An exploratory project on the taxonomic and genetic diversity of decapods in three ocean subregions (Northeast Pacific, Canadian Arctic, and Northwest Atlantic), which were sampled in 2022, was undertaken by the Arctic Working Group under the Canada-U.S. Fisheries and Climate Collaboration between Fisheries and Oceans Canada (DFO) and the National Marine Fisheries Service (NMFS) of the National Oceanic and Atmospheric Administration (NOAA). This collaboration framework aims to pool Canadian and U.S. data to explore the impacts of broad-scale climate change on marine biodiversity. In early summer 2022, a sampling protocol with the selection of targeted decapods was provided to DFO and NOAA collaborators. Targeted genera were collected from a total of 10 research programs across three ocean subregions and four marine regions. The Northeast Pacific samples were collected in the Bering Sea during the Northern Bering Sea Ecosystem and Surface Trawl Survey, and the Eastern and Northern Bering Sea Continental Shelf Bottom Trawl Survey of Groundfish and Invertebrate Fauna onboard the F/V Northwest Explorer, F/V Alaska Knight and F/V Vesteraalen. In the Western Canadian Arctic (mainly from Beaufort Sea and Amundsen Gulf), specimens were collected during DFO’s Canadian Beaufort Sea – Marine Ecosystem Assessment (CBS-MEA) survey onboard the F/V Frosti. In Eastern Canadian Arctic (mainly from Baffin Bay and Davis Strait), specimens were collected during DFO’s Knowledge and Ecosystem-Based Approach in Baffin Bay (KEBABB) survey onboard the CCGS Amundsen and DFO’s North Atlantic Fisheries Organization (NAFO) Subarea 0B survey onboard the R/V Tarajoq. In the Estuary and Gulf of St. Lawrence (EGSL), specimens were collected from coastal surveys (scallops, sea cucumber, snow crab, and whelk surveys) onboard the CCGS Leim and offshore during the Ecosystemic Survey onboard the CCGS Teleost. Decapods were collected from various sampling gears (benthic beam trawl, modified Atlantic Western IIA otter trawl, Bacalao trawl, shrimp trawl, Digby scallop dredge, or modified sea cucumber dredge) and identified to the lowest possible taxonomic level and photographed, when possible. All specimens were frozen at sea (n = 995). In the lab, the identifications were validated or refined with the photos and the frozen specimens. DNA was extracted for 87 specimens and a section of COI gene was amplified in order to be sequenced using Sanger method. Sequences were compared with existing data using The Basic Local Alignment Search Tool (BLAST) in the National Center for Bio-technology Information Nucleotide database (NCBI-nt, including the GenBank database) to compare scientific names, where available.The present dataset includes 391 decapod species occurrences. DNA was extracted for a subset of 87 specimens (COI gene); sequences are publicly available on BOLD data portal under project code DDAO (see supporting document "citations_references.csv" for more information).The data are presented in Darwin Core format and are separated in three files:The "Activité_décapodes_DDAO_decapods_event_en" file contains information about missions, stations and deployments, which are presented under a hierarchical activity structure.The "Occurrence_décapodes_DDAO_decapods_en" file contains the taxonomic occurrences.The "ADN_décapodes_DDAO_decapods_DNA_en" file contains the DNA derived data.For further details, please refer to the technical report available in the supporting document named "citations_references.csv". USE LIMITATION:To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

Monthly mean temperature from Bedford Institute of Oceanography North Atlantic Model (BNAM) results were averaged over 1990 to 2015 period to create monthly mean climatology for the Northwest Atlantic Ocean, which can be considered as a representation of the climatological state of the Northwest Atlantic Ocean. The BNAM model is eddy-resolving, NEMO-based ice-ocean coupled North Atlantic Ocean model developed at the Bedford Institute of Oceanography (BIO) to support DFO monitoring programs. The data available here is monthly climatology for eight selected depths (surface, 110 m, 156 m, 222 m, 318 m, 541 m, 1062 m, bottom) in 1/12 degree spatial resolution. The data for each month from 1990 until present for the entire model domain ( 8°–75°N latitude and 100°W–30°E longitude) and various depths is available upon request.The 1990-2017 model hindcast result is compared with observational data from surface drifter and satellite altimetry. The model demonstrates good skill in simulating surface currents, winter convection events in the Labrador Sea, and the Atlantic Meridional Overturning Circulation as observed at 26.5°N and 41°N. Model results have been used to interpret changes in the Labrador Current and observed warming events on the Scotian Shelf, and are reported through the annual AZMP Canadian Science Advisory Secretariat Process.When using data please cite following:Wang, Z., Lu, Y., Greenan, B., Brickman, D., and DeTracey, B., 2018. BNAM: An eddy resolving North Atlantic Ocean model to support ocean monitoring. Can. Tech. Rep. Hydrogr. Ocean. Sci. 327: vii + 18p

In 2018, Fisheries and Oceans Canada initiated the Multidisciplinary Arctic Program (MAP) – Last Ice, the first ecosystem study of the poorly characterized region of Tuvaijuittuq, where multiyear ice still resides in the Arctic Ocean. The program MAP-Last Ice takes a coordinated approach to integrate the physical, biochemical, and ecological components of the sea ice-ocean connected ecosystem and its response to climate and ocean forcings. This program provides baseline ecological knowledge for Tuvaijuittuq and, in particular, for its unique multiyear ice ecosystem. The database provides baseline data on fatty acid composition and stable isotopes signatures of sea ice communities in multi- and first-year ice in Tuvaijuittuq. The data were collected during the 2018 spring field campaign of the MAP-Last Ice Program, offshore of Canadian Forces Station (CFS) Alert, in the Lincoln Sea.

Cold-water corals are conspicuous in the waters off Eastern Canada. Despite that, there are few DNA sequence records from specimens collected in the region available in GenBank, and not all species recorded in the region have sequence data regardless of geographic origin. This can limit the use of eDNA techniques to detect and identify corals. Our objective was to sequence and publish sequences for two octocoral DNA barcoding markers: CO1 and MutS. We sequenced and deposited 36 sequences to GenBank from 19 specimens representing three sea pen taxa (Octocorallia: Pennatuloidea): Distichoptilum gracile, Pennatula aculeata, and Protoptilum carpenteri. Identification of all specimens was confirmed by B. M. Neves before submission. Specimens and DNA tissues were donated to the Canadian Museum of Nature, where they are currently stored. This publication is part 1 of a series of GenBank submissions by our lab.Specimens were collected from across the Northwest Atlantic and originate from depths ranging between 200-1924 meters. Specimens were collected as part of research vessel multispecies trawl surveys or remotely operated vehicle (ROV ROPOS) surveys. DNA was isolated and purified using the QIAgen DNeasy Blood and Tissue kit, with an initial overnight incubation with Proteinase K. Two commonly used octocoral barcoding regions were amplified using previously described primers: 1) COII8068F (McFadden et al., 2004) and COIOCTR (France and Hoover, 2002) for the CO1 gene, and 2) ND42599F (France and Hoover, 2002) and mut3458R (Sánchez et al., 2003) for the MutS gene. Amplifications were conducted using 12.5 µl of Green DreamTaq Master Mix (Thermo Fisher Scientific), 1 µl of template DNA, 0.5 µl of each 10 µM forward and reverse primers, 0.5 µl of 10 µM reverse primer, and 10.5 µl of water. Thermocycling was run as follows: 3 min of initial denaturation at 95 °C, followed by 40 cycles at 95 °C for 30 s, 30 s at annealing temperature of 48 °C, then 65 s at an extension temperature of 72 °C, and a final elongation at 72 °C for 4 min. PCR products were cleaned using Agencourt AMPure XP Beads (Beckman Coulter) and sent to The Center for Advanced Genomics, Toronto, Canada for Sanger sequencing. Sequences were visualized and aligned using Geneious Prime 2022.0.2. Obtained sequences have been deposited in GenBank under accession numbers OQ569768- OQ569784 and OQ420359- OQ420377. This work was funded by Fisheries and Oceans Canada under an Enhanced Regional Capacity grant (2020-2021) and the Marine Conservation Targets (MCT) program (2021-2024), Newfoundland and Labrador Region.

A compendium of reports that provide information about aquatic and terrestrial animals and plants, soils, surface water, groundwater and their accompanying data files and maps

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

Fisheries and Oceans Canada (DFO) conducts an annual summer multidisciplinary scientific survey with a bottom trawl in the Estuary and the northern Gulf of St. Lawrence since 1984. Over the years, this survey has been conducted on four vessels: the MV Lady Hammond (1984-1990), the CCGS Alfred Needler (1990-2005), the CCGS Teleost (2004-2021) and the CCGS Cabot (2022-current). It is important to note that the objectives, the methods used and the identification of the species during these surveys have improved over time in response to DFO requests and mandates. The data are therefore not directly comparable between these surveys. The specificities of the missions onboard the MV Lady Hammond are described below.Objectives:1. Assess groundfish populations abundance and condition2. Assess environmental conditions3. Conduct a biodiversity inventory of benthic and demersal megafauna4. Monitor the pelagic ecosystem5. Collect samples for various research projectsSurvey descriptionThe survey covers the northern Gulf of St. Lawrence, that is the divisions 4R, 4S and the northern part of division 4T of the Northwest Atlantic Fisheries Organization (NAFO). A stratified random sampling strategy is used for this survey and the fishing gear used on the MV Lady Hammond is a bottom trawl Western IIA. Standard trawling tows last 30 minutes, starting from the time the trawl touches the sea floor. Towing speed is 3.5 knots.DataFor each fishing tow, the catch is sorted and weighed by taxa; individuals are counted and biological data are collected on a sub-sample. For fish, crab and squid, size and weight are measured by individual and, for some species, sex, gonad maturity, and the weight of certain organs (stomach, liver, gonads) are also evaluated. The soft rays of the anal fin are counted for redfish and otoliths are collected for redfish and Atlantic cod. Invertebrates are weighted and counted (no individual measurements).The biological data are divided into 4 files: a “Metadata” file containing set information, a “Catches” file containing catches per set for fish taxa, a “Carbio” file containing biological and morphometric measurements per individual and a “Freql” file containing the length frequency of fish. It's important to note that this is raw data. Only sets considered successful are retained. In each set, all species are kept, with a few exceptions. For more information please contact the data management team (gddaiss-dmsaisb@dfo-mpo.gc.ca).

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.

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.

The purpose of this study was to characterize the kelp bed at Batture-aux-Alouettes, a preferred food source for the green sea urchin (Strongylocentrotus droebachiensis). The green urchin is fished commercially in Quebec and the fishing effort is concentrated on the Batture-aux-Alouettes near Tadoussac, at the mouth of the Saguenay Fjord. The study was conducted in two separate phases in 2018 and 2019. The main objective of this study was to determine the abundance and biomass of the kelp bed at Batture-aux-Alouettes. The first phase, using a stratified random sampling design, was conducted from August 21th to August 24th, 2018. Sampling of two 50 x 50 cm quadrats, separated by a distance of approximately 30 m, was conducted at eleven sites during twelve dives in the eastern section of the Batture-aux-Alouettes to collect kelp for biomass estimation and macroalgal species richness assessment. In the second phase, a total of 429 stations were first sampled between July 15 and 18, 2019 with a camera system dropped in two 50 x 50 cm quadrats. The presence or absence of kelp, percent macroalgal cover, and substrate type were assessed for each photo. As a result of this underwater photographic analysis, 129 of these stations were identified as having a presence of kelp and 88 of these stations had a presence of other algal species. To ensure equal representation of the different depth strata, the stations with kelp were divided into three depth categories: shallow (-1.7 m to 0 m), medium (0 m to 2 m) and deep (2 m to 5 m). Dives were conducted from August 13 to 15, 2019, at ten of these stations using a stratified random sampling design, taking care to ensure a balanced spatial distribution as well as an equal distribution of the different depth strata (four in the shallow, three in the medium, and two in the deep). Sampling of the 50 x 50 cm dive quadrat took place at three different distances spaced 5 m apart from a transect, i.e. at the 3 m (_3m), 8 m (_8m) and 13 m (_13m) mark. If there was little or no kelp in the quadrat, the quadrat sampling could be repeated for up to four quadrats per distance for a total area of 1 m². Two additional quadrats were conducted (_x) at two stations. Biomass assessment was also done via "cookie cutter" sampling (_CC). Divers took the same 50 x 50 cm quadrat and placed it on a selected (i.e., non-random) plot with 100% kelp cover.The three files provided (DarwinCore format) are complementary and are linked by the "eventID" key. The "event_information" file includes generic information about the event, such as date and location. The "additional_information_event_and_occurrence" file includes sample size, protocol and sampling effort. The "taxon_occurrence" file includes the taxonomy of the species observed, identified to the species or lowest possible taxonomic level. To obtain the abundance and biomass assessment of the kelp bed at Batture-aux-Alouettes, contact Rénald Belley (renald.belley@dfo-mpo.gc.ca).For quality control, the organisms were identified in the field fallowing the guide: Chabot, Robert et Anne Rossignol. 2003. Algues et faune du littoral du Saint-Laurent maritime : Guide d'identification. Institut des Sciences de la mer de Rimouski, Rimouski; Pêches et Océans Canada (Institut Maurice-Lamontagne), Mont-Joli. 113 pages. The taxonomy was checked against the World Register of Marine Species (WoRMS) to match recognized standards and using the R obistools and worrms libraries. The WoRMS match was placed in the "scientificNameID" field of the occurrence file. All sample 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.