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Data for Freshwater mollusc community screening - classical and eDNA monitoring to detect rare, indicator and invasive species

https://doi.org/10.5878/68mj-8k45
The data belongs to the study Freshwater mollusc community screening - classical and eDNA monitoring methods to detect rare, indicator and invasive species. Tables and figures represent in detail the sample localities of 15 Swedish lakes and rivers. The study was focusing on Plankton samples and two kind of sediment samples (Kick-net and M42 method) at two sampling times (spring and autumn). Species were found through a) classical morphological studies where freshwater molluscs were determined by hand with a stereoscopic microscope; b) with barcoding by the cytochrome c oxidase subunit I (COI) gene and c) through eDNA metabarcoding analysis (Illumina sequencing). The main focus was on pea clams, but even other benthic freshwater molluscs and organisms could be detected. COI barcode data were analyzed for a Barcode Tree with MEGA version 11.0.13 (https://www.megasoftware.netOpens in a new tab) (Stecher et al., 2020). Metabarcoding data were analyzed with the Apscale pipeline (https://github.com/DominikBuchner/apscaleOpens in a new tab, Buchner et al., 2022).
Download data and documentation (12 files / 1.42 MiB)

Data files

  • FigureS1A_C_NCBI_BOLD_240625.docx
    457.66 KiB
  • FigureS2_InvasiveSpecies.png
    125.31 KiB
  • SupplementaryTable1_SampleSites.docx
    21.89 KiB
  • SupplementaryTable2_SequencesBarcodeTree.docx
    35.61 KiB
  • SupplementaryTable3_Morphological_Records_FM_240829b.xlsx
    40.44 KiB
  • SupplementaryTable4A_List_InvasiveSpecies.docx
    14.92 KiB
  • SupplementaryTable4B__Results_InvasiveSpecies_Metabarcoding.xlsx
    12.83 KiB
  • SupplementaryTable5A_IndicatorList_.xlsx
    91.05 KiB
  • SupplementaryTable5B_Indicator_list_NCBI_BOLD.DataFootprint.xlsx
    161.97 KiB
  • SupplementaryTable5C_Results_IndicatorSpecies_Metabarcoding.xlsx
    296.24 KiB
  • Thumbs.db
    10.5 KiB

Documentation files

  • ReadmeFileDataSetFreshwaterMolluscCommunityScreening.pdf
    182.65 KiB

Citation and access

Data access level:

Creator/Principal investigator(s):

Research principal:

Principal's reference number:

  • FP2018/20

Data contains personal data:

No

Citation:

License:

Language:

Method and outcome

Time period(s) investigated:

Data format/data structure:

Species and taxons:

Samples/material Collected from scientific collection/biobank

Name:

Göteborgs Naturhistoriska Museum

Type(s) of sample:

Tissuce samples from barcodes individutal and voucher material that were collected (freshwater molluscs)

Data collection Field/Intervention experiment

Mode of collection:

Field/Intervention experiment

Description of the mode of collection:

The material was collected by using three different methods along a 50 m line transect at each aquatic habitat: 1) Plankton net: zooplankton net, 200 um size, drawn in a semi-circle at 0, 25 and 50 meters 2) Kick net: Wildcon D net, 500 um, vertical in front of the collector's feet, at 0, 25 and 50 meters 3) Swedish M42 method for monitoring bottom fauna in lakes' littorals and rivers - independent selection Version 1:2, 2016-11-01 (Swedish Agency for Marine and Water Management), with 30 sub-samples along the transect. The samples were stored in a 500ml LDPE bottle (VWR) filled with 96% ethanol in a cool box in field and then transferred to a -20°C freezer in the lab until DNA extraction was carried out.

Time period(s) for data collection:

2019-09 - 2021-07

Data collector:

Geographic coverage

Geographic location:

Geographic description:

Lakes and rivers in Sweden - region Norrbotten (Öst-Kieratj, Harrijåkkå, Aborrträsket), Bohuslän (Aröds å, Bodeleån, Risån, Nedre Bäveån, Stora Skarsjön, Ivarsbosjön, Stora Tokevattnet, Restevattnet), Skaraborg (Flämsjön, Stora Bjursjön, Vristulven, Östen)

Administrative information

Responsible department/unit:

School of Bioscience

Funding

Funding agency:

Award number:

2018-01003_Formas

Award title:

End biodiversity loss through improved tracking of threatened invertebrates

Topic and keywords

Standard för svensk indelning av forskningsämnen 2025:

INSPIRE topic categories:

Keywords:

Relations

Homepage:

Is supplemented by:

original metabarcoidng files (fastq files) in the ENA catalogue (European Nucleotide Archive)Opens in a new tab

Publications

Citation:

Authors: Sonja Leidenberger, Vollrath Wiese, Finja Schaumann, Felix Pleiss, Kathrin Langen, Sarah J. Bourlat Journal: Science of the Total Environment accepted

Contact

Metadata

Version 1
doris
University of Skövde
Published: