Insektmobilen - National citizen science and DNA metabarcoding survey of flying insects in June 2018 and 2019

Cecilie Svenningsen; Anders P. Tøttrup

doi:10.15468/m48e3e

Insektmobilen - National citizen science and DNA metabarcoding survey of flying insects in June 2018 and 2019

Citation

Svenningsen C, P. Tøttrup A (2024). Insektmobilen - National citizen science and DNA metabarcoding survey of flying insects in June 2018 and 2019. Version 1.11. Natural History Museum of Denmark. Occurrence dataset https://doi.org/10.15468/m48e3e accessed via GBIF.org on 2024-12-15.

Description

The Insectmobile (Insektmobilen) is a research project at the National History Museum of Denmark, University of Copenhagen, with the goal to investigate the diversity of flying insects in Denmark. In the summer of 2018, 2019 and 2020 almost 400 volunteers collected flying insects using large custom made insect nets mounted on the roof of their cars. The bulk insect samples were processed with a non-destructive DNA extraction DNA metabarcoding protocol (dx.doi.org/10.17504/protocols.io.bmunk6ve) and sequences were assigned taxonomy by importing the fasta file into GBIF's sequence ID tool (https://www.gbif.org/tools/sequence-id). The sequences were queried against a 99% clustered version of the BOLD Public Database v2024-01-06 public data (COI-5P sequences). The dataset contains unidentified sequences and potential errors and contaminants. For example, even though the primers used were developed as universal primers targeting freshwater insects, you will find other phyla, classes etc. We share these sequences and associated data for the data to be as open as possible, but please do reannotate sequences and filter the data for your specific needs prior to using the data for analysis. Please be aware that the samples may contain gut content of sampled insects and eDNA. Sequence identification certainty is captured in the identificationRemarks field. The bit score is the required size of a sequence database in which the current match could be found just by chance. The bit score is a log2 scaled and normalized raw score. Each increase by one doubles the required database size (2bit-score). The expect value is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the score of the match increases. Hence, a low expect value is better. How much of the query(input) sequence aligns with the match in the the reference database, in percent. Badges representing different identity thresholds (match types); Blast exact match = identity >= 99% and queryCoverage >= 80%. This is within the threshold of the OTU, Blast ambiguous match = identity >= 99% and queryCoverage >= 80%, but there is at least one more match with similar identity, Blast close match = identity < 99% but > 90% and queryCoverage >= 80%. It is something close to the OTU, maybe the same genus, Blast weak match = there is a match, but with identity < 90% or/and queryCoverage < 80%. Depending on the quality of the sequence, bit score, identity and expect value, a higher taxon could be inferred from this, Blast no match = no match to the reference database.

Sampling Description

Study Extent

Sampling was carried out in Denmark in the month of June of 2018 and 2019.

Sampling

We recruited citizen scientists to drive with car nets in close proximity to their home address in June and July 2018. The car net was funnel- shaped with a detachable sampling bag at the far end for sample collection. Metal guy- line adjusters enabled adjustment to car length and allowed the net to be used on most car types (Figure 1). The measurements of the net were as follows: front height: 75 cm; front width: 100 cm; length: 140 cm; width of sampling bag: 29 cm; mesh size at the bottom (grey fabric): 2 × 1 mm; and mesh size for the rest of the net (white fabric): ~0.3 mm. Custom tent poles (L: 209 cm, D: 8 mm) supported the opening of the net Citizen scientists were recruited by the Natural History Museum of Denmark (NHMD). The citizen scientists received a simple sampling protocol, and video tutorials and FAQ sheets along with the sampling equipment. Sampling of each route was carried out once during two time intervals on the same day: between 12 and 15 h (midday) and again between 17 and 20 h (evening) with a maximum speed of 50 km/h and weather conditions of at least 15°C, an average wind speed of maximum 6 m/s and no rain. Insects were collected in individual sampling bags that were placed in 96% pure ethanol and stored in double-sealed plastic bags before the citizen scientists sent the samples back to the research institution.

Method steps

Please consult the following publications and their supplementary material for more information: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ddi.13532 https://resjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/icad.12694 https://royalsocietypublishing.org/doi/full/10.1098/rsbl.2020.0833 https://www.protocols.io/view/insects-and-dna-metabarcoding-insectmobile-laborat-261ge46qdv47/v1

Taxonomic Coverages

The project targeted flying insects specifically, but a universal primer was used. We have included all sequences and associated taxonomic assignments although some may appear odd, it is our hope that updated reference database may improve the taxonomy of the sequences in the long run and hence their re-usability.

Symphypleona
rank: order
Protura
rank: class
Clionaida
rank: order
Arthropoda
rank: phylum
Peyssonneliales
rank: order
Hydrozoa
rank: class
Amphipoda
rank: order
Chromista
rank: kingdom
Hildenbrandiales
rank: order
Hemiptera
rank: order
Sarcoptiformes
rank: order
Rotifera
rank: phylum
Nemertea
rank: phylum
Haptoglossa
rank: class
Opiliones
rank: order
Artiodactyla
rank: order
Palaeonemertea
rank: class
Coronatae
rank: order
Clitellata
rank: class
Phasmida
rank: order
NA
rank: kingdom
Annelida
rank: phylum
Monostilifera
rank: order
Enchytraeida
rank: order
Polychaeta
rank: class
Florideophyceae
rank: class
Bubarida
rank: order
Cyprinidae
rank: order
Bangiales
rank: order
Hoplonemertea
rank: class
Arachnida
rank: class
Chordata
rank: phylum
Rhodophyta
rank: phylum
Gigartinales
rank: order
Ceramiales
rank: order
Julida
rank: order
Diplopoda
rank: class
Ixodida
rank: order
Crassiclitellata
rank: order
Thysanoptera
rank: order
Neuroptera
rank: order
Longidoridae
rank: order
Dermaptera
rank: order
Mammalia
rank: class
Haplosclerida
rank: order
Bdelloidea
rank: order
Pycnogonida
rank: class
Anthoathecata
rank: order
Collembola
rank: class
Ephemeroptera
rank: order
Araneae
rank: order
Scopalinida
rank: order
Dorylaimida
rank: class
Mesostigmata
rank: order
Plecoptera
rank: order
Rhipidiales
rank: order
Oomycota
rank: phylum
Gastropoda
rank: class
Lepidoptera
rank: order
Echinodermata
rank: phylum
Mollusca
rank: phylum
Demospongiae
rank: class
Leptomitales
rank: order
Diptera
rank: order
Peronosporea
rank: class
Cumacea
rank: order
Entomobryomorpha
rank: order
Chromadorea
rank: class
Polyxenida
rank: order
Trichoptera
rank: order
Bangiophyceae
rank: class
Porifera
rank: phylum
Eurotatoria
rank: class
Polymastiida
rank: order
Ploima
rank: order
Plantae
rank: kingdom
Pantopoda
rank: order
Animalia
rank: kingdom
Pseudoscorpiones
rank: order
Tardigrada
rank: phylum
Phyllodocida
rank: order
Parachela
rank: order
Desmacellida
rank: order
Archinemertea
rank: order
Littorinimorpha
rank: order
Poecilosclerida
rank: order
Nematoda
rank: phylum
Orthoptera
rank: order
Zygentoma
rank: order
Rhabditida
rank: order
NA
rank: order
Coleoptera
rank: order
Rhodymeniales
rank: order
Odonata
rank: order
Insecta
rank: class
Mecoptera
rank: order
Hymenoptera
rank: order
Comatulida
rank: order
Cypriniformes
rank: class
Saprolegniales
rank: order
Peronosporales
rank: order
Ochrophyta
rank: phylum
NA
rank: class
Psocodea
rank: order
Scyphozoa
rank: class
Trombidiformes
rank: order
Leptothecata
rank: order
Albuginales
rank: order
Malacostraca
rank: class
Stylommatophora
rank: order
Poduromorpha
rank: order
Bathynellacea
rank: order
Isopoda
rank: order
Protura
rank: order
Eutardigrada
rank: class
Crinoidea
rank: class
NA
rank: phylum
Cnidaria
rank: phylum

Geographic Coverages

Data was collected in Denmark.

Bibliographic Citations

Contacts

Cecilie Svenningsen
originator
position: Data administrator
Global Biodiversity Information Facility
DK
email: csvenningsen@gbif.org
userId: https://orcid.org/0000-0002-9216-2917

Anders P. Tøttrup
originator
position: Associate Professor
Natural History Museum of Denmark
DK
email: aptottrup@snm.ku.dk
userId: https://orcid.org/0000-0001-8776-9629

Cecilie Svenningsen
metadata author
position: Data administrator
Global Biodiversity Information Facility
DK
email: csvenningsen@gbif.org
userId: https://orcid.org/0000-0002-9216-2917

Isabel Calabuig
distributor
position: Node Manager & Data curator
DanBIF, Danish Biodiversity Information Facility
DK
email: icalabuig@snm.ku.dk
homepage: http://snm.ku.dk/english/staffsnm/staff/?pure=en/persons/88409
userId: https://orcid.org/0000-0001-5515-7900

Cecilie Svenningsen
administrative point of contact
position: Data administrator
Global Biodiversity Information Facility
DK
email: csvenningsen@gbif.org
userId: https://orcid.org/0000-0002-9216-2917

Anders P. Tøttrup
administrative point of contact
position: Associate Professor
Natural History Museum of Denmark
DK
email: aptottrup@snm.ku.dk
userId: https://orcid.org/0000-0001-8776-9629