GBIF User Club

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21 January 2020

Our guest will be Cecilie Svenningsen. Cecilie is a PhD student at the Natural History Museum of Denmark, UCPH, Denmark, in the Citizen Science group. She received her MSc in Biology with a specialization in Ecology from UCPH in 2017 where she studied the gut microbiome of insects with DNA metabarcoding. During her studies, she carried out various insect-related projects and currently work on the citizen science project ‘Insektmobilen’ or ‘InsectMobile’, which is funded by Aage V. Jensen Naturfond from 2017-2020.

Summary

Insects are generally under-represented in biodiversity databases although it is the most speciose terrestrial animal group. Recent reports have revealed that insects are declining at alarming rates across the globe which emphasizes the need for more data to assess, monitor and conserve insect biodiversity. Cecilie will present the citizen science project Insektmobilen/InsectMobile which aims to study the spatio-temporal distribution of flying insects in Denmark across various land-use/land-cover intensities. Insect bulk samples are collected with rooftop car nets by citizen scientist and processed with a DNA metabarcoding protocol. Citizen science sampling is carried out during the month of June 2018 and 2019 along >400 predefined 5 km routes with a car net mounted on the rooftop of the participant’s car under specific weather conditions. Each route is designed to fit into one of five different land-cover categories: forest, urban, agriculture, dry nature/open nature and wet nature. The key data resources for taxonomic assignment of sequence reads are the International Barcode of Life’s reference database which is queried through GBIFs recently available Sequence ID tool for the CO1 primer set and a custom protocol using the taxize package in R for the 16S dataset. The Sequence ID tool in GBIF has greatly improved taxonomic assignment of insect OTUs compared to other tools which processes less input data at a time and provides limited output. Another key data resource is publically available land-use/land-cover data. We are currently investigating possibilities to process large datasets and ‘flag’ detected species which are in the IUCN red list, are new species occurrences for Denmark, trait-based data, habitat association, etc. Metadata and morphological data are stored and updated in individual databases, and the majority of the bioinformatics are carried out on a HPC cluster. Sequence errors are removed with DADA2 and the LULU algorithm is used to remove erroneous OTUs in R. All data analysis is carried out in R. The project is the first large systematic survey of all groups of flying insects in Denmark and will generate 1,200 sampling events/bulk insect samples from >350 localities which will be uploaded to GBIF.

GBIF User Club is a coffee-and-cookies seminar series for the greater Copenhagen area were we share the data use experiences in an informal atmosphere. I hope the message reached the interested ones in CMEC and in the Museum branches. Feel free to bring other topics to debate, suggest a topic you want to learn about or nominate yourself as a speaker for the later slots. You are welcome to fw the message to the interested colleagues.

Venue
The Zoological Museum, Conference room, II floor
Location
Copenhagen
Country or area
Denmark
When
21 January 2020 14:00 - 15:30