AndreaBozzo/ceres-open-data-index huggingface dataset:
Scientific trawl surveys of American lobster (Homarus americanus) and rock crab (Cancer irroratus) in the Magdalene Island

A research survey on American lobster (Homarus americanus) and rock crab (Cancer irroratus) has been carried out annually on the Magdalen Islands since 1995 to assess the abundance and structure of populations in this area. The survey is carried out during the first two weeks of September and covers the southern part of the Magdalen Islands, from "Baie de Plaisance" to "Grande-Entrée", extending slightly eastwards between "Havre-aux-Maisons" and "Grande-Entrée". The survey lasts 8 to 15 days, depending of the weather conditions, and covers a maximum of 48 stations. Approximately half of the stations are surveyed in duplicate (two tows per station). The tows always cover 500 meters, with a slightly variable trawl opening (as explained above), averaging around 10 meters.

The gear used is a Nephrops trawl, a benthic trawl originally developed for langoustine fishing in Brittany, but slightly modified to target lobster. The trawl is deployed from the CCGS Leim and the harvested organisms are hauled aboard and sorted. Cephalothorax length, sex and shell stage are recorded for all lobsters. This is supplemented by information on reproductive conditions for certain size classes, and dissections of 25 males and 25 females per mission. Rock crabs are also included in the survey and are counted with additional measurements of shell width, sex and shell condition that are recorded on predetermined stations. For other stations individuals data are collected depending on the time available between trawl hauls.

The publication contains 4 files; the "Information_stations" file which contains the data of the stations, the "Data_homard_lobster_survey" file which contains the measurements of each lobster, the "Nombre_crabe_crab_number" file which contains the count of rock crabs, the "Mesure_crabe_crab_measurement" file contains the characteristics measured for each crab. Each of the files can be linked by the "date", "st", "tr" columns. The “bat” column notes the boat code, because the gear is not deployed in the same way on each boat.

*This record consist of raw data and quality has not been verified

Associated species are identified and semi-quantitatively counted directly on the sorting table, and the results are presented in the following publication: https://open.canada.ca/data/en/dataset/99cb7034-f3d5-4da4-a5bc-e81315cfb8eb

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Forecasted Changes in Growth Potential, Egg Survival and Thermal Habitat Suitability for Cod Species in the Northwest Atlantic and Eastern Canadian Arctic

Polar cod (Boreogadus saida), Atlantic cod (Gadus morhua), and Greenland cod (Gadus macrocephalus) are prominent gadid species within the northwest Atlantic Ocean in terms of their ecological and socio-economic importance but it is unclear how climate-induced changes in ocean temperature may alter their distributions by the end of the century (2100). We used physiologically based species distribution models to predict how ocean warming will influence the availability of suitable habitat for early life-stages in these marine gadids. We applied CMIP5 ocean temperature projections to egg survival and juvenile growth models for Polar cod, Atlantic cod, and Greenland cod to create predicted suitability raster surfaces for these metrics across four climatology periods (1981–2005, 2026–2050, 2051–2075, 2076–2100). The analysis focused on the projected changes in temperature in ocean shelf areas where ocean depth is ≤400 m. We created an integrated habitat suitability index by combining the suitability surfaces for egg survival and growth potential to predict areas and periods where thermal conditions were suitable for both life stages. The resulting surfaces indicate that suitable thermal habitat for the juvenile life stages of all three species will shift poleward, but the magnitude of the shift and the overall area of thermally suitable habitat remaining will differ across species and life stages through time. Modelled layers are provided in NetCDF format by metric (egg survival, growth potential, habitat suitability). Data layers for Polar cod, Atlantic cod, and Greenland cod are included within each NetCDF file as variables across time. Note that in this study we refer to Gadus macrocephalus/ogac as Greenland cod since Gadus ogac is thought to be a junior synonym of Gadus macrocephalus (Carr et al., 1999). For more details on the methods and results for this analysis see Cote et al. (2021).

References:

Carr, S. M., Kivlichan, D. S., Pepin, P., & Crutcher, D. C. (1999). Molecular systematics of gadid fishes: implications for the biogeographic origins of Pacific species. Canadian Journal of Zoology, 77(1), 19–26. https://doi.org/10.1139/cjz-77-1-19

Cote, D., Konecny, C. A., Seiden, J., Hauser, T., Kristiansen, T., & Laurel, B. J. (2021). Forecasted Shifts in Thermal Habitat for Cod Species in the Northwest Atlantic and Eastern Canadian Arctic. Frontiers in Marine Science, 8(November), 1–15. https://doi.org/10.3389/fmars.2021.764072

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Fish Habitat Assessment Output from Bay of Quinte Suitability Modelling: High Water Level (75.4m ASL) - Spawning Habitat - Low Vegetation Association Species (All Temperature Windows)

Fish Habitat Assessment Output: 2 of 16

High Water Level (75.4m ASL) - Spawning Habitat - Low Vegetation Association Species (All Temperature Windows)

Habitat suitability was assessed for the Bay of Quinte Area of Concern, at a 3 m grid resolution, using the Habitat Ecosystem Assessment Tool (HEAT), temperature algorithms, vegetation models, and water level input. Habitat classifications were based on three variables: depth (elevation), vegetation, and substrate; and modified by temperature suitabilities. The final suitability maps were based on documented habitat and temperature associations for the fish in the area. Different life stages (spawning requirements, nursery habitat, adult habitat) were modeled for the years of 1972-2011. Suitability values were scaled from 0 (not suitable) to 1 (highly suitable) and converted to suitability classes of very low, low, medium, and high. The final maps for each guild – life stage combination are maximum suitability values from the 39-year period modelled.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Winter surface conditions – Helicopter survey

Mean 2014 to 2023 winter surface conditions in the Estuary and Gulf of St. Lawrence. The survey has been taking place every year in March. Surface conditions are described by temperature, salinity and nutrient concentration (mmol/m3) interpolated on a 10km x 10km grid.

Purpose

Since many years, the Department of Fisheries and Oceans Canada (DFO) has been conducting annual surveys, at different periods of the year, in the Estuary and Gulf of St. Lawrence, each having many objectives including assessment of environmental conditions.

However, these surveys, carried out on vessels, did not cover the winter period. Since 1996, a regional monitoring program, conducted by Maurice-Lamontagne Institute scientists, is taking place in order to fill this gap. The annual helicopter survey is undertaken in the beginning of March to evaluate physical oceanographic conditions of waters up to 200 m and surface water nutrient contains.

These surveys are usually sampled from a Canadian Coast Guard helicopter but from an icebreaker in 2016 and 2017.

Data from regional monitoring programs are combined with the ones from the Atlantic Zone Monitoring Program (AZMP) to produce annual reports (physical, biological and a Zonal Scientific Advice) which are available at the Canadian Science Advisory Secretariat (CSAS), (http://www.dfo-mpo.gc.ca/csas-sccs/index-eng.htm).

Galbraith, P.S., Chassé, J., Caverhill, C., Nicot, P., Gilbert, D., Pettigrew, B., Lefaivre, D., Brickman, D., Devine, L., and Lafleur, C. 2017. Physical Oceanographic Conditions in the Gulf of St. Lawrence in 2016. DFO Can. Sci. Advis. Sec. Res. Doc. 2017/044. v + 91 p.

Devine, L., Scarratt, M., Plourde, S., Galbraith, P.S., Michaud, S., and Lehoux, C. 2017. Chemical and Biological Oceanographic Conditions in the Estuary and Gulf of St. Lawrence during 2015. DFO Can. Sci. Advis. Sec. Res. Doc. 2017/034. v + 48 pp.

Additional Information

Water sampling for nutrient analysis is done from Niskin bottles according to AZMP sampling protocol:

Mitchell, M. R., Harrison, G., Pauley, K., Gagné, A., Maillet, G., and Strain, P. 2002. Atlantic Zonal Monitoring Program sampling protocol. Can. Tech. Rep. Hydrogr. Ocean Sci. 223: iv + 23 pp.

Nitrate titration is carried out according to the following method ((nitrite + nitrate) – nitrite):
 
Nitrite + nitrate: Armstrong, FAJ, CR Stearns, JDH Strickland (1967) The measurement of upwelling and subsequent biological processes by means of the Technicon Autoanalyzer and associated equipment. Deep-Sea Res 14(3) 381-389.

Nitrite: American Public Health Assoc. (1971) Standard Methods for the examination of water and wastewater. 13th edition, pp. 240-243, Washington D.C.

Phosphate: Murphy, J, JP Riley (1962) A modified single solution method for the determination of phosphate in natural waters. Anal Chim. Acta 27 : 30.

Silicate: Strickland, JDH, TR Parsons (1972) A Practical Handbook of Seawater Analysis, second edition. Fish Res Board Can, Bulletin 167, 310 pp.

The surface water temperature and salinity are determined from CTD profiles.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Characteristics of Environmental Data Layers for Use in Species Distribution Modelling in the Maritimes Region

Species distribution models (SDMs) are tools that combine species observations of occurrence, abundance, or biomass with environmental variables to predict the distribution of a species in unsampled locations. To produce accurate predictions of occurrence, abundance or biomass distribution, a wide range of physical and/or biological variables is desirable. Such data is often collected over limited or irregular spatial scales, and require the application of geospatial techniques to produce continuous environmental surfaces that can be used for modelling at all spatial scales. Here we provide a review of 102 environmental data layers that were compiled for the entire spatial extent of Fisheries and Oceans Canada’s (DFO) Maritimes Region. Variables were obtained from a broad range of physical and biological data sources and spatially interpolated using geostatistical methods. For each variable we document the underlying data distribution, provide relevant diagnostics of the interpolation models and an assessment of model performance, and present the final standard error and interpolation surfaces. These layers have been archived in a common (raster) format at the Bedford Institute of Oceanography to facilitate future use. Based on the diagnostic summaries in this report, a subset of these variables has subsequently been used in species distribution models to predict the distribution of deep-water corals, sponges, and other significant benthic taxa in the Maritimes Region.

Cite this data as: Beazley, Lindsay; Guijarro, Javier, Lirette; Camille; Wang, Zeliang; Kenchington, Ellen (2020). Characteristics of Environmental Data Layers for Use in Species Distribution Modelling in the Maritimes Region. Published July 2023. Ocean Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/34a917cb-a0e3-403c-91c7-af3dc20628b1

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Contaminants in fish database

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.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Fish Habitat Assessment Output from Bay of Quinte Suitability Modelling: Average Water Level (75.0m ASL) - Nursery Habitat - High Vegetation Association Species (All Temperature Windows)

Fish Habitat Assessment Output: 11 of 16

Average Water Level (75.0m ASL) - Nursery Habitat - High Vegetation Association Species (All Temperature Windows)

Habitat suitability was assessed for the Bay of Quinte Area of Concern, at a 3 m grid resolution, using the Habitat Ecosystem Assessment Tool (HEAT), temperature algorithms, vegetation models, and water level input. Habitat classifications were based on three variables: depth (elevation), vegetation, and substrate; and modified by temperature suitabilities. The final suitability maps were based on documented habitat and temperature associations for the fish in the area. Different life stages (spawning requirements, nursery habitat, adult habitat) were modeled for the years of 1972-2011. Suitability values were scaled from 0 (not suitable) to 1 (highly suitable) and converted to suitability classes of very low, low, medium, and high. The final maps for each guild – life stage combination are maximum suitability values from the 39-year period modelled.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Fish Habitat Assessment Output from Bay of Quinte Suitability Modelling: High Water Level (75.4m ASL) - Nursery Habitat - Low Vegetation Association Species (All Temperature Windows)

Fish Habitat Assessment Output: 4 of 16

High Water Level (75.4m ASL) - Nursery Habitat - Low Vegetation Association Species (All Temperature Windows)

Habitat suitability was assessed for the Bay of Quinte Area of Concern, at a 3 m grid resolution, using the Habitat Ecosystem Assessment Tool (HEAT), temperature algorithms, vegetation models, and water level input. Habitat classifications were based on three variables: depth (elevation), vegetation, and substrate; and modified by temperature suitabilities. The final suitability maps were based on documented habitat and temperature associations for the fish in the area. Different life stages (spawning requirements, nursery habitat, adult habitat) were modeled for the years of 1972-2011. Suitability values were scaled from 0 (not suitable) to 1 (highly suitable) and converted to suitability classes of very low, low, medium, and high. The final maps for each guild – life stage combination are maximum suitability values from the 39-year period modelled.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Argo Canada

Argo is a key component of the Global Ocean Observing System (GOOS) with an array of about 4,000 autonomous instruments reporting on ocean conditions.  These floats collect data on ocean temperature and salinity, and in some cases, additional properties that characterize the ocean’s biological and chemical processes. Established in 1999,  Argo represents an international collaboration involving contribution from more than 30 nations. 

Data from Argo floats are made publicly available within 24 hours of collection time, for free. The data provide valuable information on changes to the Earth's climate and hydrological cycle. They are used for a variety of purposes, such as assessing climate change, improving weather forecasts and developing ocean models.

Argo Canada, led by Fisheries and Oceans Canada, has been a key contributor to the International Argo Program since its inception in 2001 .  The program has been supported by contributions  from Department of Environment and Climate Change Canada, Department of National Defense, Dalhousie University, University of Victoria and Ocean Networks Canada.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Violet tunicate (Botrylloides violaceus) - Aquatic Invasive Species Program - Newfoundland and Labrador Region

AIS NL Biofouling Species 

Fisheries and Oceans Canada's (DFO) National Marine Biofouling Monitoring Program conducts annual field surveys to monitor the introduction, establishment, spread, species richness, and relative abundance of native and some non-native species in Newfoundland and Labrador (NL) Region since 2006. Standardized monitoring protocols employed by DFO's NL, Maritimes, Gulf, and Quebec regions include biofouling collector plates deployed from May to October at georeferenced intertidal and shallow subtidal sites, including public docks, and public and private marinas and nautical clubs. Initially, (2006-2017), the collectors consisted of three 10 cm by 10 cm PVC plates deployed in a vertical array and spaced approximately 40 cm apart, with the shallowest plate suspended at least 1 m below the surface to sample subtidal and shallow intertidal species (McKenzie et al 2016a). Three replicate arrays were deployed at least 5 m apart per site. Since 2018, collector networks have been modified to improve statistical replication, including up to 10 individual collectors deployed per site at 1 m depth and at least 5 m apart (as above) from May to October. Since 2006, seven invasive biofouling organisms have been detected in Newfoundland and Labrador harbours, marinas and coastal areas.

Should be cited as follows: DFO Newfoundland and Labrador Region Aquatic Invasive Species Marine Biofouling Monitoring Program. Published March 2024. Coastal and Freshwater Ecology, Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, Newfoundland and Labrador.

Reference:

Tunicates

Violet tunicate (Botrylloides violaceus) 2007
The violet tunicate was first detected in NL waters in 2007 in Belleoram, Fortune Bay on wharf structures and vessels (McKenzie et al. 2016b). This colonial tunicate forms irregular shaped colonies usually of a solid color (orange, purple, yellow or cream). It is currently found in relatively small colonies in four harbours in NL; Placentia Bay (1), Fortune Bay (1), Conception Bay (1) and the west coast of NL (2). The data provided here indicates the detections of this AIS in coastal NL.


From 2018-2022, the Coastal Environmental Baseline Program provided additional support to enhance sampling efforts in Placentia Bay.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Margaree River and Tributaries Water Temperatures

PURPOSE:
To record hourly water temperatures throughout the Margaree watershed.

DESCRIPTION:
The Department of Fisheries and Oceans (DFO) has been deploying water temperature monitoring equipment since spring 1993 in the Margaree River watershed. Coverage has changed throughout the time series and there is little documentation regarding equipment used. In recent years data have been collected using VEMCOs.
            
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
Coastal Environmental Baseline Program (Maritimes Region), Port of Saint John region conductivity, temperature and depth data

The Coastal Environmental Baseline Program is a multi-year Fisheries and Oceans Canada initiative designed to work with Indigenous and local communities and other key parties to collect coastal environmental data at six pilot sites across Canada (Port of Vancouver, Port of Prince Rupert, Lower St. Lawrence Estuary, Port of Saint John, Placentia Bay, and Iqaluit).  The goal of the Program is to gather local information in these areas in effort to build a better understanding of marine ecological conditions.  The Maritimes region has developed a physical oceanography program to align with the oceanographic interests and data needs of local communities and stakeholders, with the goal of sharing this information via open data.  Starting in 2019, oceanographic parameters including temperature, salinity, depth, turbidity and currents have been continuously monitored at a series of locations covering a broad range of environments in the Port of Saint John and approaches vicinity, including the lower Saint John and Kennebecasis rivers, coastal fringe marshes and embayments, as well as the Musquash estuary Marine Protected Area (MPA).  This dataset includes CTD data starting in 2019 and turbidity data from August 2020.  Data collection methods range from bottom-mounted instruments in water depths of 10-50 meters, buoyant surface moorings, and hard-mounted instruments in intertidal zones. Intertidal data is interrupted during some low tide events, where the water level drops below the sensor, resulting in loss of functionality for periods up to 1-2 hours.  Overall this dataset captures a dynamic balance between salt and fresh water on the highly tidal lower Saint John river, coastal seasonal dynamics in near-shore marine environments in the Musquash MPA, and the constant fluctuations of intertidal creeks and marshes.

Update 2 - April 2025: included 2023-24 data
Update 1 - Nov 2023: included 2022 data; removed daylight savings errors from 2019, 2020 and 2021; updated position for Evandale surface mooring.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada
Fixed gear sentinel fisheries program - northern Gulf of St. Lawrence

In place since fall 1994, the sentinel fisheries program is the result of a collaboration between Fisheries and Oceans Canada (DFO) and Quebec and Newfoundland commercial fishermen's associations. Under this program, contracts are awarded by tender to fishermen’s associations to carry out fishing activities according to scientific protocols developed by DFO. The main objective of this survey is to collect data that will be used to calculate abundance indices for the northern Gulf of St. Lawrence Atlantic cod stock.

Description of fixed gears survey

The fixed gear sentinel fisheries of the northern Gulf of St. Lawrence are conducted in the sub-division 3Pn and the divisions 4R, 4S of the Northwest Atlantic Fisheries Organization (NAFO) using fixed gillnets or longlines (other fishing gears were also used at the start of the program). Fishing activities with nets must have a mesh size of 5 ½ inches (140mm) and are limited to a maximum of 6 to 20 nets depending on the region and capture and the target immersion time is between 19 to 24 hours. Longline fishing activities, for its part, must be carried out with traditional J #16 or C #12 hooks. The maximum number of hooks varies from 500 to 1000, depending on the catch, and the target immersion time is 4 to 6 hours. Data are collected by observers at sea or by technicians.

Data

For each fishing activity, the total catch is sorted and weighed by species. For each species other than Atlantic cod, the number of individuals caught is noted. Atlantic cod are then measured at the fork (cm). Other biological data such as weight (total, gonad, liver and stomach), age, sex and maturity can then be collected on a subsample of cod.

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, a “Freql” file containing the length frequency of fish.

The data collected as part of this program is available below. It is important to note, however, that 1) only traits deemed successful have been retained; 2) historical data may contain inaccuracies; 3) the most recent survey is not available for validation purposes.

Organization: Fisheries and Oceans Canada | Pêches et Océans Canada