Harbour seals reside throughout the year around Newfoundland and Labrador (NL). The first systematic survey for harbour seals occurred along the NL Shelf during July and August 2021 to obtain counts of hauled out individuals and assess distribution. Grey seals are seasonal residents in NL, mainly present in the summer and autumn months. Grey seals were also recorded during the survey as these two species can share haul-out locations. Surveys were flown along the coastline with a Bell 429 helicopter with photographs taken of hauled out seals. This data includes the counts of hauled out harbour, grey and unknown seals seen during the survey. Adjusted counts are also provided, which assign the unknown seals to species based on the number of positively identified harbour and grey seals from each survey day. The realized survey coverage (survey tracks) is also included. Cite this data as: Hamilton, C.D., Goulet, P.J., Stenson, G.B., and Lang, S.L.C. 2024. Data of: Counts of harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) from an aerial survey of the coast of the Newfoundland Shelf and Sandwich Bay, Labrador during the summer of 2021This data can be found in: Hamilton, C.D., Goulet, P.J., Stenson, G. B., and Lang, S.L.C. 2023. Counts and spatial distribution of harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) from an aerial survey of the coast of the Newfoundland Shelf and Sandwich Bay, Labrador during the summer of 2021. Can. Tech. Rep. Fish. Aquat. Sci. 3566: v + 39 p. https://publications.gc.ca/site/eng/9.927831/publication.html DFO. 20XX. Stock assessment of Atlantic harbour seals (Phoca vitulina vitulina) in Canada for 2019-2021. DFO Can. Sci. Advis Sec. Sci. Advis. Rep. 2023/XXX. Lang, S.L.C., St-Pierre, A.P., Hamilton, C.D., Mosnier, A., Lidgard, D.C., Goulet, P., den Heyer, C.E., Bordeleau, X., Irani, A.I., and Hammill, M.O. 20XX. Population status assessment and Potential Biological Removal (PBR) for the Atlantic harbour seal (Phoca vitulina vitulina) in Canadian waters. DFO Can. Sci. Advis. Sec. Res. Doc. 2024

Harbour seals (Phoca vitulina) are found along temperate and Arctic marine coastlines of the Northern Hemisphere. They are found in coastal waters of the northern Atlantic and Pacific Oceans, as well as those of the Baltic and North Seas. In Canada, they may be found off the coastal waters of British Columbia, Nunavut, Manitoba, Ontario, Quebec, New Brunswick, Prince Edward Island, Nova Scotia, and Newfoundland and Labrador.Population trends and abundance of harbour seals in British Columbia are assessed based on aerial surveys conducted during 1966-2019. Based on counts conducted in Index Areas distributed throughout the province, the trend observed in the Strait of Georgia appears to be generally indicative of harbour seal populations throughout British Columbia. Total abundance of harbour seals on the B.C. coast in 2008 was estimated to be on the order of about 105,000 (95% confidence interval of 90,900 to 118,900) seals. Total abundance was re-estimated in 2022 (estimate and CI pending completion of CSAS process). Historic reconstructions indicate the population was depleted by a period of commercial harvesting during 1879-1914, and subsequently maintained below natural levels by predator control programs until the early 1960s. Already depleted, the population could not sustain a second period of intense commercial harvesting during 1962-1968 and was further depleted, but now appears to have fully recovered.

The initial objective of this dataset was to study the seasonal movement patterns of harbour seals (Phoca vitulina) in the St. Lawrence Estuary and Sable Island. This study was part of a larger program that studied the foraging behavior of the species.Ten harbour seals were captured using gillnets from 1994 to 1998 at three sites in the St. Lawrence Estuary (Bic, n=1 individual; île Blanche, n=1; Métis-sur-Mer, n=5) and one site on Sable Island (n=3 individuals). The individuals were equipped with a satellite-linked time-depth recorder (Type3.10, Wildlife Computers) equipped with an Argos tag and placed on the back of the neck. For most individuals, satellite tracking began in September and continued until the following spring.The dataset consists of series of geographic locations of ten harbor seals with associated dates and times and movement speeds calculated from successive locations.The location data were only filtered based on the validity class provided by Argos. Class Z locations were excluded.

Most of the data were collected during aerial surveys carried out at low tides during June and August 1994-1997, 2000 and 2001. June and August are respectively pupping and moulting seasons, when the haulout sites are intensively used by seals. Features in this layer show the Harbour seal distribution and the mean abundance for all aerial surveys (tables 3 and 5, figures 3 and 5 from Robillard et al. 2005). In the estuary, areas of high abundance have more than 30 individuals, areas of medium abundance have between 10 and 30 individuals and areas of low abundance have fewer than 10 individuals. In the Gulf, areas of high abundance have more than 50 individuals and areas of medium to low abundance have fewer than 50 individuals. Unpublished data obtained from Parks Canada and Sepaq were also used to identify important haulout areas in the Saguenay Fjord sector and in Pointe-aux-Vaches tidal flat sectors, which have been categorized in this dataset as high abundance areas.Data are valid only during summer (except for the Pointe-aux-Vaches flats identified as mainly frequented in autumn by Parc Canada), because spring and fall distributions of the Harbour seal are unknown. Data shown in the Estuary and the Gulf of St. Lawrence are a picture of the situation in 2005 because it is the most recent mapping available for this specie. The distribution of the Harbour seal is non-uniform among the different concentration areas but is similar between June and August. However, Harbour seals tend to decrease their presence along the south shore and the Lower Estuary in August to the benefit of the Saguenay River colonies. Abundance classes are arbitrary but fit with the published results of haulout site utilization from Robillard et al. (2005).Data sources :Parks Canada. 2021. Personal communication. Harbor seal monitoring data on the Pointe-aux-Vaches tidal flat. Parks Canada and SÉPAQ, 2020. Données du suivi du phoque commun dans le fjord du Saguenay. Unpublished data.Robillard, A., V. Lesage, and M.O. Hammill. 2005. Distribution and abundance of harbour seals (Phoca vitulina concolor) and grey seals (Halichoerus grypus) in the Estuary and Gulf of St. Lawrence, 1994–2001. Can. Tech. Rep. Fish. Aquat. Sci. 2613: 152 pp.

Data were collected during aerial surveys carried out at low tides in June and August 1994-1997, 2000 and 2001. June and August are respectively pupping and moulting seasons, when the haulout sites are intensively used by seals. Features in this layer show the Grey seal distribution and mean abundance for all aerial surveys (tables 4 and 6, figures 4 and 6 from Robillard et al. 2005). In the estuary, areas of high abundance have more than 25 individuals, areas of medium abundance have between 5 and 25 individuals and areas of low abundance have fewer than 5 individuals. In the Gulf, areas of high abundance have more than 70 individuals and areas of medium to low abundance have fewer than 70 individuals.Data are valid only during summer because Grey seals in the Estuary and northern Gulf migrate to the southern Gulf of St. Lawrence in the fall. These seals will spend the winter on Sable Island, on the ice shelf in the Northumberland Strait or on neighboring islands. During the summer, in the Estuary and the Gulf of St. Lawrence, its distribution is not uniform between the different concentration areas identified, but it is similar between June and August. However, there are some areas where Grey seals are more abundant in August than in June. Abundance classes are arbitrary but fit with the published results of haul-out sites utilization from Robillard et al. (2005). Data shown are a picture of the situation in 2005 because it is the most recent mapping available for this species.Data sources and references:Lavigueur, L., Hammill, M.O., and Asselin, S. 1993. Distribution et biologie des phoques et autres mammifères marins dans la région du parc marin du Saguenay. Rapp. manus. can. sci. halieut. aquat. 2220: vi + 40.Lesage, V., and Hammill, M.O. 2001. The status of the grey seal, Halichoerus grypus, in the Northwest Atlantic. Can. Field-Nat. 115(4): 653-662.Robillard, A., V. Lesage, and M.O. Hammill. 2005. Distribution and abundance of harbour seals (Phoca vitulina concolor) and grey seals (Halichoerus grypus) in the Estuary and Gulf of St. Lawrence, 1994–2001. Can. Tech. Rep. Fish. Aquat. Sci. 2613: 152 pp.

Layer that includes the known information on potential haul-out sites for the harbour seal and gray seal in the Estuary and Gulf of St. Lawrence according to a literature review of documents produced between 1978 and 2000.Additional InformationPotential haul-out sites for the harbor seal and gray seal were produced according to a literature review of the following documents:Andersen, A. et M. Gagnon. 1980. Les ressources halieutiques de l'estuaire du Saint-Laurent. Rapp. can. ind. sci. halieut. aquat., 119: iv + 56 p.Argus Groupe-Conseil inc. 1992. Synthèse et analyse des connaissances relatives aux ressources naturelles du Saguenay et de l'estuaire maritime du Saint-Laurent. Parc marin du Saguenay. Service canadien des parcs, région du Québec.Biorex. 1995. Cartographie des ressources halieutiques et de leurs habitats dans l'estuaire moyen du Saint-Laurent. Rapport au ministère des Pêches et des Océans, Région du Québec, Division de la gestion de l'habitat du poisson. 36 p. + annexes. Biorex. 1996. Base de données géoréférencées sur les ressources halieutiques et leurs habitats : estuaire maritime du Saint-Laurent et fjord du Saguenay. Rapport au ministère des Pêches et des Océans, Région du Québec, Division de la gestion de l'habitat du poisson. Volume 1 : 38 p. + annexes et Volume 2 : 34 p. + annexes.Chevrier, V. 1994. Cartographie des habitats du poisson aux Îles-de-la-Madeleine. Rapport technique no. 1. Réalisé en collaboration avec le M.P.O., Attention Frag'Îles et la M.R.C. des Îles-de-la-Madeleine. 24 p. + 1 ann. + 36 cartes.Comité de la zone d'intervention prioritaire (ZIP) de la Côte-Nord du golfe. 1999. Inventaire des habitats côtiers et marins sensibles de la Basse-Cote-Nord : Rapport final, présenté à Pêches et Océans Canada par le Comité ZIP Côte-Nord du Golfe. 126 p.Comité de protection de la santé et de l'environnement de Gaspé inc. (C.P.S.E.G.). 1996.Communication personnelle par Carol Fournier, MPO. 1999. Communications personnelles par Gosselin, J-F-. 1996. Desaulniers, J. 1989. Étude des populations de pinnipèdes de l'Archipel-de-Mingan et relation entre l'activité de chasse au phoque et la sécurité publique 1987 à 1989. Parcs Canada. Région du Québec. Service de la conservation des ressources naturelles.Enquêtes auprès des pêcheurs. 1995.Lavigne, P.-J. 1978. La chasse estivale du phoque dans le Saint-Laurent. Rapport non publié. 65 p. Pêches et Océans Canada, Région du Québec.Lesage, Véronique. 2000. Communication personnel.Lesage, V., M. O. Hammill, and K.M. Kovacs. 1995. Harbour seal (Phoca vitulina) and Grey seal (Halichoerus grypus) abundance in the St. Lawrence estuary. Can. Manuscr. Rep. Fish. Aquat. Sci. 2307: iii + 19 p.Naturam Environnement inc. 1996. Caractérisation physique et biologique de l'habitat du poisson du secteur de Pointe-aux-Outardes. Realisé pour le compte de la Corporation du Parc régional de Pointe-aux-Outardes. 196 p.

PURPOSE:Understanding and predicting species range shifts is crucial for conservation amid global warming. This study analyzes life-history traits of four seal species (ringed (Pusa hispida Schreber, 1775), bearded (Erignathus barbatus Pallas, 1811), harp (Pagophilus groenlandicus Erxleben, 1777), and harbour (Phoca vitulina Linnaeus, 1758) seals) in the Canadian Arctic using data from Inuit subsistence harvests. Bearded seals are largest, followed by harp seals, harbour seals, and ringed seals. Seasonal blubber depth patterns show minimal variation in bearded seals, whereas harbour and ringed seals accumulate fat in open-water seasons and use it during ice-covered seasons. Endemic Arctic seals (ringed and bearded) exhibit greater longevity and determinate body growth, reaching maximum size by 5 years, while harbour and harp seals grow indeterminately, physically maturing around 10-15 years. Age of maturation varies, with ringed and harbour seals being more sensitive to environmental fluctuations. Most bearded seals reproduce successfully each year, while ringed seals exhibit more variability in their annual reproductive success. Analysis of isoprenoid lipids in liver tissue indicates that ringed and bearded seals rely on ice-algal production, whereas harp and harbour seals depend on open-water phytoplankton production. Bearded seals appear more specialized and potentially face less competition, while harp seals may adapt better to changing habitats. Despite expected range shifts to higher latitudes, all species exhibit tradeoffs, complicating predictions for the evolving Arctic environment. DESCRIPTION:This dataset contains the data reported in Steven H. Ferguson, Jeff W. Higdon, Brent G. Young, Stephen D. Petersen, Cody G. Carlyle, Ellen V. Lea, Caroline C. Sauvé, Doreen Kohlbach, Aaron T. Fisk, Gregory W. Thiemann, Katie R. N. Florko, Derek C. G. Muir, Charmain D. Hamilton, Magali Houde, Enooyaq Sudlovenick, and David J. Yurkowski. 2024. A comparative analysis of life-history features and adaptive strategies of Arctic and subarctic seal species - who will win the climate change challenge? Canadian Journal of Zoology 2024-0093.R1The data set includes species, location, harvest date, sex, age, standard length, girth, fat depth, teste size, parity status, pregnancy status, corpora lutea (n), corpus albicans (n), follicles (n). This dataset includes raw, unfiltered, and unprocessed historical data provided by harvesters that have not been screened for outliers. Individual users should screen the data for their specific use.Cite these data as:Steven H. Ferguson, Jeff W. Higdon, Brent G. Young, Stephen D. Petersen, Cody G. Carlyle, Ellen V. Lea, Caroline C. Sauvé, Doreen Kohlbach, Aaron T. Fisk, Gregory W. Thiemann, Katie R. N. Florko, Derek C. G. Muir, Charmain D. Hamilton, Magali Houde, Enooyaq Sudlovenick, and David J. Yurkowski. 2024. Arctic and Aquatic Research Division, Fisheries and Oceans Canada, Winnipeg, MB. https://open.canada.ca/data/en/dataset/ea9ff038-8b16-11ef-8cce-55cc7f028297

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

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.

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.