Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects

by Axel Hausmann, Stefan Schmidt and Jérome Morinière | Apr 7, 2019 | iBOL Nation Activity

Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects

Marbled white (Melanargia galathea). PHOTO CREDIT: Stefan Schmidt

Since DNA barcoding started in Germany 13 years ago, barcodes of some 55,000 species have been assembled from all continents, and the Zoologische Staatssammlung München (ZSM) is now globally among the top three providers of barcoding voucher specimens, reflecting the analysis of more than 250,000 specimens. In less than a decade, DNA barcodes of more than 24,000 German species of metazoans have been assembled as part of two major national DNA barcoding initiatives: the ‘Barcoding Fauna Bavarica’ (BFB) and the ‘German Barcode of Life’ (GBOL) projects.

Ring Ouzel (Turdus Torquatus Alpestris). PHOTO CREDIT: Stefan Schmidt

Bumblebee (Bombus sp.). PHOTO CREDIT: Stefan Schmidt

DNA barcoding activities in Germany have resulted in several major data releases, for example with Coleoptera (Hendrich et al., 2015, Raupach et al., 2016, 2018, Rulik et al., 2017), Diptera (Morinière et al., 2019 accepted), aquatic insects (Ephemeroptera, Plecoptera, Trichoptera, Morinière et al., 2017), Heteroptera (Raupach et al., 2014, Havemann et al., 2018 ), Hymenoptera (Schmidt et al., 2015, 2017, Schmid-Egger et al., 2018), Lepidoptera (Hausmann et al., 2011a, 2011b), Neuroptera (Morinière et al., 2014), Orthoptera (Hawlitschek et al., 2017), Araneae and Opiliones (Astrin et al., 2016), and Myriapoda (Spelda et al., 2011, Wesener et al., 2015).

In addition to extending the DNA barcode library, Germany has invested in examining the potential of DNA metabarcoding for the rapid assessment of species assemblages as part of studies that address a range of different research questions, including Malaise trap surveys (Morinière et al., 2016, Hardulak et al.,, in prep), analysis of feces for dietary inference (Hawlitschek et al., 2018), species identification in forensic entomology (Chimeno et al., 2019), and food composition studies (Gerdes et al., 2019, Michel & Hardulak, submitted).
Germany will strive to maintain its role as a major contributor to the global DNA barcode library and will aim to make a substantial contribution to the BIOSCAN initiative.

References:

Astrin JJ, Höfer H, Spelda J, Holstein J, Bayer S, Hendrich L, Huber BA, Kielhorn KH, Krammer HJ, Lemke M, Monje JC, Morinière J, Rulik B, Petersen M, Janssen H, Muster C (2016) Towards a DNA barcode reference database for spiders and harvestmen of Germany. PLoS ONE 11: e0162624. https://doi.org/10.1371/journal.pone.0162624

Chimeno C, Morinière J, Podhorna J, Hardulak L, Hausmann A, Reckel F, Grunwald JE, Penning R, Haszprunar G (2019) DNA barcoding in forensic entomology – Establishing a DNA reference library of potentially forensic relevant arthropod species. Journal of Forensic Sciences 64: 593–601. https://doi.org/10.1111/1556-4029.13869

Hausmann A, Haszprunar G, Hebert PDN (2011) DNA barcoding the geometrid fauna of Bavaria (Lepidoptera): successes, surprises, and questions. PLoS ONE 6: e17134. https://doi.org/10.1371/journal.pone.0017134

Hausmann A, Haszprunar G, Segerer AH, Speidel W, Behounek G, Hebert PDN (2011) Now DNA-barcoded: the butterflies and larger moths of Germany (Lepidoptera: Rhopalocera, Macroheterocera). Spixiana 34: 47–58.

Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ (2018) From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 6: e4577. https://doi.org/10.7717/peerj.4577

Hawlitschek O, Morinière J, Lehmann GUC, Lehmann AW, Kropf M, Dunz A, Glaw F, Detcharoen M, Schmidt S, Hausmann A, Szucsich NU, Caetano-Wyler SA, Haszprunar G (2017) DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Molecular Ecology Resources 17: 1037–1053. https://doi.org/10.1111/1755-0998.12638

Hawlitschek O, Fernández-González A, Balmori-de la Puente A, Castresana J (2018) A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal. PLoS ONE 13: e0201763. https://doi.org/10.1371/journal.pone.0201763

Hendrich L, Morinière J, Haszprunar G, Hebert PDN, Hausmann A, Köhler F, Balke M (2015) A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD. Molecular Ecology Resources 15: 795–818. https://doi.org/10.1111/1755-0998.12354

Michel M, Hardulak LA, Meier-Dörnberg T, Morinière J, Hausmann A, Back W, Haszprunar G, Jacob F, Hutzler M (2019) High throughput sequencing as a novel quality control method for industrial yeast starter cultures. BrewingSience (accepted)

Morinière J, Hendrich L, Balke M, Beermann AJ, König T, Hess M, Koch S, Müller R, Leese F, Hebert PDN, Hausmann A, Schubart CD, Haszprunar G (2017) A DNA barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera). Molecular Ecology Resources 17: 1293–1307. https://doi.org/10.1111/1755-0998.12683

Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele JW, Hebert PDN (2019) A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Molecular Ecology Resources (accepted)

Morinière J, Hendrich L, Hausmann A, Hebert P, Haszprunar G, Gruppe A (2014) Barcoding fauna Bavarica: 78% of the Neuropterida fauna barcoded! PLoS ONE 9: e109719. https://doi.org/10.1371/journal.pone.0109719

Raupach M, Hannig K, Moriniere J, Hendrich L (2016) A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. ZooKeys 592: 121–141. https://doi.org/10.3897/zookeys.592.8316

Raupach MJ, Hannig K, Morinière J, Hendrich L (2018) A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). ZooKeys 759: 57–80. https://doi.org/10.3897/zookeys.759.24129

Raupach MJ, Hendrich L, Küchler SM, Deister F, Morinière J, Gossner MM (2014) Building-up of a DNA barcode library for True Bugs (Insecta: Hemiptera: Heteroptera) of Germany reveals taxonomic uncertainties and surprises. PLoS ONE 9: e106940. https://doi.org/10.1371/journal.pone.0106940

Rulik B, Eberle J, von der Mark L, Thormann J, Jung M, Köhler F, Apfel W, Weigel A, Kopetz A, Köhler J, Fritzlar F, Hartmann M, Hadulla K, Schmidt J, Hörren T, Krebs D, Theves F, Eulitz U, Skale A, Rohwedder D, Kleeberg A, Astrin JJ, Geiger MF, Wägele JW, Grobe P, Ahrens D (2017) Using taxonomic consistency with semi-automated data pre-processing for high quality DNA barcodes. Methods in Ecology and Evolution 8: 1878–1887. https://doi.org/10.1111/2041-210X.12824

Schmid-Egger C, Achterberg K van, Neumeyer R, Morinière J, Schmidt S (2017) Revision of the West Palaearctic Polistes Latreille, with the descriptions of two species – an integrative approach using morphology and DNA barcodes (Hymenoptera, Vespidae). ZooKeys 713: 53–112. https://doi.org/10.3897/zookeys.713.11335

Schmid-Egger C, Straka J, Ljubomirov T, Blagoev GA, Morinière J, Schmidt S (2018) DNA barcodes identify 99 percent of apoid wasp species (Hymenoptera: Ampulicidae, Crabronidae, Sphecidae) from the Western Palearctic. Molecular Ecology Resources. 19(2):476–484. https://doi.org/10.1111/1755-0998.12963

Schmidt S, Schmid-Egger C, Morinière J, Haszprunar G, Hebert PDN (2015) DNA barcoding largely supports 250 years of classical taxonomy: identifications for Central European bees (Hymenoptera, Apoidea partim). Molecular Ecology Resources 15: 985–1000. https://doi.org/10.1111/1755-0998.12363

Schmidt S, Taeger A, Morinière J, Liston A, Blank SM, Kramp K, Kraus M, Schmidt O, Heibo E, Prous M, Nyman T, Malm T, Stahlhut J (2017) Identification of sawflies and horntails (Hymenoptera, “Symphyta”) through DNA barcodes: successes and caveats. Molecular Ecology Resources 17: 670–685. https://doi.org/10.1111/1755-0998.12614

Spelda J, Reip H, Oliveira Biener U, Melzer R (2011) Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZooKeys 156: 123–139. https://doi.org/10.3897/zookeys.156.2176

Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J, Lindner N (2015) First results of the German Barcode of Life (GBOL) – Myriapoda project: Cryptic lineages in German Stenotaenia linearis (Koch, 1835) (Chilopoda, Geophilomorpha). ZooKeys 510: 15–29. https://doi.org/10.3897/zookeys.510.8852

Written by

Axel Hausmann

Zoologische Staatssammlung München, Munich, Germany

Stefan Schmidt

Zoologische Staatssammlung München, Munich, Germany

Jérome Morinière

Zoologische Staatssammlung München, Munich, Germany

← Summary of National Barcoding Activities for Portugal The Austrian Barcode of Life (ABOL) Initiative →

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The Austrian Barcode of Life (ABOL) Initiative

by Nikolaus Szucsich, Michaela Sonnleitner, Elisabeth Haring and Helmut Sattmann | Apr 7, 2019 | iBOL Nation Activity

The Austrian Barcode of Life (ABOL) Initiative

Participants of the 5^th ABOL meeting in Austria. PHOTO CREDIT: Austrian Barcode of Life

The common long-term aim to generate and provide DNA barcodes for all species of animals, plants, and fungi recorded from Austria is the binding force of the Austrian Barcode of Life (ABOL) initiative.

A number of independently funded projects currently generate DNA barcode data and all of them are committed to open access data sharing. In only 5 years, ABOL has come close to collecting barcodes for 10 per cent of Austrian biodiversity; about 6,250 named species are currently stored on the Barcode of Life Database (BOLD).

The coordination of ABOL is funded by the Ministry of Education, Science, and Research at the Natural History Museum in Vienna and involves, apart from the recruitment of projects, the maintenance of its working database and webpage, as well as the organization of workshops and annual meetings. The 5^th ABOL meeting took place from the 6^th– 7^th of December 2018 at the Natural History Museum Vienna and involved about 180 participants. The meeting included information and updates about running projects and the potential of DNA barcoding in Austria.

Building the reference library necessary for the genetic identification of organisms is the main goal of ABOL. It seeks to stimulate biodiversity research by acquiring funds, fostering diverse applications of DNA barcoding, building up and exchanging skills within the network, and increasing public awareness for biodiversity. ABOL considers itself a platform for the coordination and promotion of all research dealing with Austrian biodiversity.

According to its decentralized structure, ABOL unites all relevant Austrian institutions involved in biodiversity research. Representatives from museums, universities, biosphere parks, national parks, research institutions, researchers, federal and regional conservation departments, and scientific societies all contribute to the achievement of ABOL’s aims.

The various representative working with ABOL. PHOTO CREDIT: Austrian Barcode of Life

Written by

Nikolaus Szucsich

Natural History Museum Vienna, Vienna, Austria

Michaela Sonnleitner

Natural History Museum Vienna, Vienna, Austria

Elizabeth Haring

Natural History Museum Vienna, Vienna, Austria

Helmut Sattmann

Natural History Museum Vienna, Vienna, Austria

← Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects Update from the Norwegian Barcode of Life Network (NorBOL) →

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Summary of National Barcoding Activities for Portugal

by Filipe Costa | Apr 7, 2019 | iBOL Nation Activity

Summary of National Barcoding Activities for Portugal

Sintra Coast, Portugal. PHOTO CREDIT: Public Domain

Written by

Filipe Costa

University of Minho, Braga, Portugal

Barcoding activities in Portugal have been particularly dynamic over the past couple of years. On the marine front, a key framework for progress has been the research grant NEXT-SEA (http://nextsea.org, Centre of Molecular and Environmental Biology (CBMA), University of Minho). It aims to develop and implement autonomous multi-parameter monitoring stations for in situ deployment which will include artificial substrates for bethic colonisation. DNA metabarcoding has been used to monitor macrozoobenthos colonisation of these substrates and to assess the spatial variability of estuarine meiofauna in northwest Iberia.

A recently granted research project (NIS-DNA coordinated by CBMA) intends to apply DNA metabarcoding to monitor non-indigenous species (NIS) in ports and marinas across the country, including the Azores and Madeira archipelagos. A continuing effort has been dedicated to populating the reference libraries for marine life. Among other examples, a current PhD thesis is fully dedicated to investigating cryptic diversity in polychaetes (Annelida) of the north-eastern Atlantic.

The CIBIO-InBIO research centre at the University of Porto has been providing an impressive contribution to the reference libraries for terrestrial organisms, especially insects, among which 2,400 species have already been barcoded. Also at CIBIO-InBIO, there are various ongoing projects developing or applying metabarcoding approaches with particular focus on the bioassessment of freshwater ecosystems.

Finally, a noteworthy event was the launching of a new supercomputer facility named Minho Advanced Computing Centre (MACC) at the University of Minho, which will provide an exceptional opportunity for a significant improvement of iBOL’s bioinformatics capacity and for the development of large-scale bioinformatics research projects through MACC and iBOL partnerships.

← Finland Takes a Leap into the BIOSCAN Age Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects →

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Finland Takes a Leap into the BIOSCAN Age

by Marko Mutanen | Apr 7, 2019 | iBOL Nation Activity

Finland Takes a Leap into the BIOSCAN Age

Six thousand specimens of sawflies recently processed for DNA barcoding as part of the FinBOL project. PHOTO CREDIT: Vlad Dinca

Written by

Marko Mutanen

Ecology and Genetics Research Unit, University of Oulu, Finland

DNA barcoding first gained momentum in Finland in 2011 with the launch of the national Finnish Barcode of Life (FinBOL) initiative, initially funded by three major national funders – the Kone Foundation, the Finnish Cultural Foundation as well as the University of Oulu. FinBOL’s main goal is to build a DNA barcode reference library for the species of Finland.

Since 2015, the Academy of Finland has funded barcoding activities through the Finnish Biodiversity Information Facility (FinBIF) which brings together all information about Finnish species under the Laji.fi portal, including links to the DNA barcodes available on the Barcode of Life Database (BOLD).

With approximately 40,000 species known and 48,000 estimated, Finland’s biodiversity is relatively modest in comparison to most other countries. The fauna and flora are, however, among the best investigated globally, and roughly one-half of the species are presently represented with sequence data on BOLD. Some major groups, such as butterflies, moths, and caddisflies, already have barcode sequences for virtually all species. Many experts have been closely engaged with the project and this continued collaboration will be integral to reaching our goal.

Recently, the Academy of Finland provided €2.7M to FinBIF 2.0 to further strengthen the national biodiversity infrastructure. With this remarkable governmental support, we aim to add thousands of species to the DNA barcode library by the end of 2022. To reach this goal, we take advantage of the unprecedented progress in high-throughput sequencing technology that also facilitates the recovery of full barcode sequences from old museum specimens when fresh specimens are not available.

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