Hugues P. Benoît

Impacts of environmental change and direct and indirect harvesting effects on the dynamics of a marine fish community

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 to similarities in their ecological traits. We selected traits based on a priori beliefs of how each should reflect susceptibility to changes in a different external factor potentially affecting the community. We found evidence for an effect of ocean climate and top-down effects of fishing and seal predation, but not for bottom-up effects of prey availability on adult fishes. Mean body length in the community decreased dramatically in the 1990s. This reflected the removal of large-bodied fishes by fishing and sharp increases in the abundance of small fishes. The biomass of small fish was inversely correlated with an index of predation on those fish by larger fish...

Can the data from at-sea observer surveys be used to make general inferences about catch composition and discards?

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 obse...

Accounting for length- and depth-dependent diel variation in catchability of fish and invertebrates in an annual bottom-trawl survey

Diel variation in the catchability of 51 species of fish and 13 invertebrate taxa from an annual bottom-trawl survey of the southern Gulf of St. Lawrence was examined using generalized linear (Poisson) models. Two approaches were used: comparative fishing based on spatially paired day and night tows, and statistical control of spatio-temporal effects in regular survey data. The two approaches provided remarkably similar results. Furthermore, species-specific results were consistent between survey time periods where different vessels were used, and were quite comparable to results from other studies conducted in separate geographic areas. Where sufficient data existed, we considered both length and depth dependencies in diel variation in catchability. We commonly found significant length dependency for groundfish species and the pervasive pattern was for higher nighttime catches of small fish, the magnitude of the effect generally decreasing with increasing length. In contrast, water depth had a much less important impact, except for a few species. When considered jointly, however, patterns in length/depth dependency were not always clear. Given length-dependent geographic and bathymetric patterns in species distribution, the potential for confounding length and depth dependencies exists and correction factors for diel variation in catchability need to be applied cautiously.

Changes in Seasonal Nearshore Zooplankton Abundance Patterns in Lake Ontario following Establishment of the Exotic Predator Cercopagis pengoi

ABSTRACT 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 establishment of C. pengoi was followed by changes in the zooplankton community, seasonal patterns in nearshore zooplankton collected from May to October 1995–2000 were examined. Early summer density of small zooplankton was similar in all years while late summer and fall densities were significantly lower in 1998–2000 than in 1995–1997. The declines of small zooplankton coincided seasonally with the peak in C. pengoi density. Other possible causes for the observed changes in small zooplankton are less likely. High levels of fish predation should have resulted in smaller zooplankton in 1998–2000 than in 1995–1997 and larger declines in Daphnia than other groups. This was not observed. There was no significant decline in chlorophyll-α concentrations or changes in temperature between 1995–1997 and 1998–2000. Therefore, the declines in density of small zooplankton were most likely the result of C. pengoi predation. The effect of C. pengoi establishment on alewives is increased competition for zooplankton prey but C. pengoi has replaced a portion of the zooplankton biomass and adult alewife diet formerly dominated by Diacyclops thomasi and Bosmina longirostris.

Modelling spatial zero-inflated continuous data with an exponentially compound Poisson process

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 certain quantity of biomass drawn from an exponential distribution. In an application of the LOL, two latent structures are proposed to account for spatial dependencies between zero values at different scales within a hierarchical Bayesian framework. The LOL is compared to the delta-gamma (ΔΓ) distribution using bottom-trawl survey data. Results of this case study emphasize that the LOL provides slightly better fits to learning samples with a very high proportion of zero values and small strictly positive abundance data. Additionally, it offers better predictions of validation samples.

Comment on "Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery".

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 stock requires more defensible analyses.

Compound Poisson‐gamma vs. delta‐gamma to handle zero‐inflated continuous data under a variable sampling volume

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 the process of capturing clusters of biomass during a sampling event. Regardless of the approach, the effort involved in obtaining a sample (henceforth called the sampling volume, but could also include swept areas, sampling durations, etc.), which can potentially be quite variable between samples, needs to be taken into account when modelling the resulting sample biomass. This is achieved empirically for the DG approach (using a generalized linear model with sampling volume as a covariate), and theoretically for the CPG approach (by scaling a parameter of the model). In this study, the consequences of this disparity between approaches were explored first using theoretical arguments, then using simulations and finally by applying the approaches to catch data from a commercial groundfish trawl fishery. The simulation study results point out that the DG approach can lead to poor estimates when far from standard idealized sampling assumptions. On the contrary, the CPG approach is much more robust to variable sampling conditions, confirming theoretical predictions. These results were confirmed by the case study for which model performances were weaker for the DG. Given the results, care must be taken when choosing an approach for dealing with zero-inflated continuous data. The DG approach, which is easily implemented using standard statistical softwares, works well when the sampling volume variability is small. However, better results were obtained with the CPG model when dealing with variable sampling volumes.

Survival of European plaice discarded from coastal otter trawl fisheries in the English Channel

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 one of the most discarded in the coastal otter trawl fishery in the English Channel. The objective of this study is to provide the most reliable estimates of plaice survival after release in commercial conditions, and to identify the factors that influence survival rates. A captivity experiment was conducted in January-February in the English fishery to assess the survival of discarded plaice as a function of a semi-quantitative index of fish vitality, which has been demonstrated to be a good proxy of fish survival in comparable fishing and environmental conditions. This study examined the potential of this index to estimate discard survival in three trials from the English and French fisheries and at three different seasons. The vitality index was then used to analyse the influence of several factors (fishing practices, environmental conditions and fish biological characteristics) on the discard survival. The survival rates for plaice were accurately estimated at 62.8% in January-February, 66.6% in November and 45.2% in July. While these rates remained substantial whatever the fishing, environmental or fish biological conditions, the time fish spent on the deck, the bottom and air temperatures, the tow depth and the fish length had a significant influence on plaice survival. In practice, plaice survival could be enhanced by releasing the fish early during catch sorting and avoiding exposure to extreme air temperatures.