Project

German Barcode of Life

Goal: GBOL is a national network of various natural history museums and other biodiversity research institutions in Germany. The GBOL partners provide their professional taxonomic expertise and existing infrastructure (collections / biobanks, databases, bioinformatics platforms and laboratories) to comprehensively collect, catalog, describe, and sequence the animal, plant and fungi species in Germany. While the focus in GBOL during the first phase (2012-2015) was laid on the creation of a reference database, we will now also develop different applications of DNA barcoding in the second project phase (2016-2018). Sequence and metadata generated in GBOL will be integrated in the global barcode reference database " BOLD ".
www.bolgermany.de

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Dirk Ahrens
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Saproxylic beetles (Coleoptera) are important for biomonitoring to evaluate the state of ecological conservation of forest ecosystems. However, beetle larvae are rarely considered due to their difficult identification. Here, we evaluate the use of beetle larvae, alongside adult specimens, for monitoring. Forty sifting samples from deadwood structures were analysed from eight different forest sites near Münster (Germany). Larvae were identified by matching with DNA sequences (COI) of identified adults (from GBOL database/BOLD) using various standard DNA‐based species delimitation methods. Our main objective was to figure out whether larvae can be sampled, barcoded, and identified successfully on a larger scale, and whether the inclusion of larval data improved the ecological and taxonomic results of the survey. Altogether we found 129 species as larvae and 313 as imagos. Four larva species could not be identified to species level because of a lack of a match with adult reference sequences. Among all sifting samples, 41% of the species recorded as larva were not found as imago. The inclusion of larvae increased the expected species richness and generated a more precise differentiation between the sites in respect of saproxylic species richness and assemblage composition. Moreover, almost 30% of identified larvae are not morphologically described, so they cannot be identified morphologically. This study showed that the use of larvae could considerably improve the accuracy of ecological surveys, particularly at meso‐ and microhabitat level, while for higher level, geographical scales sequencing and sampling efforts would be at the moment excessive. Larvae identified by matching with DNA sequences (COI) of identified adults (from GBOL database/BOLD) were used for deadwood monitoring on eight different forest sites near Münster (Germany). The inclusion of larvae increased the expected species richness and generated a more precise differentiation between the sites in respect of saproxylic species richness and assemblage composition. This study showed that the use of larvae could considerably improve the accuracy of ecological surveys, particularly at meso‐ and microhabitat level.
Jerome Moriniere
added a research item
The German Barcode initiatives (BFB & GBOL) generated a reference library of 16,000 German animal species which is now ready for effective biodiversity assessment. We pre-sorted one single malaise trap sample (1 week) into 12 groups of arthropod orders (Coleoptera, Hymenoptera, Lepidoptera, Diptera, Hemiptera, Araneae, Collembola, Blattodea, Neuroptera & Mecoptera, Psocoptera, Orthoptera, Plecoptera) and extracted each group separately. An aliquot of each DNA extract was combined to simulate a non-sorted sample. Each DNA extract was amplified with 4 different primer sets targeting the CO1-5’ fragment and PCR products (150-400bp) and sequenced separately using an Illumina MiSeq, resulting in 1.5 million sequences and 5500 clusters (CD-HIT-EST, 98%). We used a total of 100,000 DNA barcodes of reliably identified, central European Hymenoptera, Coleoptera, Diptera and Lepidoptera downloaded from BOLD to establish a reference sequence database for a local custom BLAST, which allowed us to identify Barcode Index Numbers (BINs) for each cluster sequence obtained from the NGS analyses.
Matthias F Geiger
added a research item
DNA metabarcoding of macroinvertebrates is increasingly used for aquatic bioassessment and -monitoring. A major strength of metabarcoding is the high taxonomic resolution provided while the inability to deliver reliable abundance data is regarded a main drawback. Data on the potential of metabarcoding to disentangle site-specific and seasonal variation with presence/absence data have been poorly explored. In addition, the robustness of ecological status assessments compliant with the European Water Framework Directive (Directive 2000/60/EG) have only been compared in few studies, none of which adressed changes across seasons. Therefore, we here investigated seasonal as well as site-specific effects on macroinvertebrate communities at six river sites in a near-natural (Sieg) and urban (Emscher) German river through metabarcoding. Furthermore, we evaluated the usability of the method for ecological status assessments. Our data showed distinct seasonal effects on OTU composition at the near-natural river Sieg. However, ecological status assessment was constant through seasons and comparable to assessments based on available morphological identification. In contrast to the river Sieg, we found strong site and stressor-specific impacts in the heterogeneous urban river Emscher. Here, ecological status assessment varied between sampling sites ranging from good to bad status but was largely consistent between seasons. Our study demonstrates the ability of presence/absence metabarcoding data to reliably assess invertebrate community composition in streams and infer environmental (natural or anthropogenic) impacts. Together with the technical robustness, our study encourages the wider adoption of the technique in stream bioassessment and -monitoring.
Michael J. Raupach
added a research item
The genus Notiophilus Duméril, 1806 is a distinctive taxon of small, diurnal and morphologically similar beetles exhibiting large eyes and widened second elytral intervals. In this study we analysed the effectiveness of DNA barcodes to discriminate 67 specimens that represent 8 species of Notiophilus from Central Europe. Interspecific K2P distances below 2.2% were found for N. biguttatus (Fabricius, 1779) and N. quadripunctatus Dejean, 1826, whereas intraspecific distances with values > 2.2% were revealed for N. rufipes Curtis, 1829. An additional phylogenetic analysis of all available species revealed a close relationship of N. directus Casey, 1920, N. semistriatus Say, 1823, N. simulator Fall, 1906 and N. sylvaticus Dejean, 1831, possibly indicating a radiation of these species in North America. Low support values of most other nodes, however, do not allow additional phylogenetic conclusions.
Matthias F Geiger
added 4 research items
Metabarcoding is a powerful, increasingly popular tool for biodiversity assessment, but it still suffers from some drawbacks (specimen destruction, separation, and size sorting). In the present study, we tested a non-destructive protocol that excludes any sample sorting, where the ethanol used for sample preserving is filtered and DNA is extracted from the filter for subsequent DNA metabarcoding. When tested on macroinvertebrate mock communities, the method was widely successful but was unable to reliably detect mollusc taxa. Three different protocols (no treatment, shaking, and freezing) were successfully applied to increase DNA release to the fixative. The protocols resulted in similar success in taxa detection (6.8-7 taxa) but differences in read numbers assigned to taxa of interest (33.8%-93.7%). In comparison to conventional bulk sample metabarcoding of environmental samples, taxa with pronounced exoskeleton and small-bodied taxa were especially underrepresented in ethanol samples. For EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa, which are important for determining stream ecological status, the methods detected 46 OTUs in common, with only 4 unique to the ethanol samples and 10 to the bulk samples. These results indicate that fixative-based metabarcoding is a non-destructive, time-saving alternative for biodiversity assessments focussing on taxa used for ecological status determination. However, for a comprehensive assessment on total invertebrate biodiversity, the method may not be sufficient, and conventional bulk sample metabarcoding should be applied.
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.
Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on matching the composition of assemblages of organisms identified using morphological criteria present in aquatic ecosystems to those expected in the absence of anthropogenic pressures. Through decade-long and difficult intercalibration exercises among networks of regulators and scientists in European countries, a pragmatic biomonitoring approach was developed and adopted, which now produces invaluable information. Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, data acquisition is often slow due to a lack of taxonomic experts for many taxa and regions and time-consuming morphological identification of organisms. High-throughput genetic screening methods such as (e)DNA metabarcoding have been proposed as a possible solution to these shortcomings. Such “next-generation biomonitoring”, also termed “biomonitoring 2.0”, has many advantages over the traditional approach in terms of speed, comparability and costs. It also creates the potential to include new bioindicators and thereby further improves the assessment of aquatic ecosystem health. However, several major conceptual and technological challenges still hinder its implementation into legal and regulatory frameworks. Academic scientists sometimes tend to overlook legal or socioeconomic constraints, which regulators have to consider on a regular basis. Moreover, quantification of species abundance or biomass remains a significant bottleneck to releasing the full potential of these approaches. Here, we highlight the main challenges for next-generation aquatic biomonitoring and outline principles and good practices to address these with an emphasis on bridging traditional disciplinary boundaries between academics, regulators, stakeholders and industry.
Jerome Moriniere
added 11 research items
As part of the German Barcode of Life campaign, over 3500 arachnid specimens have been collected and analyzed: ca. 3300 Araneae and 200 Opiliones, belonging to almost 600 species (median: 4 individuals/species). This covers about 60% of the spider fauna and more than 70% of the harvestmen fauna recorded for Germany. The overwhelming majority of species could be readily identified through DNA barcoding: median distances between closest species lay around 9% in spiders and 13% in harvestmen, while in 95% of the cases, intraspecific distances were below 2.5% and 8% respectively, with intraspecific medians at 0.3% and 0.2%. However, almost 20 spider species, most notably in the family Lycosidae, could not be separated through DNA barcoding (although many of them present discrete morphological differences). Conspicuously high interspecific distances were found in even more cases, hinting at cryptic species in some instances. A new program is presented: DiS-tats calculates the statistics needed to meet DNA barcode release criteria. Furthermore, new generic COI primers useful for a wide range of taxa (also other than arachnids) are introduced.
Forensic entomology aims to use insects to estimate the post mortem interval of a carcass. A major problem however is the rapid, exact, and reliable identification of the insect species. Eggs and early larval stages of many insects share similar features, making it difficult to distinguish between species based on morphology. Often, collected larvae need to be reared under constant conditions to the imago, which offers better differential features. This time consuming method is not beneficial if fast species identification is crucial. A promising alternative is species identification using molecular markers. The Bavarian State Collection of Zoology (SNSB-ZSM) uses DNA barcoding to obtain genetic fingerprints of all animals, fungi, and plants found in Germany. Approximately 17,000 animal species were already successfully barcoded and more than 100,000 barcode sequences were provided for the international Barcode of Life Database (BOLD). In this study, we created a DNA barcode reference library for arthropod species playing an important role in forensic entomology and we applied NGS techniques in order to obtain simultaneous species identifications of bulk samples. We investigated insects, which were extracted from 30 human bodies and stored in 50mL Falcon tubes, provided by the local morgue. For reference library construction, we sorted out visually distinct morphospecies and different developmental stages of all sample containers; tissue samples were removed from each specimen and transferred into 96 well plates for subsequent DNA extraction. Sequence data and trace files were then uploaded to BOLD. In a second step, we tested the potential of bulk extractions and subsequent species identification using NGS and the application of the barcode reference data in one single analysis step. The analysis of the NGS data comparison with the BOLD database revealed 31 different BINs of insect species, of which only 13 could be identified by references of the forensic insect library which we created on BOLD. The whole procedure took a total of 30 working hours from DNA extraction to species identification for the whole bulk sample, which clearly indicates that NGS is especially promising, as it saves time and costs in comparison to conventional methods. This study illustrates that DNA Barcoding might be a promising addition for forensic entomologists, because it facilitates accurate and fast species identification of all developmental stages even when specialized taxonomists are lacking.
This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more. The barcode results are largely congruent with traditional taxonomy as only five closely allied pairs of species could not be discriminated by barcodes. As well, 90% of the species possessed sufficiently deep sequence divergence to be assigned to a different Barcode Index Number (BIN). In fact, 56 species (11%) were assigned to two or more BINs reflecting the high levels of intraspecific divergence among their component specimens. Fifty other species (9.7%) shared the same Barcode Index Number with one or more species, but most of these species belonged to a distinct barcode cluster within a particular BIN. The barcode data contributed to clarifying the status of nearly half the examined taxonomically problematic species of bees in the German fauna. Based on these results, the role of DNA barcoding as a tool for current and future taxonomic work is discussed. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley Sons & Ltd.
Vera Rduch
added a research item
The German Barcode of Life project (GBOL), funded by the German Federal Ministry of Education and Research, is a national DNA barcoding campaign targeting the fauna, flora and fungi of Germany. GBOL aims at compiling an open access DNA barcode reference database via collecting, sharing, processing and depositing samples in conventional and molecular collections. A consortium of natural history collections, botanical gardens, and universities works closely together with experienced and enthusiastic external taxonomic experts, including committed citizen scientists. The target list for mammals follows the German Red List and comprises 103 taxa at species level including also vagrant and extinct species. Target lists allow to evaluate taxonomic coverage achieved and to address completeness and gaps. Until now, the GBOL node at Zoological Research Museum A. Koenig accessed more than 1,200 mammal samples, covering 91% of the target taxa and resulting in 933 barcodes. Further, GBOL contributed to several research projects, e.g. small mammal monitoring in the Eifel National Park or population genetics in common hamster (Cricetus cricetus). Several species of mammals on the GBOL target list are still missing from the reference database. Our goal is to include several (2-7) specimens from each of the federal states in order to cover the molecular diversity over the range of each species in Germany. Samples consist of tissue, blood or hair from museum specimens, dead or living animals. Any inquiries and contributions that help filling the gaps and improving the significance of the barcode reference library are highly welcome! Download list of missing mammals at https://uni-bonn.sciebo.de/s/DnjoTR57siKAt8K#pdfviewer
Jerome Moriniere
added 3 research items
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status. This study represents a major step towards a DNA barcode reference library as it delivers coverage for two thirds of Germany's EPT species including 2,613 individuals belonging to 363 identified species. As such, it provides coverage for 38 of 44 families (86%) and practically all major bioindicator species. DNA barcode compliant sequences (>500bp) were recovered from 98.74% of the analyzed specimens. Whereas most species (325 - 89.53%) were unambiguously assigned to a single Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, 9 Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of these additional BINs formed nearest neighbor clusters, reflecting the discrimination of geographical subclades of a currently recognized species. BIN sharing was uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both maximum pairwise and nearest neighbor distances were substantially higher for Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution. This article is protected by copyright. All rights reserved.
Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High‐quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1‐5P’ DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high‐quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.
The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordi- nal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1 - 5 ’ fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage � 10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming pre- sorting process will yield approximately 30% more high score BINs compared to the non- sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.
Michael J. Raupach
added an update
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of ‘taxonomics’. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from highthroughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
 
Michael J. Raupach
added an update
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina//Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
 
Michael J. Raupach
added a research item
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara . In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris . Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species ( Sigara , Callicorixa ), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima . Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
Matthias Lutz
added a research item
The German Barcode of Life (GBOL) project is a large-scale DNA barcoding initiative to assess the biodiversity of animals, fungi, and plants of Germany. Here we introduce the subproject focusing on rust fungi (Pucciniales, Basidiomycota). This is the only group of fungi represented in the initial 3.5-year phase of the project. The goal of the rust project is a complete DNA-barcode sequence library for the roughly 500 rust species reported for Germany. The DNA barcode database will link the extensive information available on morphology, ecology, and host range studies with barcoding data linked to individual specimens. Rust fungi are exceptionally well studied in Central Europe. A significant number of cryptic species may be recovered; alternatively, several species described from different hosts may need to be merged. Further, the full life cycles and host relationships, particularly of some host-alternating species, await elucidation. These data will allow identification of rust specimens in museum collections, which to date could not be identified be- cause of missing discriminatory spore states. Most DNA samples are extracted from herbarium specimens of the fungus collections preserved at the Natural History Museum Karlsruhe in Karlsruhe Germany, but targeted collecting of additional speci- mens will also be necessary. In the first phase of the project, primer selection and optimization were found to be essential for successful generation of DNA barcodes. The internal transcribed spacer (ITS) rDNA region and the large subunit of the rDNA are suitable common fungal barcode markers. To facilitate high-throughput barcoding, methods have been developed for semiautomatic DNA extraction from herbarium specimens and polymerase chain reactions in 96 well plates. Currently the following groups are extensively DNA-barcoded: Uromyces pisi s.l., an especially complicated complex of species, and the genera Melampsora and Coleosporium. An example of an as-yet unidentified Coleosporium species on invasive Solidago (goldenrod) is presented.
Vera Rduch
added a research item
Maintenance of high levels of biodiversity through conservation depends on correctly identified species. The GBOL (German Barcode of Life) project, funded by the German Federal Ministry of Education and Research, is a national DNA barcoding campaign for assessing the genetic diversity of animals, fungi and plants in Germany. Professional taxonomists closely work together with enthusiastic and active external taxonomic experts, including committed citizen scientists, to establish this library of biodiversity. In case of mammals the target list follows the German Red List and comprises 103 taxa at the species level. Focussing on terrestrial species it also includes vagrant species, as well as species that are extinct on a global or local scale. Until now, GBOL archived more than 1,200 samples, covering 87 % of the target taxa. Samples consist of tissue, blood or hair from classical museum specimens, dead or living animals. The importance of the target list grows with the progress in taxonomic coverage achieved, as gaps can be identified and addressed more specifically. Since our goal is to cover the molecular diversity over the range of each species in Germany, we want to include several (2 - 7) specimens from each of the federal states. This pragmatic approach enables quick queries for the presence of taxa or the coverage of particular taxa and helps coordinating sampling efforts. Because there are still „missing taxa‟ of mammals on the GBOL target list (http://tinyurl.com/GBOL-mammal) –also in other animal groups – we are looking for people from different fields that want to contribute by providing samples. Any inquiries and contributions that help increasing the number of taxa covered and improve the significance of the barcode reference library are highly welcomed!
Michael J. Raupach
added 4 research items
Since 1994, Hemigrapsus penicillatus, an Asian brush-clawed shore crab, spreads along Northeast Atlantic coasts. There is evidence that the most recently described and widely accepted sibling species of H. penicillatus, namely Hemigrapsus takanoi, represents the Asian brush-clawed brachyuran crab in Europe. Morphological characteristics are considered insufficient for species discrimination, and molecular analyses were recommended but have to date not been performed in Europe. To clarify the identity of the non-indigenous Asian brush-clawed crab species, which has been invading intertidal alien Crassostrea reefs in the Wadden Sea, we analysed more than 3.5 kpb of mitochondrial and nuclear genes of individuals from invaded German sites and from native Japanese sites. In addition to molecular analyses, we also document key morphological and morphometric characteristics of the same individuals to provide a comparative description. While morphological identification was not confidently feasible, our molecular results confirm the existence of Hemigrapsus takanoi as a closely related species to H. penicillatus and have identified H. takanoi to be the alien brush-clawed crab species in Germany. Furthermore, most of the analysed specimens from Japan and all additional NCBI-listed brush-clawed crabs from Japan, Korea and China which were traditionally classified as H. penicillatus in Asia, are de facto H. takanoi.
In most cases, adult fish can be easily identified based on the analysis of morphological characteristics. In contrast to this, a successful identification of processed specimens or early life cycle stages might be quite challenging. Here we present an in situ hybridization (ISH) approach for reliable species identification. Oligonucleotide probes targeting the small ribosomal subunit (18S rRNA) were developed and tested for the identification of the three commercially important fish species Merluccius merluccius, Scomber scombrus, and Trachurus trachurus. These species are routinely monitored by triennial ichthyoplankton surveys in the Northeast Atlantic. Our results demonstrated a species specific hybridization and staining for all three target species using a combination of helper, competitor and probes. The Trachurus trachurus probe can also be used to identify Trachurus mediterraneus which can be found further South. Additionally, we showed successful hybridization by a subsequent use of probes. The application of in situ hybridization may represent a robust, fast and cheap alternative for the identification of fish species in comparison to other molecular approaches.
Dirk Ahrens
added a research item
1. In recent years, large-scale DNA barcoding campaigns have generated an enormous amount of COI barcodes, which are usually stored in NCBI's GenBank and the official Barcode of Life database (BOLD). BOLD data are generally associated with more detailed and better curated meta-data, because a great proportion is based on expert-verified and vouchered material, accessible in public collections. In the course of the initiative German Barcode of Life (GBOL), data were generated for the reference library of 2,846 species of Coleoptera from 13,516 individuals. Accepted Article This article is protected by copyright. All rights reserved. 2. Confronted with the high effort associated with the identification, verification and data validation, a bioinformatic pipeline, "TaxCI" was developed that i) identifies taxonomic inconsistencies in a given tree topology (optionally including a reference data set), ii) discriminates between different cases of incongruence in order to identify contamination or misidentified specimens, iii) graphically marks those cases in the tree, which finally can be checked again and, if needed, corrected or removed from the dataset. For this, "TaxCI" may use DNA-based species delimitations from other approaches (e.g., mPTP) or may perform implemented threshold-based clustering. 3. The data-processing pipeline was tested on a newly generated set of barcodes, using the available BOLD records as a reference. A data revision based on the first run of the TaxCI tool resulted in the second TaxCI analysis in a taxonomic match ratio very similar to the one recorded from the reference set (92 vs 94%). The revised dataset improved by nearly 20% through this procedure compared to the original, uncorrected one. 4. Overall, the new processing pipeline for DNA barcode data allows for the rapid and easy identification of inconsistencies in large datasets, which can be dealt with before submitting them to public data repositories like BOLD or GenBank. Ultimately, this will increase the quality of submitted data and the speed of data submission, while primarily avoiding the deterioration of the accuracy of the data repositories due to ambiguously identified or contaminated specimens.
Matthias F Geiger
added an update
Out now: the first interim report for the first year (2016) of the second phase of GBOL. Only available in German - sorry colleagues.
 
Matthias F Geiger
added an update
Informationsveranstaltung zu Anwendungsgebieten DNA-basierter Artbestimmung (DNA-barcoding)
Das finale Programm für unsere Veranstaltung am Montag, 6. März 2017, ab 13:00 im Museum Koenig in Bonn zu Anwendungsgebieten DNA-basierter Artbestimmung steht nun! Hierzu laden wir herzlich ein! Die Veranstaltung deckt mit anschaulichen Kurzvorträgen u.a. folgende Themengebiete ab und soll zu Diskussionen und möglichen Synergien zwischen den Teilnehmern führen:
- Übersicht mit Erklärung zu DNA-Barcoding generell und Initiativen in Deutschland und Europa (Schwerpunkt Referenzdaten) - Potential für Umweltmonitoring - Potential für Gewässergütebewertung - Naturwissenschaftliche Forensik - Genetische Ressourcen in Deutschland - Zoll & Artenschutz - Lebensmittelanalytik - Agrar & Forstwirtschaft
 
Matthias F Geiger
added an update
Am Montag den 6. März 2017 findet ab 13:00 eine Informationsveranstaltung am Museum Koenig in Bonn zu Anwendungsgebieten DNA-basierter Artbestimmung statt. Hierzu laden wir Sie herzlich ein! Die Veranstaltung deckt mit anschaulichen Kurzvorträgen u.a. folgende Themengebiete ab und soll zu Diskussionen und möglichen Synergien zwischen den Teilnehmern führen: - Übersicht mit Erklärung zu DNA-Barcoding generell und Initiativen in Deutschland und Europa (Schwerpunkt Referenzdaten) - Potential für Umweltmonitoring - Potential für Gewässergütebewertung - Naturwissenschaftliche Forensik - Genetische Ressourcen in Deutschland - Zoll & Artenschutz - Lebensmittelanalytik - Agrar & Forstwirtschaft Gerne stehe ich für Rückfragen zur Verfügung.
 
Matthias F Geiger
added 2 research items
Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conservation depends on correctly identified species. To this aim, the German Federal Ministry of Education and Research is funding the GBOL project, a consortium of natural history collections, botanic gardens, and universities working on a barcode reference database for the country's fauna and flora. Several noticeable findings could be useful for future campaigns: (i) validating taxon lists to serve as a taxonomic backbone is time-consuming, but without alternative; (ii) offering financial incentives to taxonomic experts, often citizen scientists, is indispensable; (iii) completion of the libraries for widespread species enables analyses of environmental samples, but the process may not hold pace with technological advancements; (iv) discoveries of new species are among the best stories for the media; (v) a commitment to common data standards and repositories is needed, as well as transboundary cooperation between nations; (vi) after validation, all data should be published online via the BOLD to make them searchable for external users and to allow cross-checking with data from other countries.
Matthias F Geiger
added 4 research items
Result of the BIN discordance analysis (BOLD, September 25th 2015) for all BINs.
Compilation of all specimens not identified to species level with embedded links leading to the respective BIN or specimen page on BOLD for an easy entry point to start refinements of taxonomic placements.
J. Wolfgang Wägele
added an update
The GBOL Team is currently implementing a first set of application studies...
 
Matthias F Geiger
added a project goal
GBOL is a national network of various natural history museums and other biodiversity research institutions in Germany. The GBOL partners provide their professional taxonomic expertise and existing infrastructure (collections / biobanks, databases, bioinformatics platforms and laboratories) to comprehensively collect, catalog, describe, and sequence the animal, plant and fungi species in Germany. While the focus in GBOL during the first phase (2012-2015) was laid on the creation of a reference database, we will now also develop different applications of DNA barcoding in the second project phase (2016-2018). Sequence and metadata generated in GBOL will be integrated in the global barcode reference database " BOLD ".