GBOL III: Dark Taxa

GBOL III: Dark Taxa

GBOL III: Dark Taxa

Researchers launch new BIOSCAN project that aims to illuminate thousands of new insect species on Germany's doorstep.

A “pixelated” Diptera.

Currently, around 1.4 million species of animals are known. For tropical regions, many species are still unknown, with estimates of global biodiversity ranging from five to 30 or even 100 million species. More recent studies suggest that there are about 10 million species on our planet. In contrast to the tropics, the Central European fauna is considered to be very well studied. However, specialists have mostly concentrated on less diverse and easy-to-study organisms, neglecting the species-rich, often taxonomically difficult groups, like many Diptera and Hymenoptera. This led to a mismatch between high species numbers and a small number of researchers, often referred to as the ‘taxonomic impediment’. This is most prominent for the megadiverse faunas of tropical regions. Less known is that this also applies, to some extent, for countries with a long history of taxonomic research like Germany, covering 200 or more years. For example, for the compilation of the German checklist of Hymenoptera, 32 specialists were available for 247 species of digger wasps (Crabronidae), while for parasitoid wasps of the family Ichneumonidae one specialist had to deal with 3,332 species.

In Germany, about 48,000 species of animals have been documented, including about 33,300 species of insects. In little-studied groups such as insects and arachnids, preliminary results of earlier DNA barcoding initiatives indicate the presence of thousands of species that are still awaiting discovery. Among the groups with a particularly large suspected number of unknown species are the Diptera (flies) and the Hymenoptera (in particular, the parasitoid wasps). With almost 10,000 known species each, these two insect orders account for two-thirds of the German insect fauna, underlining their importance.

Bar Graph depicting availability of taxonomic expertise for major insects orders in Germany.

“Dark taxa” are, as a rule, small-sized and rich in species, and have therefore been largely ignored by taxonomists. This is reflected by the number of undescribed species in these taxa, combined with a low chance to get specimens identified by specialists.

The insight that there are not only a few but many unknown species in Germany is a result of the earlier German Barcode of Life projects GBOL I and II, both supported by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) and the Bavarian Ministry of Science (project Barcoding Fauna Bavarica). The projects aimed at making all German species reliably, quickly and inexpensively identifiable by DNA barcodes. Since the first project was launched about ten years ago, more than 25,000 animal species have been barcoded, in collaboration with national and international partners. Among them are mostly well-known groups such as butterflies, moths, beetles, grasshoppers, spiders, bees and wasps.

Two scatterplots demonstrating relationship between body size (top) and species richness (bottom) in German Diptera

Relationship between body size (top) and species richness (bottom) in German Diptera1

Despite their popularity, these groups represent only a fraction of the total inventory of German insects. In Germany there are 170 butterfly species, 81 dragonfly and damselfly species, 87 species of grasshoppers, katydids and crickets, and 580 species of ground beetles, all of which are well-studied. Taken together, these 918 species stand for only a small fraction (2.8%) of the German insect fauna. They are morphologically well identifiable, have manageable species numbers, can easily be monitored during daytime and are therefore regarded as relevant in nature conservation and often used for monitoring species diversity. Conversely, however, this means that the vast majority of the native species diversity has been largely ignored in nature conservation and in general and applied research.

Circular tree depicting Nematocera (midges) and Brachycera (flies)
A circular neighbour‐joining tree for the two suborders of flies, Nematocera and Brachycera1. Each line in the tree corresponds to a distinct Barcode Index Number (BIN). Whereas for two of the “big four” insect orders, the Lepidoptera and Coleoptera, the number of German species are very precisely known, the numbers for the Diptera and Hymenoptera must rely on rough estimates. 

This applies in particular to the Diptera (flies). The observation that estimates of the number of species of native Diptera have been far too low was not only a result of the DNA barcoding projects at the ZSM, but became clear in a recent study by Paul Hebert and his team2. In this large-scale study, DNA barcodes of about one million insects were analyzed. Based on this study, Canada’s gall midges alone are estimated to include about 16,000 species, suggesting the existence of at least two million species on earth. That would be more species of gall midges worldwide than all previously described animal species combined.

The little-known or unknown species, referred to as ‘dark taxa’, are the subject of another BMBF-funded DNA barcoding project that is being carried out at the ZSM in collaboration with other German natural history museums and institutions. The project focuses on Diptera and Hymenoptera (in particular, parasitoid wasps), each with a large proportion of ‘dark taxa’. The new project, funded by a grant of 5.3 million Euro, starts July 1st 2020, with 12 PhD students at three major natural history institutions in Bonn (Zoological Research Museum Alexander Koenig), Munich (SNSB – Zoologische Staatssammlung München) and Stuttgart (State Museum of Natural History Stuttgart), to address a range of questions related to the taxonomy of German ‘dark taxa’, targeting selected groups of Diptera and parasitoid Hymenoptera.

Detailed photo of a Eulophidae specimen
Yellow Mymaridae specimen

Small parasitoid wasps of the families Eulophidae (top) and Mymaridae (bottom), both group with possibly hundreds of new species in Germany that still await discovery.

Among the major aims of GBOL III is assessing of the performance of DNA barcoding for species identification of ‘dark taxa’, and assessing the species detection ability of DNA barcodes in mass samples that are obtained from metabarcoding studies. Other aims of the project include the development of a platform for managing OTU-based taxonomic data, developing a pipeline for reliable and fast barcoding of small and poor-quality samples, and training of the next generation of taxonomists.

GBOL III is designed to make an important contribution to the global BIOSCAN initiative of the Centre for Biodiversity Genomics. It helps to lay the foundations for a global biomonitoring system to record the biodiversity of our planet on a large geographical scale in times of rising temperatures, increasing weather extremes and receding ice, and to track its changes as a result of global environmental changes.

References:

1. Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele J, 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 19: 900–928. https://doi.org/10.1111/1755-0998.13022

2. Hebert PDN, Ratnasingham S, Zakharov EV, Telfer AC, Levesque-Beaudin V, Milton MA, Pedersen S, Jannetta P, deWaard JR (2016) Counting animal species with DNA barcodes: Canadian insects. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150333. https://doi.org/10.1098/rstb.2015.0333

Written by

Axel Hausmann

Axel Hausmann

SNSB - Zoologische Staatssammlung München, Munich, Germany

Lars Krogmann

Lars Krogmann

State Museum of Natural History Stuttgart, Stuttgart, Germany

Ralph S. Peters

Ralph S. Peters

Zoological Research Museum Alexander Koenig, Bonn, Germany

Vera Rduch

Vera Rduch

Zoological Research Museum Alexander Koenig, Bonn, Germany

Stefan Schmidt

Stefan Schmidt

SNSB - Zoologische Staatssammlung München, Munich, Germany

July 10, 2020

doi: 10.21083/ibol.v10i1.6242

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Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects

Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects

Thirteen Years of DNA Barcoding in Germany – Achievements and Prospects

In less than a decade, DNA barcodes of more than 24,000 German species have been assembled resulting in several major data releases and publications.
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

Axel Hausmann

Zoologische Staatssammlung München, Munich, Germany

Stefan Schmidt

Stefan Schmidt

Zoologische Staatssammlung München, Munich, Germany

Jérome Morinière

Jérome Morinière

Zoologische Staatssammlung München, Munich, Germany

April 7, 2019

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