Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of fish and marine mammal species whose DNA has been detected in water samples collected between 2019 and 2021 using the mitochondrial marker MiFish (12S).The surveys were carried out in the summer of 2019 (July 14-18) and (July 30 - August 5), in the fall of 2020 (October 27-28) and in the summer-fall of 2021 (May 31 - June 3 ) and (August 24-25) between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 1-50 meters depth in 91 stations, with 1 to 3 replicates per station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissues or PowerWater extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. The libraries were prepared either by Génome Québec (2019, 2020) or by the Genomics Laboratory of the Maurice-Lamontagne Institute (2021), then sequenced on a NovaSeq 4000 PE250 system by Génome Québec. The bioinformatics analysis of the sequences obtained was carried out using an analysis pipeline developed in the genomics laboratory. A first step made it possible to obtain a table of molecular operational taxonomic units (MOTU) using the cutadapt software for the removal of the adapters and the R package DADA2 for the filtration, the fusion, removal of chimeras and compilation of data. The MOTUs table was then corrected using the R package metabaR to eliminate the tag-jumping and take contaminants into consideration. Samples showing a strong presence of contaminating MOTUs were removed from the dataset. The MOTUs were also filtered to remove all remaining adapter sequences and also retain only those of the expected size (around 170 bp). Finally, taxonomic assignments were made on the MOTUs using the BLAST+ program and the NCBI-nt database. Taxonomic levels (species, genus or family) were assigned using a best match method (Top hit), with a threshold of 95%. Only assignments at the level of fish and marine mammals were considered, and the taxa detected were compared to a list of regional species, and corrected if necessary. The species detections of the different replicas have been combined.The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute.This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems.Data were also published on SLGO platform : https://doi.org/10.26071/ogsl-2239bca5-c24a

A research survey of scallops (mainly sea scallop Placopecten magellanicus, but also Icelandic Scallop Chlamys islandica) using a dredge was carried out by DFO (Fisheries and Oceans Canada) every 1 or 2 years since 1992 in the Magdalen Islands (fishing area 20). The main objective of this research survey was to assess Sea Scallop stocks. Another objective was to document taxa associated with scallop habitat according to a fixed random sampling plan. Occurrences for the year 2021 and 2022 are presented by species (or taxon) by station. Starting in 2021, catches were weighed, and specimens photographed, with information available upon request. The taxonomic and geographical validity of the data was checked and the World Register of Marine Species served as the taxonomic authority for naming all taxa recorded during the survey. Epibenthic invertebrates (mainly molluscs, echinoderms and crustaceans) as well as demersal fish were identified from the dredge catches. The historical dataset is available at the following link : https://open.canada.ca/data/en/dataset/71732ad5-5c70-4dbf-916d-a94e1380c53bThe study area is located south of the Magdalen Islands and the sampling of scallop beds is carried out at depths of generally around 25 to 35 m. A random selection of sampling stations is carried out from a fixed station grid. Sampling is done along transects at these randomly drawn stations in the study area. Sampling is done with a lined Digby scallop dredge (20 mm mesh) over approximately 500 m along the seabed. The four baskets of the dredge are examined for all scallops, and starting in 2022, also for all fishes. One basket (first on the starboard side) is sorted and examined for associated species. Most specimens are counted by taxa. Those that are too small and numerous, or colonial, are noted for presence or relative abundance. Special cases are occasionally conserved for taxonomic analysis, for example, ascidians (to monitor for invasive species) and sponges (to document new species). The availability of photos and some conserved specimens enables future review. Changes are anticipated in the identifications, notably for Bryozoan, Hydrozoa, and Porifera, that are currently the focus of research efforts.

Spiny dogfish (Squlaus acanthias), is a species found in Atlantic Canadian waters which is encountered mostly in commercial fisheries. Pop-up Satellite Archival Tags (PSAT) from Wildlife Computers were applied to spiny dogfish from 2008 to 2009 to collect data on depth (pressure), temperature and ambient light level (for position estimation). Deployments were conducted in Canada on commercial fishing vessels from August to October. Wildlife Computers PSAT Mk10 (N=6) were used and 3 of 6 tags reported. One tag was found washed up on shore and was returned. The spiny dogfish tagged ranged in size from 80 cm to 96 cm Fork Length (curved); all 6 were female. Time at liberty ranged from 75 – 234 days and the 43 tags that reported remained on the sharks for the programmed duration. Raw data transmitted from the PSAT’s after release was processed through Wildlife Computers software (GPE3) to get summary files, assuming a maximum swimming speed of 2m/s, NOAA OI SST V2 High Resolution data set for SST reference and ETOPO1-Bedrock dataset for bathymetry reference. The maximum likelihood position estimates are available in .csv and .kmz format and depth and temperature profiles are also in .csv format. Other tag outputs as well as metadata from the deployments can be obtained upon request from: warren.joyce@dfo-mpo.gc.ca or heather.bowlby@dfo-mpo.gc.ca.

A research survey of scallops (mainly sea scallop Placopecten magellanicus, but also Icelandic Scallop Chlamys islandica) using a dredge was carried out by DFO (Fisheries and Oceans Canada) every 1 or 2 years since 1992 in the Magdalen Islands (fishing area 20). The main objective of this research survey was to assess Sea Scallop stocks. Another objective was to document taxa associated with scallop habitat according to a fixed random sampling plan. Occurrences by species (or taxon) are presented by station. The taxonomic and geographical validity of the data was checked and the World Register of Marine Species served as the taxonomic authority for naming all taxa recorded during the survey. Epibenthic invertebrates (mainly molluscs, echinoderms and crustaceans) as well as demersal fish were identified from the dredge catches. The current data starting in 2021 are available at the following link : https://open.canada.ca/data/en/dataset/6529a4b0-f863-4568-ac71-1fa26cf68679The study area is located south of the Magdalen Islands and the sampling of scallop beds is carried out at depths of 10 to 38 m, generally around 25 to 35 m. A random selection of sampling stations is carried out from a fixed station grid. Sampling is done along transects at these randomly drawn stations in the study area. Sampling is done with a lined Digby scallop dredge (20 mm mesh) over approximately 500 m along the seabed. The four baskets of the dredge are examined for all scallops. Next, a basket (the first on the starboard side) is sorted and examined for associated species. Most specimens are counted by taxon. The presence or relative abundance of undersized and numerous, or colonial, organisms is noted. Special cases are sometimes retained for taxonomic analysis, for example, ascidians (to monitor invasive species) and sponges (to document new species).

Speckled Dace (Rhinichthys osculus) are listed under the Species at Risk Act (SARA) as endangered. These fresh water fish, of the family Cyprinidae, are found in Canada only in the Kettle Valley of British Columbia. Proposed critical habitat was based on minimum viable population analysis and assumed densities of fish. From October 19th to the 22nd of 2015, night time pole seining surveys were conducted to enumerate Speckled Dace in proposed critical habitat on the West Kettle River; one of three rivers containing Speckled Dace. The estimated population abundance of Speckled Dace within the survey area was 8,978 (6,143-11,814), however only 1,014 of these are estimated to be adults.

The mako shark (Isurus oxyrinchus), is a species found in Atlantic Canadian waters which is encountered in commercial and recreational fisheries. Pop-up Satellite Archival Tags (PSAT) from Wildlife Computers were applied to mako sharks from 2011 to 2013 to collect data on depth (pressure), temperature and ambient light level (for position estimation). Deployments were conducted in Canada on commercial vessels, typically in summer and fall from July to October. Two types of tag models were deployed: Mk10 (N=28), and MiniPAT (N=9) and 28 of 37 tags reported (one female shark was recaptured). The mako sharks tagged ranged in size from 80 cm to 229 cm Fork Length (curved); 13 were female, 17 were male, and 7 were unknown sex. Time at liberty ranged from 0 – 185 days and 6 tags remained on for the programmed duration. Raw data transmitted from the PSAT’s after release was processed through Wildlife Computers software (GPE3) to get summary files, assuming a maximum swimming speed of 2m/s, NOAA OI SST V2 High Resolution data set for SST reference and ETOPO1-Bedrock dataset for bathymetry reference. The maximum likelihood position estimates are available in .csv and .kmz format and depth and temperature profiles are also in .csv format. Other tag outputs as well as metadata from the deployments can be obtained upon request from: warren.joyce@dfo-mpo.gc.ca or heather.bowlby@dfo-mpo.gc.ca.

The greenland shark (Somniosus microcephalus), is a species found in Atlantic Canadian waters which is occasionally encountered in commercial fisheries. Pop-up Satellite Archival Tags (PSAT) from Wildlife Computers were applied to greenland sharks from 2006 to 2009 to collect data on depth (pressure), temperature and ambient light level (for position estimation). Deployments were conducted in Canada on commercial vessels throughout the year and in Cumberland Sound (Pangirtung) on a scientific expedition in April 2008. A variety of tag models were deployed: PAT 4 (n=1) and Mk10 (N=15) and 14 of 16 tags reported. Greenland sharks tagged ranged in size from 250 cm to 549 cm Total Length (curved); 3 were female, 9 were male, and 4 were of unknown sex. Time at liberty ranged from 48 – 350 days and 9 tags remained on the sharks for the programmed duration. Raw data transmitted from the PSAT’s after release was processed through Wildlife Computers software (GPE3) to get summary files, assuming a maximum swimming speed of 2m/s, NOAA OI SST V2 High Resolution data set for SST reference and ETOPO1-Bedrock dataset for bathymetry reference. The maximum likelihood position estimates are available in .csv and .kmz format and depth and temperature profiles are also in .csv format. Other tag outputs as well as metadata from the deployments can be obtained upon request from: warren.joyce@dfo-mpo.gc.ca or heather.bowlby@dfo-mpo.gc.ca.

11 tagged Blue whales (Balaenoptera musculus) were tracked during the daytime movements as well as the feeding behaviour in the St. Lawrence River estuary. Kernel density was applied to derminate the high density feeding areas of all individuals combined (30, 40, 50, 60, 75, 95 %).Doniol-Valcroze T, Lesage V, Giard J, Michaud R, 2012. Challenges in marine mammal habitat modelling: evidence of multiple foraging habitats from the identification of feeding events in blue whales. Endang Species Res, Vol. 17 : 255–268, doi : 10.3354/esr00427(English version only)

Since 1985, research surveys targeting scallops—primarily the sea scallop (Placopecten magellanicus) and, to a lesser extent, the Icelandic scallop (Chlamys islandica)—have been conducted by Fisheries and Oceans Canada (DFO) at one- or two-year intervals around the Magdalen Islands (fishing area 20A). The main objective of this survey is to assess the status of sea scallop stocks. The study area is situated south of the Magdalen Islands, where scallop beds are typically sampled at depths ranging from approximately 25 to 35 m. Sampling stations are randomly selected from a predetermined fixed grid, with sampling conducted along transects at these randomly assigned locations within the study area. Each station is sampled using a lined Digby scallop dredge (20 mm mesh size), towed for roughly 500 m across the seabed.This publication includes three files: the file biometriePetoncle_20, which contains detailed biometric data (species, size, weights and sex) from 1998 to 2024; the file taillePetoncle_20, which provides the size of the individuals sampled from 2009 to 2024; and the file traitPetoncle_20 which contains the abundances and densities per tow from 2009 to 2024. Data on abundances and densities per tow from 1998-2008 is available upon request.This dataset is updated every one to two years as data becomes available. A cleaning of aberrant data has been carried out. However, there is missing data in various columns of the dataset – use the data with caution. If you have any questions please contact DFO.DataManagementSAISB-GestionDonneesDAISS.MPO@dfo-mpo.gc.ca or the author. For certain time periods, associated species are identified and semi-quantitatively counted directly on the sorting table, and the results are presented in the following publications: - https://open.canada.ca/data/en/dataset/6529a4b0-f863-4568-ac71-1fa26cf68679- https://open.canada.ca/data/en/dataset/71732ad5-5c70-4dbf-916d-a94e1380c53b 

Basic biological data for all fish caught during the 2012 BSMFP expedition. Includes identification, weight, length (total, fork, and, standard), liver weight, gonad weight, sex and maturity level.