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.

During the period of 1987 to 1994, Robin J. LeBrasseur and N. Brent Hargreaves lead a juvenile salmon predation research project in Alberni Inlet and Barkley Sound BC. This dataset contains the research survey catch data and individual fish examinations data.

PURPOSE:To characterize food webs of lake fish communities using stable isotopes, gut content morphology and DNA. DESCRIPTION:Data sets containing fish species caught in Miramichi Lake, McKiel Lake and Nashwaak Lake. USE LIMITATION:To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

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

Catch, effort, location (latitude, longitude), relative abundance indices, and associated biological data from groundfish multi-species bottom trawl surveys in West Coast Haida Gwaii.Introduction The West Coast Haida Gwaii (WCHG) synoptic bottom trawl survey was first conducted annually from 2006 to 2008 and has since been repeated every second year on even numbered years. The survey was not impacted by the COVID-19 pandemic. This survey is one of a set of long-term and coordinated surveys that together cover the continental shelf and upper slope of most of the British Columbia coast. The other surveys are the Queen Charlotte Sound (QCS) survey, the Hecate Strait (HS) survey, the West Coast Vancouver Island (WCVI) survey, and the Strait of Georgia (SOG) survey. The objectives of these surveys are to provide fishery independent abundance indices of all demersal fish species available to bottom trawling and to collect biological samples of selected species. The survey follows a random depth-stratified design and the sampling units are 2 km by 2 km blocks. The synoptic bottom trawl surveys are conducted by Fisheries and Oceans Canada (DFO) in collaboration with the Canadian Groundfish Research and Conservation Society (CGRCS), a non-profit society composed of participants in the British Columbia commercial groundfish trawl fishery. The Queen Charlotte Sound and West Coast Haida Gwaii surveys are conducted under collaborative agreements, with the CGRCS providing chartered commercial fishing vessels and field technicians, while DFO provides in-kind contributions for running the surveys including personnel and equipment. The Hecate Strait, West Coast Vancouver Island, and Strait of Georgia surveys are conducted by DFO and have typically taken place on a Canadian Coast Guard research vessel. Until 2016 this vessel was the CCGS W.E. Ricker. From 2021 onwards, this vessel was the CCGS Sir John Franklin. In years when a coast guard vessel has not been available, the Hecate Strait, West Coast Vancouver Island, and Strait of Georgia surveys have taken place on chartered industry vessels. Data from these surveys are also presented in the groundfish data synopsis report (Anderson et al. 2019).EffortThis table contains information about the survey trips and fishing events (trawl tows/sets) that are part of this survey series. Trip-level information includes the year the survey took place, a unique trip identifier, the vessel that conducted the survey, and the trip start and end dates (the dates the vessel was away from the dock conducting the survey). Set-level information includes the date, time, location, and depth that fishing took place, as well as information that can be used to calculate fishing effort (duration) and swept area. All successful fishing events are included, regardless of what was caught.CatchThis table contains the catch information from successful fishing events. Catches are identified to species or to the lowest taxonomic level possible. Most catches are weighed, but some are too small (“trace” amounts) or too large (e.g. very large Big Skate). The unique trip identifier and set number are included so that catches can be related to the fishing event information (including capture location).BiologyThis table contains the available biological data for catches which were sampled. Data may include any or all of length, sex, weight, age. Different length types are measured depending on the species. Age structures are collected when possible for species where validated aging methods exist and are archived until required for an assessment; therefore, all existing structures have not been aged at this time. The unique trip identifier and set number are included so that samples can be related to the fishing event and catch information.BiomassThis table contains relative biomass indices of species that have been captured in every survey of the time series. The coefficient of variation and bootstrapped 95% confidence intervals are provided for each index. The groundfish data synopsis report (Anderson et al. 2019) provides an explanation of how the relative biomass indices are derived. Note that we do not calculate a biomass index for the 2014 West Coast Haida Gwaii survey, as this survey was incomplete due to operational problems.

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

The Fish Pathology Program (FPP) located at the Pacific Biological Station in Nanaimo has been assessing the health of aquatic animals since the early 1970’s. Utilizing traditional diagnostic methods, the FPP has supported internal and external clients to provide clinical data and management advice on the health of aquatic animals. The dataset contains information from diagnostic fish health cases coming from the Salmonid Enhancement Program, Research, Public and I&T submissions. Data contained in the database includes pathogen findings from submitted cases from all of the Pacific Region.The publication of The Fish Health Database will comply with public release recommendations documented in recommendation twenty two, made in volume three of the Final Report (October 2012) submitted by the Cohen Commission of Inquiry into the Decline of the Sockeye Salmon in the Fraser River.

Since 1991, an annual fishery-independent acoustic survey of early fall (September-October) concentrations of Herring has been conducted in the sGSL. The standard annual survey area occurs in the 4Tmno areas where both NAFO Div. 4T Herring spawning components aggregate in the fall. The survey uses a random stratified design of parallel transects within predefined strata. Surveys are conducted at night and use two vessels: an acoustic vessel to quantify the fish schools biomass using a hull-mounted 120 KHz split-beam transducer, and a fishing vessel to sample aggregates of fish with a pelagic trawl (details in LeBlanc et al. 2015; see also LeBlanc and Dale 1996).Trawl samples are used to separate the estimated biomass by spawning component and age, determine species composition, and size distribution for the estimation of the target strength (LeBlanc and Dale 1996; LeBlanc et al. 2015).A standardized abundance index is generated from this acoustic survey. This index includes catch-at-age data since 1994.This survey also provides the age-disaggregated acoustic abundance index for ages 2 to 10 for spring spawners and fall spawners.

The contaminants in fish database is a compilation of contaminant data analysed from fish tissue at the Fresh Water Institute from 1970 to 2005. Data include lab number, region, analysis, organs, species, lake, form (whole fish, headon dressed, headless dressed), weight, and length and contaminant concentrations. Total mercury was the predominant contaminant measured. Results were expressed as ppm or ppb based on the parameter analyzed. Concentrations are expressed based on wet weight.

The Great Lakes Fish Biodiversity Science Database is a compilation of fish community and habitat data from DFO Science surveys, primarily related to freshwater fishes of conservation concern in the Great Lakes basin. Data include: sampling site location, date, fish species and counts, and associated habitat information. Project-specific details including purpose/objectives and study methodology are often reported in the DFO Canadian data report of fisheries and aquatic sciences series.