A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae)

Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae)

A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).

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.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

High molecular diversity in Carabus (Hygrocarabus) variolosus and C. nodulosus

The Carabus subgenus Hygrocarabus contains two taxa: C. variolosus and C. nodulosus, the species or subspecies status of which is handled far from uniform in the literature. Both taxa show a similar morphology, the shape of the tip of the aedeagus provides a reliable morphological marker for identification. We analysed two mitochondrial gene parts (COI-5’ and COI-3’) and a nuclear one (ITS2). High diversity was found showing specific geographical patterns. Introgressive hybridisation was detected but interpreted not as an argument for subspecies status because high genetic distances indicated that it must have taken place in former times. In a laboratory hybridisation experiment, the male did not accept the female of the other taxon, supporting the conclusion that these are separate species. A series of refuges was expected for the period of ice ages. Although only the taxon C. variolosus is listed in Annex II and IV of the EU Habitats Directive, C. nodulosus also falls under this listing, as at the time of including the species into the Annexes in 2004, the two taxa were considered subspecies and hence the listing would include both, independent of later taxonomic revisions.

A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae)

Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichusadstrictus Eschscholtz, 1823/Pterostichusoblongopunctatus (Fabricius, 1787) and Pterostichusnigrita Paykull, 1790/Pterostichusrhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molopspiceus (Panzer, 1793), Pterostichuspanzeri (Panzer, 1805), Pterostichusstrenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.

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.

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

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.