Hugues P. Benoît

Hugues P. Benoît
Fisheries and Oceans Canada | DFO · Gulf Fisheries Centre

32.54
 · 
PhD
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Projects
Projects (3)
Project
Quantify key bio-physical environmental drivers of fish stocks productivity and develop approaches to integrate environmental effects in stock assessment and management
Project
Consultant in the case study 2.2 "Algarve purse seine" - Procedural and technological changes to purse seining with mixed catches of low value by-catch, and undersized target species leading to slipping; developing a commercially viable, low-impact alternative to current fishing practices
Research
Research items (82)
Article
The diet of repeat‐spawner Atlantic salmon Salmo salar was investigated using carbon and nitrogen stable‐isotope values from the outer growth band of scales, which reflect the fish’s consumption and growth during their most recent marine phase. Isotope values for S. salar displaying different spawning strategies were compared between and within the...
Article
Full-text available
Like many marine species around the globe, several stocks of Atlantic cod (Gadus morhua) live in increasingly hypoxic waters. In the Gulf of Saint Lawrence (GSL) in Canada, the deep channels traversing the semi-enclosed sea exhibit year-round hypoxia, identified as one of the limiting factor for the recovery of GSL cod in its northern part. While m...
Article
Full-text available
The effects of two different slipping methods on the survival, physical and physiological response of sardines, Sardina pilchardus, captured in a purse-seine fishery were investigated in southern Portugal. Sardines were collected and transferred into holding tanks onboard a commercial fishing vessel after being captured, crowded and deliberately re...
Data
Survival estimates for sardine using Kaplan-Meier survival curves (dashed line), overlaid with the predictions from the selected mixture-distribution survival model M3 (solid lines with 95% confidence bands) for the three treatment replicates (1–3): Control, standard slipping (SS) and modified slipping (MS). (TIF)
Article
Decapod shrimps typically occupy lower trophic levels, often as omnivores, and many have high population turnover rates, which makes shrimp populations susceptible to changes in predator abundance and environmental change. The increased biomass of northern shrimp Pandalus borealis in many parts of the NW Atlantic has been associated with the collap...
Article
Senescence is the physiological deterioration of adult organisms leading to an age-specific decline in fitness principally associated with an increase in mortality rate (actuarial senescence) and decline in fecundity (reproductive senescence). Senescence is common in natural populations of many taxa; however, there are few examples among fishes, ev...
Technical Report
Full-text available
There are two basic pieces of information required for implementing Fisheries and Oceans Canada’s (DFO) Policy on Managing the Impacts of Fishing on Sensitive Benthic Areas: The identification and delineation of Significant Benthic Areas, and The overlap between these Significant Benthic Areas and fishing activities. This analysis builds on the m...
Article
Due primarily to regulatory factors, skates (family Rajidae) account for nearly half the total bycatch discarded during commercial fishing operations in the U.S. portion of the Northwest Atlantic Ocean. In this region the New England scallop dredge fishery has the second highest skate discard rate; however, no information regarding their resiliency...
Article
Discard mortality (DM) estimates are vitally important to fisheries management. Commercial fishery DM estimates, for example, can help calculate total fishing mortality and biologically acceptable catch limits. The winter skate, Leucoraja ocellata, is the only species within the US portion of the western North Atlantic that is targeted in the skate...
Article
Species that have a high likelihood of surviving the discarding process have become great concern since the European Union reformed the Common Fisheries Policy and enacted a landing obligation prohibiting the discarding any individuals of species under quota. Among species presenting an elevated survival potential, plaice (Pleuronectes platessa) is...
Article
By 2019, the Common Fisheries Policy will prohibit discarding in all European fisheries of any pelagic, demersal or shellfish species for which removals are managed by TACs and quotas or minimum sizes. However, the regulation allows for exemptions from the prohibition for species for which scientific evidence demonstrates high survival rates associ...
Technical Report
Full-text available
Significant Benthic Areas are defined in DFO’s Ecological Risk Assessment Framework (ERAF) as “significant areas of cold-water corals and sponge dominated communities”, where significance is determined “through guidance provided by DFO-lead processes based on current knowledge of such species, communities and ecosystems”. Here we provide maps of th...
Technical Report
Full-text available
Herring (Clupea harengus) is a key prey species in the diets of numerous fishes, marine mammals, seabirds, and large pelagic predators in many North Atlantic ecosystems, including the southern Gulf of St. Lawrence (sGSL; NW Atlantic, Canada). Like many small pelagic forage fish species, predation can be a significant source of mortality in Herring,...
Article
We study methods to estimate regression and variance parameters for over-dispersed and correlated count data from highly stratified surveys. Our application involves counts of fish catches from stratified research surveys and we propose a novel model in fisheries science to address changes in survey protocols. A challenge with this model is the lar...
Technical Report
Full-text available
Models of probability of occurrence and predicted biomass distribution have been created using random forest (RF) machine learning techniques for different invertebrate taxa in the Gulf of St. Lawrence. Response data were derived from by-catch data collected from DFO research vessel trawl surveys following a stratified random design based on depth...
Technical Report
Kernel density estimation (KDE) utilizes spatially explicit data to model the distribution of a variable of interest. It is a simple non-parametric neighbour-based smoothing function that relies on few assumptions about the structure of the observed data. It has been used in ecology to identify hotspots, that is, areas of relatively high biomass/ab...
Technical Report
Full-text available
Kernel density estimation (KDE) utilizes spatially explicit data to model the distribution of a variable of interest. It is a simple non-parametric neighbour-based smoothing function that relies on few assumptions about the structure of the observed data. It has been used in ecology to identify hotspots, that is, areas of relatively high biomass/ab...
Article
Pershing et al (Science, 13 November 2015, p. 809) concluded that recent warming in the Gulf of Maine contributed to the collapse of Gulf of Maine cod. We argue that this conclusion is based on a flawed analysis of the population dynamics of this cod stock. We believe that understanding the potential role of climate change in the collapse of this s...
Article
Full-text available
Open access link: http://icesjms.oxfordjournals.org/cgi/reprint/fsw058?ijkey=BuTWCAewKazxV4l&keytype=ref In recent years, the recreational contribution to the total catch of Atlantic cod (Gadus morhua) in the Gulf of Maine (GOM) has increased with recreational discards outnumbering recreational landings by 2:1. However, the discard mortality (DM...
Technical Report
Full-text available
Important areas for biologically diverse communities were identified for the first time using data from ecosystem surveys including bottom trawl and plankton net sampling as well as seabird observations in the Northern and Southern Gulf of St. Lawrence. Taxonomic richness was examined by group for demersal fish, benthic invertebrates, pelagic taxa...
Article
Full-text available
The analysis of biomass time-series from standardized surveys, particularly comparing patterns of variation and their supposed relationship with drivers, can provide insight into how fish species and communities as a whole respond to environmental, trophic, and fishing-related drivers of change in ecosystems. Here we describe and compare the common...
Article
The post-release mortality of discarded fish can represent an additional source of mortality that is important to understand for effective marine fisheries management. To best estimate these mortality rates under near-natural conditions, a refrigerated flow-through seawater system was developed for short-term holding experiments at-sea aboard comme...
Article
Numerous studies have shown that, at spatial scales of metres to several kilometres, animals balance the trade-off between foraging success and predation mortality by increasing their use of safer but less profitable habitats as predation risk increases. However, it is less clear whether prey respond similarly at the larger spatiotemporal scales of...
Article
The top-down effects of predators on ecosystem structure and dynamics have been studied increasingly. However, the nature and consequence of trophic interactions between upper-trophic-level predators have received considerably less attention. This is especially the case in marine systems due to the inherent challengesof studying highly mobile marin...
Article
Conservation concerns and new management policies such as the implementation of ecosystem-based approaches to fisheries management are motivating an increasing need for estimates of mortality associated with commercial fishery discards and released fish from recreational fisheries. Traditional containment studies and emerging techniques using elect...
Article
Full-text available
Conservation concerns and new management policies such as the implementation of ecosystem-based approaches to fisheries management are motivating an increasing need for estimates of mortality associated with commercial fishery discards and released fish from recreational fisheries. Traditional containment studies and emerging techniques using elect...
Article
Improved understanding of the dynamics of populations at low abundance is needed in the face of global biodiversity loss. We examined the dynamics of depleted demersal fish populations in the southern Gulf of St. Lawrence, Canada. Twenty years ago, a number of these populations collapsed due to overexploitation. Since then, others have declined to...
Article
There is limited understanding of the relationship between mobile gear fishing intensity and themagnitude of the resulting perturbation in marine benthic communities. Theory predicts that instan-taneous fishing-induced mortality should generally scale directly with fishing intensity. This study useda before–after-impact experimental design with 16...
Article
High natural mortality is preventing the recovery of collapsed stocks of Atlantic cod and white hake in the southern Gulf of St Lawrence, Canada. Predation by grey seals has been proposed as an important cause of this high mortality. We determined the contribution of cod and hake to the diet of grey seals collected along the west coast of Cape Bret...
Conference Paper
The population of Atlantic cod in the southern Gulf of St. Lawrence collapsed in the early 1990s due to overfishing. Fishing mortality has been at negligible levels since then, but the population has continued to decline. This lack of recovery results from dramatic increases in the natural mortality of adult cod. Among the potential causes for this...
Conference Paper
There is increasing interest in understanding discard related losses as part of an ecosystem approach to fisheries, a more fulsome accounting of fishing mortality in stock assessments and in promoting the conservation of principally released species. Though these objectives could be achieved by obtaining reliable estimates of discard mortality that...
Conference Paper
Due primarily to regulatory factors, skates (family Rajidae) account for nearly half the total bycatch discarded during commercial fishing operations in the U.S. portion of the Northwest Atlantic Ocean. Although the New England scallop dredge fishery has the second highest skate discard rate, no information regarding their resiliency to interaction...
Article
Ecological data such as biomasses often present a high proportion of zeros with possible skewed positive values. The Delta-Gamma (DG) approach, which models separately the presence–absence and the positive biomass, is commonly used in ecology. A less commonly known alternative is the compound Poisson-gamma (CPG) approach, which essentially mimics t...
Conference Paper
Due primarily to regulatory factors, skates from the family Rajidae account for nearly half the total bycatch discarded during commercial fishing operations in the U.S. portion of the Northwest Atlantic Ocean. However, despite the rigors of capture and handling, and mounting management and conservation concerns, few studies have investigated the po...
Article
Biomass samples from marine scientific surveys are commonly used to investigate spatial and temporal variations in stock abundances. Biomass records are often characterized by a high proportion of zeros on the one hand, and occasional large catches on the other. These features induce a modeling challenge when trying to understand the state of popul...
Article
Estimating fishery impacts on commercially unimportant species is often hindered by limited and possibly biased data for landed and discarded catch, and poor information on discard mortality. The three skate (family Rajidae) species occurring in southern Gulf of St Lawrence (Canada) exemplify this problem. Assessing the contribution of fishing to i...
Data
Reliable catch statistics are essential for assessing fishing impacts on individual stocks. However, fisheries that capture a mixture of stocks or species for which catch statistics are not disaggregated pose a challenge. Nonetheless, catch composition can be inferred given information on fishing date and location and a prevalent role of season and...
Article
Determining the sustainability of fishing mortality for discards requires information on discard amounts as well as capture and release mortality rates. Formal estimates of these rates are costly and only available for a limited number of species and fisheries. In their absence, proxies for discard mortality could inform risk assessments of fishing...
Article
Reliable catch statistics are essential for assessing fishing impacts on individual stocks. However, fisheries that capture a mixture of stocks or species for which catch statistics are not disaggregated pose a challenge. Nonetheless, catch composition can be inferred given information on fishing date and location and a prevalent role of season and...
Article
Chaput, G., and Benoît, H. P. 2012. Evidence for bottom–up trophic effects on return rates to a second spawning for Atlantic salmon (Salmo salar) from the Miramichi River, Canada. – ICES Journal of Marine Science, 69: 1656–1667. Increased return rates of consecutive repeat-spawning Atlantic salmon (Salmo salar) have been noted in the Miramichi Rive...
Article
Full-text available
Obtaining a representative estimate of discard mortality for population and ecosystem assessments is very challenging. This can only rarely be done directly by recovering tagged discarded individuals. Instead, semi-quantitative measures of individual fish vitality or physical condition, obtained by onboard observers prior to discarding, can be used...
Article
Full-text available
Metrics representative of key ecosystem processes are required for monitoring and understanding system dynamics, as a function of ecosystem-based fisheries management (EBFM). Useful properties of such indicators should include the ability to capture the range of variation in ecosystem responses to a range of pressures, including anthropogenic (e.g....
Article
Full-text available
A key aspect of ecosystem-based fisheries management is assessing sustainability at multiple levels of organization beyond single target species. For this, appropriate biological reference points (BRPs) for aggregated groups of species need to be developed. But what are the potential risks and benefits of applying aggregate management measures to t...
Conference Paper
Full-text available
Understanding species distribution is a key challenge when managing harvested, endangered or invasive species. Survey data available for this kind of study often present an excess of zero. This large proportion of zero calls specific zero-inflated modelling approaches. Delta-distribution approaches are the common tool to model zero-inflated data in...
Conference Paper
Full-text available
Comprendre et étudier la distribution des espèces est un défi majeur pour la gestion d'espèces d'élevages, en voie d'extinction ou encore envahissantes. Cependant la majeure partie des données utilisées pour de telles études présentent une forte proportion de zéros. De nombreuses approches ont été développées pour faire face à ces excès de zéros. U...
Article
Full-text available
Despite 2 decades of very low fishing levels, numerous NW Atlantic demersal fish stocks have failed to recover from collapsed states or are presently collapsing. In the southern Gulf of St. Lawrence, adult natural mortality (M) appears to be the demographic rate that most limits population productivity in at least 3 species: Atlantic cod Gadus morh...
Article
Full-text available
We present a summary of variability in age and length at metamorphosis for marine fishes. Data from the literature were partitioned into taxonomic, population, and individual levels of resolution to examine the factors affecting the timing of metamorphosis. Temperature appears to be a dominant influence on timing, likely due to its effect on growth...
Article
Full-text available
We assessed the extent to which temperature interacts with maternal contributions to egg size to affect development time and size of yellowtail flounder (Pleuronectes ferrugineus) larvae at hatch. Maternal effects contributed significantly to differences in egg sizes produced by four females. Eggs from each female were incubated at five temperature...
Article
Our objectives were to describe the patterns of colonization of lentic macroinvertebrates on artificial substrates and to evaluate how this information can then be used to effectively and efficiently sample macroinvertebrates in vegetated littoral zones of lakes. Colonization of taxa in terms of both richness and density generally followed a Michae...
Article
Understanding the factors affecting the likelihood that discarded fish will die can contribute to better management of resources by enhancing the potential for successful live release and by improving the estimation of otherwise unaccounted fishing mortality. Semi-quantitative measures of individual fish vitality or physical condition, obtained by...
Article
A parsimonious model is presented as an alternative to delta approaches to modelling zero-inflated continuous data. The data model relies on an exponentially compound Poisson process, also called the law of leaks (LOL). It represents the process of sampling resources that are spatially distributed as Poisson distributed patches, each containing a c...
Article
Full-text available
Some fishery characteristics such as total discards are often inferred from data collected by at-sea observers on a subset of fishing trips. Such inference is predicated on the assumption that observed and unobserved trips are statistically exchangeable. There are two principal reasons why this may not be so. A deployment effect results from nonran...
Preprint
Full-text available
This paper describes a compound Poisson-based random effects structure for modeling zero-inflated data. Data with large proportion of zeros are found in many fields of applied statistics, for example in ecology when trying to model and predict species counts (discrete data) or abundance distributions (continuous data). Standard methods for modeling...
Article
We describe dramatic shifts in the species composition of the marine fish community of the southern Gulf of St. Lawrence using a 35-year time series of catch rates in an annual bottom-trawl survey. We attempt to understand the causes of these changes using a traits-based approach that relates the similarity among species in their abundance trends t...
Article
Cercopagis pengoi, a zooplanktivore first discovered in Lake Ontario in 1998, may reduce availability of prey for planktivorous fish. Cercoapgis pengoi is most abundant in late summer and fall. Therefore, we hypothesized that abundance of small zooplankton (bosminids and cyclopoids) species would decrease at that time. To determine if the establish...