the task to identify, name, and describe organisms, and as such, it provides necessary data for all other biological disciplines. The biodiversity crisis through which we are living draws attention to the crucial role of taxonomy in biology today. At the same time, the scientific community, as well as society in general, has become more aware of the difficulties associated with taxonomy, such as gaps in taxonomic knowledge, a lack of taxonomic infrastructure, and an insufficient number of taxonomic experts (“taxonomic impediment”). With this study, we tried to size this knowledge gap by analyzing the taxonomical studies on Aphidiinae (Hymenoptera: Braconidae) conducted from 2010 to 2021. Aphidiinae are endoparasitoids of aphids; a single specimen completes its development inside the living aphid host, which are used in biological control programs. Here, we summarize the knowledge gathered over the last dozen years and discuss it in a general context.

Abstract

Taxonomic impediment is one of the main roadblocks to managing the current biodiversity crisis. Insect taxonomy is the biggest contributor to the taxonomic impediment, both in terms of the knowledge gap and the lack of experts. With this study, we tried to size the knowledge gap by analyzing taxonomical studies on the subfamily Aphidiinae (Hymenoptera: Braconidae) conducted from 2010 to 2021. All available taxonomic knowledge gathered in this period is critically summarized: newly described species, detection of alien species, published identification keys, etc. All findings are discussed relative to the current state of general taxonomy. Future prospects for taxonomy are also discussed.

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.

Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species

Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.

Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany

Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.

Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem

Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.

Tiny wasps, huge diversity - A review of German Pteromalidae with new generic and species records (Hymenoptera: Chalcidoidea)

Background

Despite their ecological and economic importance, hymenopteran parasitoids are severely understudied. Even in countries with a long taxonomic history such as Germany, dating back to the 18th century and including prolific figures like Christian Gottfired Nees von Esenbeck and Otto Schmiedeknecht, those species-rich groups are seldom the subject of comprehensive research efforts, leaving their true diversity unknown. This is often due to their small size of a few millimetres on average, leading to difficulties in their identification and examination. The chalcidoid family Pteromalidae is no exception to this neglect. So far, 735 species have been reported from Germany. Estimating the diversity of this group is not possible, but it has to be assumed that many more species are still to be discovered in Germany.

New information

With this study, we improve the knowledge on pteromalid diversity and present new records of 17 genera and 41 species, previously unknown to occur in Germany. We also match and describe previously unknown sexes of two species, based on DNA barcode data. The results of this study were generated as part of the German Barcode of Life Project. The newly-recorded species are illustrated and notes on the biology and distribution are given. The ecological significance of Pteromalidae and potential value as indicators for nature conservation efforts are briefly discussed.

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.

The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions

DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.

A molecular-based identification resource for the arthropods of Finland

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.

Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956

Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.

Congruence between morphology-based species and Barcode Index Numbers (BINs) in Neotropical Eumaeini (Lycaenidae)

BACKGROUND

With about 1,000 species in the Neotropics, the Eumaeini (Theclinae) are one of the most diverse butterfly tribes. Correct morphology-based identifications are challenging in many genera due to relatively little interspecific differences in wing patterns. Geographic infraspecific variation is sometimes more substantial than variation between species. In this paper we present a large DNA barcode dataset of South American Lycaenidae. We analyze how well DNA barcode BINs match morphologically delimited species.

METHODS

We compare morphology-based species identifications with the clustering of molecular operational taxonomic units (MOTUs) delimitated by the RESL algorithm in BOLD, which assigns Barcode Index Numbers (BINs). We examine intra- and interspecific divergences for genera represented by at least four morphospecies. We discuss the existence of local barcode gaps in a genus by genus analysis. We also note differences in the percentage of species with barcode gaps in groups of lowland and high mountain genera.

RESULTS

We identified 2,213 specimens and obtained 1,839 sequences of 512 species in 90 genera. Overall, the mean intraspecific divergence value of CO1 sequences was 1.20%, while the mean interspecific divergence between nearest congeneric neighbors was 4.89%, demonstrating the presence of a barcode gap. However, the gap seemed to disappear from the entire set when comparing the maximum intraspecific distance (8.40%) with the minimum interspecific distance (0.40%). Clear barcode gaps are present in many genera but absent in others. From the set of specimens that yielded COI fragment lengths of at least 650 bp, 75% of the a priori morphology-based identifications were unambiguously assigned to a single Barcode Index Number (BIN). However, after a taxonomic a posteriori review, the percentage of matched identifications rose to 85%. BIN splitting was observed for 17% of the species and BIN sharing for 9%. We found that genera that contain primarily lowland species show higher percentages of local barcode gaps and congruence between BINs and morphology than genera that contain exclusively high montane species. The divergence values to the nearest neighbors were significantly lower in high Andean species while the intra-specific divergence values were significantly lower in the lowland species. These results raise questions regarding the causes of observed low inter and high intraspecific genetic variation. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the montane species concerned are relatively young and hybridization is probable. The release of our data set represents an essential baseline for a reference library for biological assessment studies of butterflies in mega diverse countries using modern high-throughput technologies an highlights the necessity of taxonomic revisions for various genera combining both molecular and morphological data.

Coverage and quality of DNA barcode references for Central and Northern European Odonata

Background

Dragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches.

Methods

This study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD.

Results

Over 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges.

High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity

The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.

Mitogenomes provide insights into the phylogeny of Mycetophilidae (Diptera: Sciaroidea)

The family Mycetophilidae (Diptera: Sciaroidea) consists of more than 4,500 described species distributed worldwide. Among them, dozens of species have been reported to be economically important to cultivated mushrooms and crops. Relationships among subfamilies in Mycetophilidae have been controversial by using morphological characters or gene markers. In this study, five mycetophilid mitogenomes representing four subfamilies were sequenced and analyzed with 15 published sciaroid mitogenomes as ingroup, while another two species representing two closely related families were chosen as outgroup. All of the sequenced mitogenomes contain 37 genes arranged in the ancestral order, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region (CR). Among mycetophilid mitogenomes, Leu, Ile, Phe, and Met are the most frequently encoded amino acids (AA), with TTA (Leu), ATT (Ile), TTT (Phe) and ATA (Met) being the most frequent codons. Meanwhile, the phylogenetic results reconstructed based on PCGs, PCGs + rRNAs and AA sequences respectively show that the clade of Sciaroidea was well separated from outgroup, further confirming its monophyly. The phylogenetic relationships within Mycetophilidae were recovered as (Manotinae + Sciophilinae) + (Mycomyinae + Mycetophilinae). Mapped to the phylogram, the gene rearrangements occur frequently in the crown group, implying extremely rapid evolutionary rates in Sciaridae and Cecidomyiidae, which might be the reason why the two families have such high species diversity.

Adding DNA barcoding to stream monitoring protocols - What's the additional value and congruence between morphological and molecular identification approaches?

Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.

Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding

Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.

Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($>$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94-407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($>$200 bp). Only very short mini-barcodes (<200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $>$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.].

Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species

DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.

Toward a standardized quantitative and qualitative insect monitoring scheme

The number of insect species and insect abundances decreased severely during the past decades over major parts of Central Europe. Previous studies documented declines of species richness, abundances, shifts in species composition, and decreasing biomass of flying insects. In this study, we present a standardized approach to quantitatively and qualitatively assess insect diversity, biomass, and the abundance of taxa, in parallel. We applied two methods: Malaise traps, and automated and active light trapping. Sampling was conducted from April to October 2018 in southern Germany, at four sites representing conventional and organic farming. Bulk samples obtained from Malaise traps were further analyzed using DNA metabarcoding. Larger moths (Macroheterocera) collected with light trapping were further classified according to their degree of endangerment. Our methods provide valuable quantitative and qualitative data. Our results indicate more biomass and higher species richness, as well as twice the number of Red List lepidopterans in organic farmland than in conventional farmland. This combination of sampling methods with subsequent DNA metabarcoding and assignments of individuals according depending on ecological characteristics and the degree of endangerment allows to evaluate the status of landscapes and represents a suitable setup for large-scale long-term insect monitoring across Central Europe, and elsewhere.