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 invertebrates species whose DNA has been detected in water samples collected at 2018 using the marker COI.The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 9-52 meters depth in 40 stations with one sample par station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissue extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. Libraries at the COI locus were prepared by Genome Quebec and sequenced on an Illumina MiSeq PE250 system. The bioinformatics analysis of the sequences obtained was carried out using an in-house analysis pipeline as reported in Bourret et al. 2022. A first step made it possible to obtain a molecular operational taxonomic unit table (MOTU) using the cutadapt software for the removal of the adapters and the DADA2 R package for the filtration, fusion, chimera removal and data compilation. The MOTUs table was subsequently corrected by taking into account the negative controls, where the number of observations in the latter was removed from the linked samples. Singleton MOTUs have also been removed. Finally, the taxonomic assignments were carried out on the MOTUs using the IDTAXA classifier (present in the DECIPHIER R package) using a training set trained on the COI reference bank for Golf St-Laurent (GSL-rl v1.0, https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) and a threshold of 40. Detections with an “Unreliable due to gaps” category were reported at the genus level only.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 are also available on SLGO platform : https://doi.org/10.26071/ogsl-cd4c205b-f63b

An exploratory fishery was carried out in the Mackenzie River Delta between 1989 and 1993 at the request of the Inuvik Hunters and Trappers Committee to assess the commercial fishery potential in this area. Data collected during this exploratory fishery was used in two technical reports. Broad whitefish were the target species of this fishery (DFO Technical Report 2180), however other species such as northern pike, inconnu, and lake whitefish were also harvested (DFO Technical Report 2330).Biological data from broad whitefish (fork length, age, gonadosomatic index and instantaneous mortality) were analyzed to assess the impact of an exploratory fishery in the Mackenzie River Delta. The data were collected using variable mesh experimental gill nets and commercial harvesters' 139 mm (5.5”) mesh gill nets. The data suggest that the broad whitefish population might be separated, with larger mature spawners gathering in the main channels prior to spawning and smaller, immature or resting fish staying in side channels away from strong currents. From this analysis we conclude that the size and structure of the broad whitefish population(s) found in this area are stable at the current level of total harvest (commercial and subsistence combined) There may be room for increased harvests but to what level is uncertain.Biological data from northern pike, inconnu, and lake whitefish were analyzed to assess the impact of the fishery on population abundance and structure. All three by catch species support subsistence fisheries in the Mackenzie Delta. lnconnu and lake whitefish migrate substantial distances, crossing land claim borders and are likely fished by a variety of user groups. Northern pike, on the other hand tend to be non-migratory with localized populations that are mainly fished by people living in the near vicinity. A concern was that commercial fishing pressure might reduce the numbers of fish available to subsistence users. Based on trends in size and age frequency, age at maturity, sex ratio, growth rates, and mortality rates, we conclude that inconnu and lake whitefish populations in the Mackenzie Delta have remained healthy and stable at the current harvest levels, however northern pike populations showed a decrease in the proportion of older fish, possibly indicating over-fishing of local stocks. lnconnu and lake whitefish may be able to withstand increased harvest, but to what extent is unknown, given that little reliable information is available on subsistence harvest levels in this region. Increasing harvest levels of pike may be risky and we suggest that a reduction of current commercial harvest quotas be considered.

A novel, bay – scale (i.e. tens of km) survey method was employed to examine algal populations on the southwestern shore of Cape Breton, Canada, for the purposes of potential economic exploitation. Since traditional remote sensing methods were unlikely to be successful in these waters, underwater video and acoustic methods were applied. A transponder positioned towfish housing video camera and sidescan sonar was hauled along predetermined transects perpendicular to shore to provide information on bottom type and algal cover. The towfish data were used to ground truth echosounder data (bottom type and macrophyte canopy height) collected along 5, 10 and 20 m depth contours. The survey area was divided into six zones comprising a range of exposure, depth and bottom types. Destructive quadrat samples were collected at each depth plus shore stations to provide biomass estimates. Over thirty five taxa were enumerated, indicating depths and zones of common occurrence. Ascophyllum was abundant at some of the shore stations. The genera Chondrus, Cystoclonium, Desmarestia, Fucus, Phyllophora, Polysiphonia, and Saccharina were common at 5 m. Desmarestia and Saccharina dominated at 10 m with wet weights sometimes over 1 kg·m-2. Agarum dominated at 20 m. The towfish / echosounder grid sampling system was relatively coarse in order to cover the 140 km2 survey area within 12 days. As a result, the survey did not produce spatially detailed information. However, adequate information was gathered to describe the general characteristics of bottom type and algal cover by zone and for focusing further exploration--Abstract, p. vi.Cite this data as: Vandermeulen H. Data of: A Novel Video and Acoustic Survey of the Seaweeds of Isle Madame. Published: August 2021. Coastal Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/ebdd8f91-9131-45f0-8aec-aba9f65e3fae

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

PURPOSE:These data have been updated following a Canadian Science Advice Secretariat (CSAS) Regional Science Advisory Process. Associated publications are available in the citation section below or will be posted on the Fisheries and Oceans Canada (DFO) Science Advisory Schedule as they become available.Determine the stock status of southern Gulf of St. Lawrence Atlantic Cod. DESCRIPTION:The yearly spawning stock biomass estimates of southern Gulf of St. Lawrence Atlantic Cod were obtained using a Statistical Catch-at-Age model as part of the stock assessment to year 2023.The yearly estimates presented come from Markov Chain Monte Carlo (MCMC) simulations. The yearly median estimates are provided, along with uncertainty estimates (2.5th, 25th, 75th and 97.5th percentiles). The values are in thousands of tons of spawning stock biomass. USE LIMITATION:To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

The Department of Fisheries established a survey of demersal juvenile Atlantic cod (*Gadus morhua*) in the nearshore (<10 m deep) in 1959. This survey aimed to characterize the distribution and abundance of juvenile Atlantic cod and was based upon Norway's Flodevigen sampling program which has been conducted continuously since 1919. A 25 m seine was used to sample juvenile Atlantic cod nursery locations on the Avalon Peninsula and Northeast coast of the island of Newfoundland in September and October. The survey continued until 1964 and became known as the Fleming survey, after original initiator Alistair Fleming. The survey was reinstated by Memorial University of Newfoundland from 1992 to 1997. Multiple tows were conducted at a subset of the original 55 Fleming sites located in St. Mary's Bay, Trepassey Bay, the Southern Shore, Conception Bay, Trinity Bay, Bonavista Bay, Gander Bay, New World Island, Fortune Harbour, Badger Bay, Halls Bay and Green Bay.This data set includes several different subsets, some of which span both Fleming Survey periods (1959-1964 and 1992-1997):I. JuvCodCatch60s90s:Catches of juvenile Atlantic cod (1959-1964, 1992-1997) from the first two consecutive tows at each site. This is a summary based on JuvCodLengths90s and FlemingSurveyData60s;II. JuvCodLength90s:Lengths of all individual juvenile Atlantic cod caught for each site (1992-1997);III. SiteEnvData60s90s:Station data for Fleming data 1992-1997;IV. FlemingSurveyData60s:Fleming survey data from 1959-1964 (note there are three record types pertaining to: station data "type 1"; general species catch data including juvenile Atlantic cod grouped by age class ("1+", "Zeroes", and "Total") "type 2; and juvenile Atlantic cod (species 223) listed in length bins "type 3"; andV. FlemingBycatch60s92to96:Bycatch data from 1959-1964 & 1992-1996 from first two tows at each site. This is a summary based partly on the FlemingSurveyData60s set.

The North Shore of the Lower Estuary (Upper North Shore, Quebec) is a productive coastal system where many commercial species of benthic invertebrates are fished in the infralittoral (10-20 m) and circalittoral (20-50 m) zone. However, little data exist on the biodiversity of non-commercial species and the environmental characteristics of the benthic habitat in this area. Two scientific surveys were conducted in 2018 and 2019 to address this knowledge gap by developing a framework of biodiversity and environmental (water column and seafloor) data taking that will be used to determine the baseline state of the benthic ecosystem in this region.Surveys were conducted in 2018 (August 11-14) and 2019 (July 30-August 5) in the Upper North Shore region (between the towns of Forestville and Godbout). Surveys followed a fixed sampling design of eight transects perpendicular to bathymetry with stations at 10 m depth intervals in a bathymetry range of 10-50 m for a total of approximately 40 stations per survey. Specimens were collected with a beam trawl with an opening of 2.8 m. The hauls were made at a target speed of 2 knots and a target duration of 7 minutes. Start and end positions were recorded to calculate the distance traveled on each tow using the geosphere library of R. The average tow distance was approximately 425 m. The area covered at each tow was the product of the trawl opening and the distance traveled. The three files provided (DarwinCore format) are complementary and are linked by the "eventID" key. The "event_information" file includes generic event information, including date and location. The "additional_information_event_and_occurrence" file includes sample size, sampling protocol and sampling effort, among others. The "taxon_occurrence" file includes the taxonomy of the species observed, identified to the species or lowest possible taxonomic level. For abundance and biomass estimates, contact Virginie Roy (virginie.roy@dfo-mpo.gc.ca). For quality controls, all taxonomic names were checked against the World Register of Marine Species (WoRMS) to match recognized standards. The WoRMS match was placed in the "scientificNameID" field of the occurrence file. Special cases were noted in "identificationRemarks" and selected specimens were confirmed using field photos. Data quality checks were performed using the R obistools and worrms libraries. All sampling locations were spatially validated.This project was funded by DFO Coastal Environmental Baseline Program under Canada’s Oceans Protection Plan. This initiative aims to acquire environmental baseline data contributing to the characterization of important coastal areas and to support evidence-based assessments and management decisions for preserving marine ecosystems.

This dataset documents the epifauna occurrences collected from 2021 to 2024 during the Canadian Beaufort Sea Marine Ecosystem Assessment (CBS-MEA) conducted by the Department of Fisheries and Oceans (DFO). This scientific program focuses on the integration of oceanography, food web linkages, physical-biological couplings, and spatial and interannual variabilities. The program also aims to expand the baseline coverage of species diversity, abundances, and habitat associations in previously unstudied areas of the Beaufort Sea and Western Canadian Archipelago. The study took place mainly in the Canadian Beaufort Sea and the Amundsen Gulf. Sampling is done along transects at fixed stations in the study area. Catches are collected with a 3 m benthic beam trawl for 10 minutes bottom-contact time at a target speed of 2 knots and with a modified Atlantic Western IIA otter trawl for 20 minutes bottom-contact time at a target speed of 2.9 knots. A total of 32 stations were sampled for epifauna in 2021, 22 in 2022, 23 in 2023 and 22 in 2024, between 22-655 m depth. Epibenthic invertebrates were identified to the lowest taxonomic level possible and photographed. All unknown specimens are frozen. In the lab, the identifications are validated or refined with the photos and the frozen specimens.The data are presented in Darwin Core and are separated in two files:The "Activité_épifaune_CBSMEA_epifauna_event_en" file which contains information about missions, stations and deployments, which are presented under a hierarchical activity structure.The "Occurrence_épifaune_CBSMEA_epifauna_en" file that contains the taxonomic occurrences.

PURPOSE:Provide early detection of newly arrived Aquatic Invasive Species (AIS) and determine the spread, establishment and spatial distribution of existing AIS within marine waters of the southern Gulf of St. Lawrence (sGSL), DFO Gulf Region boundaries (northern and eastern coastal shores of NB, Gulf shore of NS, and PEI shoreline).DESCRIPTION:DFO Science monitors for AIS in the Gulf Region. The data collected from DFO's biofouling monitoring program provides an overview of the distribution and abundance of Aquatic Invasive Species (AIS) in the Gulf Region. This information can be used by the general public, scientists and DFO managers.Monitoring program targeting aquatic invasive species (AIS). Native biofouling species are not included in this dataset. Botrylloides violaceus: Violet tunicateBotryllus schlosseri: Golden star tunicateCiona intestinalis: Vase tunicateStyela clava: Clubbed tunicateCaprella mutica*: Japanese skeleton shrimpMembranipora membranacea: Coffin box bryozoanCarcinus maenas*: European green crabCodium fragile*: Oyster thief algaJuxtacribrilina mutabilis**: Ribbed bryozoan (JCM)*indicates species that are not included as percent cover as they are not accurately captured by the sampling method, but are included as detections.**indicates species was only integrated fully into the monitoring protocol starting in 2025.Included here is a dataset of detection and percent cover data of AIS, as well as a monitoring station dataset. Environmental data collected, including from temperature loggers, are stored but not included here. PARAMETERS COLLECTED:Air and water temperature, salinity, depth, dissolved oxygen, weather conditions, list of biofouling AIS, percent cover of AIS on PVC plates, and incidental detection of other species and AIS in surrounding area. Only species data is pushed to the Open Data platform.NOTES ON QUALITY CONTROL:Each sample and species is processed and identified in a standardized fashion using standardized DFO Science AIS protocols and taxonomic references. Data is manually entered into DFO Gulf Region's AIS Science biofouling database and randomly verified for accuracy.SAMPLING METHODS:Biofouling monitoring is conducted using PVC collector plates that are deployed in the water column approximately 1 meter below the sea surface in the spring of each year. Biofouling organisms settle on these plates which are collected in the fall of the same year. Abundances of AIS are given as percent plate cover. Physico-chemical data including temperature, conductivity, and depth as well as weather conditions are noted at each geo-referenced biofouling monitoring site during initial deployment and at time of retrieval. All biofouling organisms settled on the underside of the PVC plates are noted and percent cover of each AIS is estimated. Any AIS present at the location is also noted. A HOBO temperature and light logger was deployed.USE LIMITATION:To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

This record contains data on beluga whale locations in the Beaufort Sea and west Amundsen Gulf reported in Harwood, L.A. and P. Norton (1996). Aerial survey data from the southeast Beaufort Sea, Mackenzie River estuary and west. Amundsen Gulf, July 1992. Canadian Data Report of Fisheries and Aquatic Sciences No. 964