Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary

# Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary **I. General information** Dataset title: "Data from: eDNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary" Principle investigator: Charlotte Van Driessche ([[e-mail]](mailto:[e-mail])) Co-investigators: Teun Everts, Sabrina Neyrinck, David Halfmaerten, Pieter Verschelde, Jan Breine, Dries Bonte, Rein Brys Data collection data: April, July, September 2021 Geographic location of data collection: Belgium, Flanders (Northern Region) Keywords: biodiversity monitoring, integrated sampling, assay sensitivity, reference database, salinity, seasonal migration Principal funders: Research Foundation Flanders grants for strategic basic research (FWO-SB, grant number 1S23822N to CVD and grant number 1S01822N to TE) and the Research Institute for Nature and Forest As a result of this work, an updated version of the reference database used for metabarcoding was created which can be found here: [https://doi.org/10.5281/zenodo.10422227](https://doi.org/10.5281/zenodo.10422227). **II. Data overview and methodological information** *- Datafile: VanDriessche et al. 2024_ObiTools Count Table_Riaz.xlsx* Creation data file: the 26th of October 2023 The dataset contains eight tab pages. 1\. info_tab: an overview repeating this information but facilitating the use of the Excel file and explaining again the use of all different tabs 2\. raw_table_sorted: sorted raw count table as provided via ObiTools 3\. table_allreps_id100_all: started from raw_table_sorted, but now discarded sequences with <100% identity match with our reference database, as well as sequances with less than 500 reads across all samples. 4\. table_allreps_id100_all_frac: same as tab page 3, but in relative frequencies instead of absolute counts 5\. table_allreps_id100_agglomerate: started from tab page 3, but summed the counts of sequences with the same taxonomic assignment 6\. table_allreps_id100_aggl_frac: same as tab page 5, but in relative frequencies instead of absolute counts 7\. table_allreps_id100_agglomerated_fish: started from tab page 5, but retained only fish species and discarded samples containing <5% fish. 8\. table_allreps_id100_agglomerated_fish_f: same as tab page 7, but in relative frequencies instead of absolute counts Cells containing 'NA' in this file, refer to 'Not Available', for example when a genetic sequence was only identified to genus level and not to species level. Across all tab pages; the same lay-out is used. Column explanations are listed below: ASV: number of the amplicon sequence variant family_name: latin family name genus_name: latin genus name species_name: latin species name familie: Dutch translation of the family name categorie: Dutch translation of the large taxonomic group, e.g. fish full_name: full species name combining the information in column B, C and D sequence: actual sequence used for comparison and match with reference database ASV: same as column A Remainder of the columns include identity codes for the samples. These include: the filtercode + the season and year of sampling + the name of the sampling site + low (E) or high (V) tide + replicate 1 or 2 concurring with the fishing haul + depth level of sampling (o = deep, m = middle, b = surface) + the primer assay used (Riaz or Teleo) + the technical replicate number (1, 2 or 3) example: E2020KRW004_L21_Doel_E1O_Riaz_1 *- Datafile: VanDriessche et al. 2024_ObiTools Count Table_Teleo.xlsx* Creation data file: the 19th of September 2023 The dataset contains eight tab pages. 1\. info_tab: an overview repeating this information but facilitating the use of the Excel file and explaining again the use of all different tabs 2\. raw_table_sorted: sorted raw count table as provided via ObiTools 3\. table_allreps_id100_all: started from raw_table_sorted, but now discarded sequences with <100% identity match with our reference database, as well as sequances with less than 500 reads across all samples. 4\. table_allreps_id100_all_frac: same as tab page 3, but in relative frequencies instead of absolute counts 5\. table_allreps_id100_agglomerate: started from tab page 3, but summed the counts of sequences with the same taxonomic assignment 6\. table_allreps_id100_aggl_frac: same as tab page 5, but in relative frequencies instead of absolute counts 7\. table_allreps_id100_agglomerated_fish: started from tab page 5, but retained only fish species and discarded samples containing <5% fish. 8\. table_allreps_id100_agglomerated_fish_f: same as tab page 7, but in relative frequencies instead of absolute counts Cells containing 'NA' in this file, refer to 'Not Available', for example when a genetic sequence was only identified to genus level and not to species level. Across all tab pages; the same lay-out is used. Column explanations are listed below: ASV: number of the amplicon sequence variant family_name: latin family name genus_name: latin genus name species_name: latin species name familie: Dutch translation of the family name categorie: Dutch translation of the large taxonomic group, e.g. fish full_name: full species name combining the information in column B, C and D sequence: actual sequence used for comparison and match with reference database ASV: same as column A Remainder of the columns include identity codes for the samples. These include: the filtercode + the season and year of sampling + the name of the sampling site + low (E) or high (V) tide + replicate 1 or 2 concurring with the fishing haul + depth level of sampling (o = deep, m = middle, b = surface) + the primer assay used (Riaz or Teleo) + the technical replicate number (1, 2 or 3) example: E2020KRW004_L21_Doel_E1O_Teleo_1 *- Datafile: VanDriessche et al. 2024_Raw Stow.xlsx* Creation data file: the 20th of November 2021 The dataset contains one tab page. 1\. stow_net_raw: raw stow net fishing data in numbers of individuals per species as total catch from the stow nets and as reported also on the vis.inbo dataportal. Column explanations are listed below: Study_site: Doel, Antwerp, Steendorp or Branst Date: Date of sampling Tide: Low or High Season: Spring, Summer or Autumn Remainder of the columns include the latin species names of the species identified morphologically on the fishing vessel. **III. Sharing access and information** This dataset is licensed under a (CC0 1.0) Creative Commons Attribution Non Commercial 1.0 Generic. This data was used generated in the Research Article (manuscript): Van Driessche, C., Everts, T., Neyrinck, S., Halfmaerten, D., Verschelde, P., Breine, J., Bonte, D., & Brys, R. (2024) eDNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary. Science of the Total Environment.