AndreaBozzo/ceres-open-data-index huggingface dataset:
The fate of intracoelomic acoustic transmitters in Atlantic Salmon (Salmo salar) post-smolts and wider considerations for causal factors driving tag retention and mortality in fishes

Acoustic telemetry is a widely used method in assaying behavioural dynamics in fishes. Telemetry tags are often surgically implanted in the coelom of the animal and are assumed to have minimal rates of post-release mortality and tag shedding. However, fish are capable expelling tags and mortalities do occur following release, with the mechanism(s) underlying these effects not well understood. The purpose of this research was to address causal factors underlying tagging mortality and tag expulsion in fishes. We conducted an empirical assessment of tag retention and post-surgical mortality rates in post-smolt Atlantic salmon (Salmo salar) fitted with a dummy acoustic tag over a 92 day monitoring period. This was complimented with a meta-analysis of factors affecting tag retention and post-surgical mortality rates in the wider literature. Post-smolt salmon exhibited low rates of mortality following tag implantation (≤ 5.1%) but had high rates of tag expulsion (54.8%) and impaired growth and a foreign body response was evident. The meta-analysis showed that mortality was generally low across all studies (12.4%) and was largely unaffected by model cofactors. Tag retention rates were high among the studies investigated here (86.7%) and had a weak negative relationship with tag: body mass ratios. Our results suggest that while mortality is often low among tagging studies, including this one, caution must be exercised in assessing stationary tags as they may represent an expelled tag rather than a mortality event. Our results also indicate that tag dimensions are not nearly important as the tag: body mass ratio.

Lawrence, M.J., Wilson, B.M., Reid, G.K. et al. The fate of intracoelomic acoustic transmitters in Atlantic salmon (Salmo salar) post-smolts and wider considerations for causal factors driving tag retention and mortality in fishes. Anim Biotelemetry 11, 40 (2023). https://doi.org/10.1186/s40317-023-00351-0

Cite this data as: Lawrence, M.J., Wilson, B.M., Reid, G.K., Hawthorn, C., English. G, Black, M, Leadbeater, S., McKindsey, C.W., Trudel, M.  The fate of intracoelomic acoustic transmitters in Atlantic Salmon (Salmo salar) post-smolts and wider considerations for casual factors driving tag retention and mortality in fishes. Published October 2023. Coastal Ecosystem Science Division, Fisheries and Oceans Canada, St Andrews, NB.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Salmonid Enhancement Program (SEP) Post-Season Report Archive

The data tables for post-season production list proposed release targets and the production that actually took place for that brood year. They address production from SEP licensed facilities only, and do not contain production of steelhead or cutthroat which are provincially managed.

Post-Season Reports from brood year 2014-2019 include fry releases and in-season on hand smolt counts. Smolt release numbers were not published for those years.

Discrepancies between planned releases and actual releases may exist due to the inability to achieve target broodstock due to factors such as:

•	low escapement

•	logistical issues

•	environmental conditions such as high water levels

Discrepancies between the release target and actual release may also be caused by higher than expected survival during incubation and rearing.

Discrepancies where there is a target but no associated release may also be due to the use of an approved alternate, or “back-up” release strategy. Alternate release strategies may happen if the primary release strategy cannot be used due to common causes such as:

•	the inability to collect primary broodstock (see reasons above)

•	facility rearing capacity or logistical issues, resulting in a change in release stage

•	inaccessibility to primary release sites, resulting in releases to nearby sites

Some SEP licensed facilities also rear provincially managed Steelhead and Cutthroat Trout at the request of the Province. For more information regarding the hatchery enhancement of these species please contact the BC Ministry of Forests, Lands and Natural Resource Operations: https://www.env.gov.bc.ca/fw/contact/

This Open Data page includes the final version of the Post-Season Report as they were published for IFMP review. This site will be updated each year with the new final version of the report from two brood cycles previous.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Conceptual models of major ecosystems in Canada’s Pacific Ocean

Graphic illustrations of the major ecosystems in the Pacific region, including details on the main ecological components, key ecological interactions, environmental drivers, and relevant human activities.  Ecosystems range from the intertidal to the deep sea and include: High and low energy rocky shores, High and low energy soft shores, Rocky and soft bottom subtidal, Pelagic, Estuaries, Fjords, Hydrothermal vents, Seamounts, Bathyal plains, and Cold seeps.

See Jeffery et al. (2023) for details: https://publications.gc.ca/site/eng/9.925084/publication.html?wbdisable=true.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Escapes of cultured finfish from BC aquaculture sites

Fisheries and Oceans Canada’s (DFO’s) Pacific Aquaculture Regulations and Conditions of Licence for aquaculture in B.C. require licence holders to take various fish escape prevention measures, including maintaining infrastructure in a manner to prevent the escape of farmed fish into the environment as well as responding to remedy the cause of the escape as soon as possible. 

When there is evidence that an escape event has occurred, licence holders must report the incident to the department within 24 hours either through the Observe Record and Report Line (ORR 1-800-465-4336), or to a dedicated email mailbox, detailing the cause, time and location of the event and the species, size and number of fish involved. The licence holder must also provide fish health information about the stock, such as exposure to therapeutants. A more detailed written report is then submitted to the department within seven days.

DFO monitors BC waters for escaped Atlantic salmon through the Atlantic Salmon Watch Program (ASWP), which relies on voluntary reports from fish harvesters. A summary of [reports made to the ASWP](https://open.canada.ca/data/en/dataset/f0299fb3-73b9-4977-b96a-c83bd84ebdc4 "reports made to the ASWP") since July 2005 is available.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Canadian Atlantic Shelf Temperature-Salinity (CASTS)

The Canadian Atlantic Shelf Temperature-Salinity (CASTS) data product includes most of the historical temperature and salinity profiles collected in Atlantic Canada and the Eastern Arctic since 1873. CASTS consists of approximately 837,000 individual profiles, bin-averaged to varying resolutions up to a maximum of 5000m (1m resolution up to 1000m depth, 10m resolution up to 2000m depth, and 100m up to 5000m depth). Profile locations were restricted between 35-80 degrees North and 100-42 degrees West. Profiles were gathered from January 1873 to December 2024 and are organized into yearly NetCDF files. Profiles are uniformly formatted and quality controlled allowing users to immediately use the data product. Data fused to make this product were gathered from multiple sources, including regional archives at the Maurice-Lamontagne Institute (DFO-QC), the Bedford Institute of Oceanography (DFO-MAR) and the Northwest Atlantic Fisheries Centre (DFO-NL). Other sources of data include DFO-NL Aquaculture, the Marine Institute of Memorial University of Newfoundland, data from from international ships of opportunity archived by MEDS, the Polar Data Catalogue, etc. A complete list of sources is included in the README file.


Coyne, J., Cyr, F., Donnet, S., Galbraith, P., Geoffroy, M., Hebert, D., Layton, C., Ratsimandresy, A., Snook, S., Soontiens, N., Walkusz, W. (2023). Canadian Atlantic Shelf Temperature-Salinity (CASTS). Federated Research Data Repository. 


https://doi.org/10.20383/103.01191

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Beach Emergence Data - Capelin

Beach emergence data samples consist of capelin larvae only. These samples are extracted from various beach sites at high tidal conditions, using a modified beach seine with a plankton net fitting that was towed for 40 m along the beach edge. Data series is from 1990-2012. See Nakashima and Mowbray (2014) DFO Can Sci Advis Sec Res Doc 2013/091 v+27 p. for details.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Temporal declines in fecundity: A study of southern Gulf of St. Lawrence Atlantic herring (Clupea harengus) and implications for potential reproductive output

PURPOSE:
This data set was used to examine temporal changes in 4TVn Atlantic Herring fecundity.
            
DESCRIPTION:
This data set holds 4TVn Atlantic Herring fecundity data collected in the early 1970s, 1980s and 2022.  We used the data to examine the temporal declines in fecundity over the 3 time periods and estimated size-fecundity relationships for each spawning component in the 1970s and 2022. 
            
USE LIMITATION:
To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
PBDEs and emerging flame retardants in belugas (Delphinapterus leucas) and minke whales (Balaenoptera acutorostrata) from the St. Lawrence Estuary (Canada) and Canadian Arctic belugas

The endangered St. Lawrence Estuary (SLE) beluga population is in decline despite multiple protection measures and exposure to organohalogen contaminants have been proposed as an explanation for its lack of recovery. Elevated levels of halogenated flame retardants (HFR) were indeed observed in SLE beluga tissues during the 1990s. The objective of this dataset was to investigate the occurrence of HFRs (35 PBDE congeners and 13 emerging compounds) in the blubber of belugas (Delphinapterus leucas) and minke whales (Balaenoptera acutorostrata) from the St. Lawrence as well as belugas from Nunavik where the species is targeted by Inuit subsistence hunt.

Methods of sample and data collection were detailed in Simond et al. (2017, http://dx.doi.org/10.1016/j.envres.2017.03.058). In summary, tissue samples (blubber and skin) from the St. Lawrence region were collected on fresh beluga and minke whale carcasses stranded ashore. Tissue samples from Nunavik region were collected on beluga carcasses landed during Inuit subsistence hunt. The age of belugas was determined according to Stewart et al. (2006). Sample extraction and clean-up and HFR concentration measurements were conducted following Houde et al. (2014). HFR concentrations are reported in ng/g lipid weight. 

This dataset contains sex and age, body length, percentage of extractable lipids, an index of carcass freshness, d13C and d15N measured in skin (lipid-extracted and bulk samples, respectively), and the concentration of polybrominated and emerging flame retardants measured in blubber. The sample consists of 51 male belugas and 12 minke whales (2 males, 6 females, 4 unknown) from the St. Lawrence and 6 male belugas from Nunavik. Sample collection spans from 1997 to 2014. 

Quality control procedures included analyses of procedural method blanks, duplicate blubber samples and standard reference materials (SRM; NIST 1945 Whale Blubber) for each batch of ten samples.

The contact for the main co-authors of Simond et al. (2017, http://dx.doi.org/10.1016/j.envres.2017.03.058) are included in the file "Authors_contact_auteurs.pdf"

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Guide on best practices for seaweed harvesting in Quebec

This guide was developped for seaweed harvesters and anyone wishing to deepen their knowledge on seaweed harvesting practices. It promotes sustainable seaweed management in Quebec in the maritime zone illustrated in turquoise on the map. This guide is based on a literature review adressing seaweed harvesting conditions of multiple species harvested in Quebec and in similar climatic regions (Roy et al. 2025, in preparation). This guide aims to raise awareness on the importance of sustainable seaweed harvesting, with a focus on harvesting techniques respecting seaweed ecosystems. It is important to note that this guide is intended to serve as an informative resource promoting appropriate seaweed harvesting practices. However, it does not constitute an official regulation. The recommendations are designed to complement and not to replace existing regulations.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
South Coast Area BC Chinook Reference Fishery Biological Data

The Chinook Reference Fishery is a Pacific Salmon Strategy Initiative (PSSI)-funded, multi-year monitoring program initiated in 2023 to assess Chinook Salmon catch in South Coast BC Chinook mark-selective fisheries (MSFs). The objective of the program is to estimate the proportion of Chinook caught and released at sea (by size class), the mark rate (i.e., the proportion of hatchery-marked Chinook encountered), and the stock composition of sampled fish. Reference Fishery data will be used to evaluate the fishery-dependent estimates produced from the South Coast Area recreational catch monitoring (creel) program. This dataset contains detailed information for each Chinook Salmon sampled during the reference fishery. 

Each record includes: the catch date, which is the date the fish was sampled, and the creel sub-area, identifying the geographic location where the fish was caught. The adipose fin clipped field indicates whether the fish had a clipped adipose fin (“Y” for clipped, “N” for intact). The length (cm) column provides the fork length of the fish, measured from the tip of the nose to the fork in the tail. Genetic stock identification reported at both fine and broad spatial scales. 

The “DNA Stock X” columns represents the stock-level scale. Each fish may have up to five individual stock-level assignments based on DNA analysis, ranked from highest to lowest probability. The DNA Stock 1 column lists the most likely stock assignment—typically at the river or hatchery level—along with its associated DNA Stock Region 1, and the corresponding Probability 1, which indicates the likelihood of that assignment being correct. Similarly, DNA Stock 2, DNA Stock Region 2, and Probability 2 report the second most likely assignment and so on, down to DNA Stock 5, DNA Stock Region 5, and Probability 5. 

The “resolved stock region” represents the broader stock region and aligns closely with Canada's Stock Management Units (SMUs), which are used in salmon Integrated Fisheries Management Plans (IFMPs) and is the most appropriate for identifying stocks of concern. The “resolved stock region” is determined by summing the probability of all DNA stock assessments that corresponds to the same region. The region with the highest summed probability becomes the “resolved stock region”. The “resolved stock region probability” is the summed probability of all DNA stock Region assignments that correspond to this “resolved stock region”, providing a quantitative measure of confidence in the regional assignment. 

In cases where Probability 1 equals 1 and all subsequent probabilities are “NA,” the stock assignment was made deterministically through parentage-based tagging rather than statistical inference and therefore carries no associated uncertainty.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Ecological Risk Assessment Framework (ERAF) feasibility and suitability evaluation based on a subset of Significant Ecological Components (SEC) from the Hecate Strait - Queen Charlotte Sound Glass Sponge Reefs Marine Protected Area (HS-QCS MPA).

The Pacific Region ERAF provides a comprehensive approach for assessing all threats to marine ecosystems by evaluating cumulative risk from multiple activities to multiple ecosystem components for ecosystem-based management (EBM), improving upon international and national best practices in risk assessment that focus solely on single activities (e.g., ERAFs for assessing fisheries impacts) or single ecosystem-components (e.g., habitat-based risk assessments). This project applies the Level 2 Risk Assessment framework (O et al. 2015) to the Hecate Strait - Queen Charlotte Sound Glass Sponge Reefs Marine Protected Area (HS-QCS MPA) to determine the relative risk to the HS-QCS MPA ecosystem from anthropogenic activities.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Canadian Science Advisory Secretariat Habitat Status Reports

This series reports on human activities that may impact aquatic ecosystems or components of those ecosystems, including the nature of the activities, their extent, their interactions with ecosystem components, and interactions with other human activities on the same areas. Generally, the effects of fisheries on fish stocks were reported in the Stock Status Report series, with regard to their effects on the dynamics of the targeted stocks or bycatch. However, some types of fishing effects were more appropriately included in the HSR series.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Maritimes Regional Application of the National Framework for Assessing the Vulnerability of Biological Components to Ship-Source Oil Spills in the Marine Environment

An important contribution to fulfilling Fisheries and Oceans Canada (DFO) commitment in oil spill response planning was the development of a framework for the rapid assessment of vulnerability of marine biological components to ship-source oil spills that fall under the DFO mandate, contributing to the ecological aspects of the ‘Resources at Risk’ component of oil spill planning and response. A National framework, developed in 2017 (Thornborough et al. 2017) – uses a structured approach for assessing and screening biological components expected to be most affected by a ship-source oil spill, utilizing a suite of criteria to assess vulnerability. 

The framework identified two key phases for assessing vulnerabilities of marine components: 

1. Grouping of biological components (sub-groups) based upon shared characteristics related to oil vulnerability; and 
2. Scoring of biological sub-groups against ecological vulnerability criteria (Exposure, Sensitivity, and Recovery) to identify those most vulnerable to oil using a binary scoring system. 

For validation purposes, the National framework stressed the need to apply and test the framework in a variety of marine aquatic environments across Canada. This research document describes how the National framework was used in the Maritimes Region, to: 

1. Adapt the National framework to create appropriate sub-groups for Maritimes Region biota; 
2. Apply the National scoring criteria to Maritimes Region sub-groups, adapting scoring criteria where necessary; and 
3. Develop a rank list of sub-groups most vulnerable to a ship-source oil spill in the Maritimes Region. 

The vulnerability results from the application of the National framework in the Maritimes Region will help identify marine sub-groups that are most vulnerable to oil and will be used to inform oil spill response strategies in an effort to manage and limit the impacts of oil spills in the Region.


Cite this data as: Lander, T., Hamer, A., Merritt, V., Jones, O. and Harvey, C. 2024. Maritimes Regional Application of the National Framework for Assessing the Vulnerability of Biological Components to Ship-Source Oil Spills in the Marine Environment. DFO Can. Sci. Advis. Sec. Res. Doc. 2024/068. vii + 230 p.

For additional information please see:

DFO. 2024. Maritimes Regional Application of the National Framework for Assessing the 
Vulnerability of Biological Components to Ship-Source Oil Spills in the Marine Environment. 
DFO Can. Sci. Advis. Sec. Sci. Advis. Rep. 2024/052. https://www.dfo-mpo.gc.ca/csas-sccs/Publications/SAR-AS/2024/2024_052-eng.html

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Eelgrass (Zostera marina) study in the historical goldmining region of Goldboro, Nova Scotia (2020)

Nearshore marine construction activities often involve projects conducted directly in or adjacent to eelgrass beds and can have detrimental effects on eelgrass health, through physical destruction of beds, smothering of plants by sediment, and light reduction from turbidity. A liquefied natural gas (LNG) marine terminal is proposed to be constructed near Goldboro in Isaacs Harbour on the Eastern shore of Nova Scotia in an area where sediments are contaminated with heavy metals from historical goldmining tailings. We conducted a pre-impact assessment of the eelgrass beds in Isaacs Harbour and in adjacent contaminated and non-contaminated harbours. We used underwater video to precisely map the eelgrass bed in the direct construction footprint in Isaacs Harbour. We surveyed 169 stations along ~40 km of coastline from Wine Harbour to New Harbour to identify eelgrass presence or absence in the nearby region and provide data on the distribution and abundance of other sensitive fish habitat such as kelp and other macrophytes. Sediment samples were collected and analyzed for grain size, organic matter content and heavy metal contamination. We also collected eelgrass plants to assess plant condition using morphological and physiological metrics, and heavy metal contamination in plant tissues. The overall condition of eelgrass plants in the surveyed area fell within the range of healthy plant characteristics (morphometrics and carbohydrates reserves) seen elsewhere along the Atlantic coast. However, a few stations displayed high arsenic and mercury contamination in sediments, which translated in some cases to high contamination in eelgrass rhizomes and leaves. There would be significant risk of impact on benthic habitat and contamination of marine biota from resuspension of sediments during a construction and operation of a ship terminal in Isaacs Harbour. This pre-impact assessment will allow DFO to assess the LNG terminal construction proposal and develop appropriate mitigation and monitoring procedures. Collected data will also be used for habitat-forming species distribution modeling to inform marine spatial and conservation planning.

Vercaemer, B., O’Brien, J. M., Guijarro-Sabaniel, J. and Wong, M. C. 2022. Distribution and condition of eelgrass (Zostera marina) in the historical goldmining region of Goldboro, Nova Scotia. Can. Tech. Rep. Aquat. Sci. 3513: v + 67 p.

Cite this data as: Vercaemer, B., O’Brien, J. M., Guijarro-Sabaniel, J., Wong, M. Data of: Eelgrass (Zostera marina) study in the historical goldmining region of Goldboro, Nova Scotia (2020). Published: February 2023. Coastal Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/ee88aa17-fd30-4d4a-8924-897fd47cf560

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Coastline fetch estimates for Pacific Canada

Fetch is a proxy for wind-wave action and exposure. Estimates of fetch over a total of 39,938 km of the BC coastline were calculated at 50 m intervals, yielding 799,220 near shore fetch points. Fetch was calculated for five regions in Pacific Canada: Haida Gwaii (HG), North and Central Coast (NCC), Queen Charlotte and Johnstone Straits (QCS), Salish Sea (SoG), and West Coast Vancouver Island (WCVI). For all regions, a bearing interval of 5 degrees was used to generate fetch lines for each point along the shoreline, resulting in 72 fetch lines per point. A maximum fetch distance of 200 km was used to ensure the barrier effect of Haida Gwaii was captured.

Supplementary information provided includes the fetch geometry calculator script and user guide (Gregr 2014) and a report on the fetch processing objectives, process, and results (Gregr 2015).

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada