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We present a hierarchical model for survey comparative fishing (CF) experiments (x) to utilize data from several species (s) and x to provide improved estimates of the relative efficiency of one survey protocol compared to another. This model is applied to four flatfish s and two x conducted by Fisheries and Oceans Canada (DFO) in 1995 and 1996. We used a monotone increasing function for relative efficiency, and included spatial effects to account for this important source of variation that was not considered in previous analyses of these data. We provide detailed analyses of the anticipated impacts of the various changes in the DFO survey protocols to better understand the reliability of the results. We show that there were important differences in relative efficiency among s, x , and spatial regions, which, combined with low sample sizes and low catch rates, contributed to poor precision in the estimates of relative efficiency. We conclude that stock assessment models in the future should have a goal of using unconverted survey indices, but also include information on the relative efficiency of trawl survey protocols as prior distributions. This will more adequately account for this important source of uncertainty. [ABSTRACT FROM AUTHOR]

The status of the cod stock in the Northwest Atlantic Fisheries Organization (NAFO) Subdivision (Subdiv.) 3Ps was assessed during a Fisheries and Oceans Canada (DFO) Regional Peer Review Process meeting held November 2-7, 2020. Total landings for the 2019-20 management year (April 1-March 31) were 3,499 t, or 59% of the Total Allowable Catch (TAC). This marks the tenth consecutive season that the entire TAC has not been taken. There was no DFO research vessel (RV) survey during spring 2020 due to the pandemic. Sentinel gillnet catch rates have been very low and stable since 1999. Sentinel line trawl catch rates were below average over 2011-18, but the 2019 catch rates were relatively high. An integrated state space model resulting from the 2019 3Ps Cod Framework meeting was used to assess the status of the stock and estimate fishing mortality. The Limit Reference Point (LRP) is 66,000 t of Spawning Stock Biomass (SSB). SSB at January 1, 2021, is estimated to be 25 kt (18 kt-35 kt). The stock is in the Critical Zone (38% of Blim [27-53%]) as defined by the DFO Precautionary Approach (PA) Framework. The probability of being below Blim is >99.9%. The estimated fishing mortality rate (ages 5-8) has generally declined, from 0.16 in 2015 to 0.11 in 2019. With an assumed catch of 2,702 t in 2020, fishing mortality (F) is projected to be 0.07 (0.05-0.09) in 2020. Natural mortality (ages 5-8) was estimated to be 0.43 (0.35-0.52) in 2019. Values of natural mortality (M) during the last four years are the among the highest in the time series. Recruitment (age 2) estimates have been below the long term average since the mid-1990s. Projection of the stock to 2023 was conducted assuming. [ABSTRACT FROM AUTHOR]

Increases in natural mortality have been suggested as a potential driver for both the collapse and lack of recovery for the American plaice (Hippoglossoides platessoides) population on the Grand Bank of Newfoundland in NAFO Divisions 3LNO. However, natural mortality is among the most difficult parameters to estimate since it can be confounded with other parameters and model misspecifications. One method used to avoid this confounding involves modeling unfished components of a population where total mortality and natural mortality are equal. Here, we use a state-space metapopulation dynamics model to investigate whether there is evidence that natural mortality rates for unfished juvenile American plaice have varied since the population collapse. In addition, our model examined the degree of synchrony in age-1 recruitment signals between each management Division. The best fitting model included temporal variability in natural mortality rates, but estimates did not frequently differ from zero. This indicates that change in natural mortality rates is not an important driver of current juvenile 3LNO American plaice stock dynamics. Instead, this model identified that juvenile stock dynamics were mainly affected by variations in age-1 recruitment. Furthermore, a correlation analysis of the temporal variations in recruitment showed that trends were somewhat dissimilar between NAFO Divisions 3L and 3NO. Overall, although increases in M have been suggested by recent studies, we did not find strong evidence for this in juvenile fish. [ABSTRACT FROM AUTHOR]

The paper describes the development of a state-space model (HYBRID) for the stock assessment of Northwest Atlantic Fisheries Organization (NAFO) Subdivision 3Ps cod stock. The HYBRID model fits to the DFO RV survey (1983-2005, 2007-19) as well as the following additional survey time series: the IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer, English: French Research Institute for Exploitation of the Sea) ERHAPS (Evaluation des Ressources Halieutiques de la région 3PS) survey (1978-91), the Groundfish Enterprise Allocation Committee (GEAC) survey (1998-2005), and the sentinel gillnet and line-trawl surveys (1995-2018). The HYBRID model also fits to fisheries data with the expectation that the model can separate fishing mortality from natural mortality. Fisheries catch-at-age is fit using continuation ratio logits, and the fisheries landings are fit via censored likelihood. The use of censored likelihood for fitting landings allows the inclusion of expert opinion on reliability of landings throughout the model time series. The HYBRID model presented here starts in 1959, which is the first year for which landings data are available. The HYBRID model allows exploration of different forms for parameterization of time-varying fisheries selectivity, natural mortality, and approaches for estimation of catch-at-age data. The model formulations also differ depending on the survey series used in fitting the model. Seventeen model formulations are presented. Alternate formulations based on fishing mortality included: 1. a logistic flat topped or dome selectivity with time-blocks 2. SAM (State-space Assessment Model, Nielsen and Berg, 2014) style Multivariate Normal random walk 3. a separable age-year correlated process for fishing mortality rate (F) similar to NCAM (Cadigan 2016), and 4. option to break the processes for F in years where important events (like a moratorium) have impacted the fishery. Alternate formulation based on natural mortality included: 1. invariant natural mortality across age and years, and 2. time-varying natural mortality related to fish condition. The different model formulations are compared and evaluated on the basis of AIC (Akaike Information Criterion) values and their performance in retrospective analyses. The meeting concluded that time-varying natural mortality is an important consideration for modelling the dynamics of 3Ps cod and selecting a population model for this stock. Following the evaluations of the alternate model formulations, model formulations 11 which includes fit to sentinel data series, has F modelled using an MVN Random walk with year break for the moratorium, and has time-varying natural mortality rate (M) was considered to have utility as an assessment model for 3Ps cod stock assessment. [ABSTRACT FROM AUTHOR]

We document unprecedented abandonments and breeding failures by Northern Gannets in eastern Canada at Cape St. Mary's, Bonaventure Island, and the Magdalen Islands. These events were associated with a marine heat wave during chick rearing in the late summer of 2012. The rapid onset of abandonment at Cape St. Mary's also coincided with intense lightning and thunder during an overnight storm. Parental desertions at all colonies were transient, resolving over a period of weeks, and appeared to be food-related, resulting in the poorest breeding success on record for each of these colonies. The Northern Gannet's primary prey during the breeding season is Atlantic mackerel Scomber scombrus, which was at historically low levels in 2012; a 2018 assessment by Fisheries and Oceans Canada classified the population in the Critical Zone. Researchers studying the effects of ocean heat waves are noticing widespread changes in marine food webs, and longer-term biophysical relationships are under investigation. [ABSTRACT FROM AUTHOR]

Large-scale relationships between changes in abundance of coastal breeding Herring (Larus argentatus) and Great Black-backed (L. marinus) gulls and commercial fisheries landings of bottom-dwelling groundfish spanning 28 years in four of Canada's east coast Provinces were investigated. Herring and Great Black-backed gull abundance data were compared between survey periods prior to (1986-1990) and following (2002-2006 and 2010-2014) the widespread reduction of groundfish fishing activities due to a moratorium that began in 1992. Regionwide declines in the number of breeding Herring and Great Black-backed gulls were observed between the 1986-1990 and 2002-2006 survey periods (Herring Gull: -3.7% per year; Great Black-backed Gull: -3.6% per year) and between the two periods following the moratorium (Herring Gull: -1.6% per year; Great Black-backed Gull: -4.1% per year). Total groundfish landings reported for the study area declined by 76% between the 1990-1992 and 2002-2006 fishing periods, and declined by an additional 25% between the two periods following the moratorium. A positive relationship was found between Province-wide groundfish landings and the number of breeding Great Black-backed Gulls corrected for coasdine length. These results support the hypothesis that the moratorium reduced the availability of discards, which in turn played a role in the region's widespread decline of breeding Herring and Great Black-backed gull populations. In addition to continued declines in available discards, additional factors are likely influencing recent regional breeding population trends, including declines in available refuse and forage fish and increases in novel food sources such as expanding American mink (Neovison vison) farms. [ABSTRACT FROM AUTHOR]

The article discusses the study that investigated age-related variation in trophic niche overlap of Dovekies Alle alle collected during summer, fall and early winter, collected on Newfoundland beaches after an oil spill in early winter 2004. Findings discussed include significantly higher values of stable isotope values of nitrogen observed in adults compared to those of sub-adults during fall moult and hatch-year birds during summer, and possible overlap on wintering grounds.

Obtaining useful information on marine birds that can aid in oil spill (and other hydrocarbon release) risk and damage assessments in offshore environments is challenging. Technological innovations in miniaturization have allowed archival data loggers to be deployed successfully on marine birds vulnerable to hydrocarbons on water. A number of species, including murres (both Common, Uria aalge, and Thick-billed, U. lomvia) have been tracked using geolocation devices in eastern Canada, increasing our knowledge of the seasonality and colony-specific nature of their susceptibility to oil on water in offshore hydrocarbon production areas and major shipping lanes. Archival data tags are starting to resolve questions around behaviour of vulnerable seabirds at small spatial scales relevant to oil spill impact modelling, specifically to determine the duration and frequency at which birds fly at sea. Advances in data capture methods using voice activated software have eased the burden on seabird observers who are collecting increasingly more detailed information on seabirds during ship-board and aerial transects. Computer programs that integrate seabird density and bird behaviour have been constructed, all with a goal of creating more credible seabird oil spill risk and damage assessments. In this paper, we discuss how each of these technological and computing innovations can help define critical inputs into seabird risk and damage assessments, and when combined, can provide a more realistic understanding of the impacts to seabirds from any hydrocarbon release. [ABSTRACT FROM AUTHOR]

Abstract: Bycatch and indirect mortality associated with global fishing operations affect non-target species. Northern gannets (Morus bassanus) and other seabirds incorporate marine debris, much of it originating in fisheries, into their nests, at times resulting in entanglement. We compared the prevalence and composition of marine debris in nests at two gannet colonies in Newfoundland before and after a basin-wide ground fish closure in 1992, and at the species’ largest colony in the Gulf of St. Lawrence, where fishing effort is low. The proportion of nests with marine debris decreased following the fishery closure, and the proportion of nests with fishing gear was related exponentially to the number of gillnets set around breeding colonies. Assessing the composition of gannet nests could provide a useful index of the prevalence of fishing debris and could be used to assess entanglement risk of other animals in the marine environment over decadal scales. [Copyright &y& Elsevier]

Seabirds and other marine animals are at risk from anthropogenic activities that target them directly and those that can harm them incidentally. We integrate year-round tracking and vessel studies to assess risks for a globally important seabird population in the North-West Atlantic. The eastern Canadian Grand Bank has a rich and diverse food web that supports an abundance of apex predators. Major resource extraction industries (hydrocarbon production and fisheries) operate in the area, and, in addition to shipping and hunting, pose risks for marine birds. Understanding the relative risks has been hampered by poor information on bird distribution at sea. Here, we deployed global location sensors (loggers or geolocators) on common murres Uria aalge at Funk Island, the species' largest North American breeding colony. Adults ( n=10) were resident on the Grand Bank and in adjacent pelagic waters year round. Within 10 days of leaving the colony, males dispersed offshore (<50°W), south-south-east of Funk Island. Females departed later and spent 10-47 days in coastal waters before moving offshore. All birds were in the vicinity of offshore oil platforms during November and December, but remained outside the area of the coastal Newfoundland and Labrador murre hunt. Three of six tracked females, but only one of four tracked males moved closer to shore during January and February where vulnerability to the hunt may have increased. Vessel-based surveys confirmed the importance of offshore, shelf-edge habitats for murres in winter. Our results highlight the relative risk to wintering murres from different human activities, providing a sound scientific rationale for focusing conservation and management actions. This information is particularly timely given the continued expansion of deep-water drilling in the North-West Atlantic and increasing risk of oil pollution for seabirds attracted to platforms. [ABSTRACT FROM AUTHOR]

Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod ( Gadus morhua ) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.

In 1992, the eastern Canadian gillnet fisheries for northern cod and Atlantic salmon were largely closed. These large-scale fishery closures resulted in the removal of tens of thousands of gillnets known to inflict high levels of seabird mortality. We used this unprecedented opportunity to test the effects of gillnet removal on seabird populations. Consistent with predictions, we show that the breeding populations of divers (auks, gannets; susceptible to gillnet bycatch) have increased from pre-closure levels, whereas the populations of scavenging surface-feeders (gulls; low vulnerability to gillnet bycatch but susceptible to removal of fisheries discards) have decreased. Using the most complete series of seabird census data for the species most vulnerable to bycatch, we demonstrate a positive population response of common murres to reduction in gillnet fishing within its foraging range. These findings support the widespread but seldom documented contention that fisheries bycatch negatively impacts populations of non-target large vertebrates.