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Bibliography of the Maurice Lamontagne Institute

Daniel E. DUPLISEA

TUCKER, A., D. DUPLISEA, 2012. Bioinformatics tools in predictive ecology : applications to fisheries. Philos. Trans. R. Soc. Lond., Ser. B: Biol. Sci., 367(1586): 279-290 .

There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse.©2011 The Royal Society

TAMDRARI, H., M. CASTONGUAY, J.-C. BRÊTHES, P.S. GALBRAITH, D.E. DUPLISEA, 2012. The dispersal pattern and behaviour of Atlantic Cod (Gadus morhua) in the northern Gulf of St. Lawrence : results from tagging experiments. Can. J. Fish. Aquat. Sci., 69(1): 112-121 .

We examined how the distribution of Atlantic cod (Gadus morhua) is influenced by abiotic (temperature, salinity, depth, suitable habitat) and biotic (stock biomass) factors based on tagging–recapture data collected from 1995 to 2008 by the Department of Fisheries and Oceans Canada in the northern Gulf of St. Lawrence. We calculated a centre of gravity index and a dispersion index using only individuals recaptured more than 1 year after tagging during the summer. The centre of gravity showed a northward expansion and eastward contraction in recent years, reflecting both fish distribution and changes in fishing effort. The dispersion index was significantly related to temperature, habitat suitability, and biomass but not to salinity or depth. These results indicate that interannual fluctuations of temperature and stock abundance both influence the dispersion pattern of cod. This new information could influence spatio-temporal fisheries management strategies for northern Gulf cod.©2012 NRC Research Press

TUCKER, A., D. DUPLISEA, 2011. Integrating marine species biomass data by modelling functional knowledge. LNCS, 7014:352-363 .

Ecosystems and their underlying foodwebs are complex. There are many hypothesised functions that play key roles in the delicate balance of these systems. In this paper, we explore methods for identifying species that exhibit similar functional relationships between them using fish survey data from oceans in three different geographical regions. We also exploit these functionally equivalent species to integrate the datasets into a single functional model and show that the quality of prediction is improved and the identified species make ecological sense. Of course, the approach is not only limited to fish survey data. In fact, it can be applied to any domain where multiple studies are recorded of comparable systems that can exhibit similar functional relationships.©2011 Springer-Verlag

MCALLISTER, M., D.E. DUPLISEA, 2011. Production model fitting and projection for Atlantic redfish (Sebastes fasciatus and Sebastes mentella) to assess recovery potential and allowable harm ; Ajustement du modèle de production et projection pour le sébaste atlantique (Sebastes fasciatus et Sebastes mentella) afin d’évaluer le potentiel de rétablissement et les dommages admissibles. DFO, Canadian Science Advisory Secretariat, Research Document ; MPO, Secrétariat canadien de consultation scientifique, Document de recherche, 2011/057, 81 p .

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A recovery potential analysis was carried out for stocks of Atlantic redfish falling within three designatable units recently assessed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) as either threatened or endangered. A state-space Schaefer surplus production model was fitted to trawl survey biomass estimates considered as relative indices of abundance for these different stocks. Bayesian methods were applied for parameter estimation, evaluation of stock status and stock projections for three populations of Acadian redfish, Sebastes fasciatus, and two populations of deepwater redfish, Sebastes mentella, on the Atlantic coast of Canada for the purpose of assessing recovery potential. This stock assessment methodology has been previously applied to other Sebastes species on the Pacific coast of Canada. The state-space version of this model allowed for the inclusion of process error which can account for deviations in dynamics from surplus production assumptions. Though apparently an esoteric methodological detail, allowing a process error estimate for each year means that the model can incorporate irregular population processes such as spasmodic recruitment events which seem to characterise Atlantic redfish populations and which can invalidate non-state-space implementations of production models. Results suggest that the Laurentian Channel population of S. mentella is presently in a very low biomass state with a 0 % chance of being above 40 % of the most productive stock biomass level (0.4 Bmsy) while the northern population is doing only slightly better with 1 % chance of being above this level. There would appear to be little prospect for any allowable harm on the Laurentian channel population if the goal is to increase the biomass of the stock even to only 40 % of Bmsy. The situation is only slightly better for the northern population. Results suggest that populations of S. fasciatus, are not nearly in such a poor state as S. Mentella and the southern population in Unit 3 would appear to be healthy. The Laurentian Channel-Grand bank population of S. fasciatus would appear to be able to support a directed fishery when considered as a unit stock. The 2J3K population of S. fasciatus is not very abundant and even small fisheries on this stock would slow down its recovery to 40 % Bmsy. S. Fasciatus, taken as a whole as the Atlantic designatable unit, would appear to have a very low risk of extinction and in most places could support directed fishing.

DUPLISEA, D.E., A. FRÉCHET, 2011. A preliminary evaluation of the impacts of Grey Seal, (Halichoerus grypus), predation on the 4T ecosystem and possible effects of their removal on Cod (Gadus morhua) recovery ; Évaluation préliminaire des impacts de la prédation par le phoque gris, (Halichoerus grypus), sur l'écosystème 4T et des effets possible d'un abattage sur le rétablissement des stocks de morue (Gadus morhua). DFO, Canadian Science Advisory Secretariat, Research Document ; MPO, Secrétariat canadien de consultation scientifique, Document de recherche, 2011/003, 12 p .

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Reference points for northern Gulf of St Lawrence (nGSL) cod were updated from the estimates presented at the 2009 cod zonal assessment process held in St. John’s (Duplisea and Fréchet 2009) owing to recent changes to the weight at age vector used for the calculation of spawning stock biomass (SSB). The new weight at age vector are based mostly on surveys corrected to January of each year rather than the weight age vector from the commercial fishery. The result of this change is that weight at age used for SSB calculation has decreased in all age classes though this does not affect abundance at age. Consequently, the previous estimate for the limit reference point declined from 140,000 t to 116,000 t and the upper stock reference point based on the recruitment plateau decreased from 200,000 t to 180,000 t. It is emphasised that changes to reference points here are mostly due to rescaling SSB and though it may change the perception of stock size, the actual abundance of fish in the water did not change in the VPA. Because the commercial weight at age vector is still used for TAC calculation and risk analysis, these are unaffected by the change in weight at age vector for SSB calculation.

DUPLISEA, D., D. POWER, 2011. Recovery potential assessment of redfish (Sebastes fasciatus and S. mentella) in the northwest Atlantic. DFO, Canadian Science Advisory Secretariat, Science Advisory Report, 2011/044, 18 p .

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DUPLISEA, D., D. POWER, 2011. Évaluation du potentiel de rétablissement du sébaste (Sebastes fasciatus et S. mentella) dans l'Atlantique Nord-Ouest. MPO, Secrétariat canadien de consultation scientifique, Avis scientifique, 2011/044, 20 P .

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LINK, J.S., A. BUNDY, W.J. OVERHOLTZ, N. SHACKELL, J. MANDERSON, D. DUPLISEA, J. HARE, M. KOEN-ALONSO, K.D. FRIEDLAND, 2011. Ecosystem-based fisheries management in the Northwest Atlantic. Fish Fish., 12(2): 152-170 .

The northwest Atlantic has had a notable history of living marine resource (LMR) exploitation. There have been calls for evaluating and improving approaches to manage those resources as stocks have undergone sequential depletion, with some dramatic instances of stock declines. The need for more holistic ecosystem-based approaches to manage LMRs has been increasingly recognized as part of these calls, along with the recognition that there are broader issues to consider when managing a fishery. We discuss some of the major efforts to this end which are extant among our institutions. We emphasize current initiatives to implement ecosystem-based fisheries management in the northwest Atlantic, with a focus on how advice based on the natural sciences supports an ecosystem-based approach. We present this information as a case study within a rich historical context of fisheries science and management.©2011 Blackwell Publishing Ltd.

FRISK, M.G., D.E. DUPLISEA, V.M. TRENKEL, 2011. Exploring the abundance-occupancy relationships for the Georges Bank finfish and shellfish community from 1963 to 2006. Ecol. Appl., 21(1): 227-240 .

Abundance–occupancy (A–O) patterns were explored temporally and spatially for the Georges Bank finfish and shellfish community to evaluate long-term trends in the assemblage structure and to identify anthropogenic and environmental drivers impacting the ecosystem. Analyses were conducted for 32 species representing the assemblage from 1963 to 2006 using data from the National Marine Fisheries Service’s annual autumn bottom trawl survey. For individual species, occupancy was considered the proportion of stations with at least one individual present, and abundance was estimated as the mean annual number of fish captured per station. Intraspecific relationships were estimated to provide information on utilization of space by a species. Multispecies interspecific relationships over all species for each year were fitted to estimate assemblage structural changes over the time series. Results indicated that the slopes and strengths of interspecific A–O relationships significantly declined over the duration of the time series, and this decline was significantly related to groundfish landings. However, the rate of decline was not constant, and a breakpoint analysis of interspecific slopes indicated that 1973 was a period of ‘‘state’’ change. More importantly a jackknife-after-bootstrap analysis indicated that the early 1970s followed by the 1990s were periods of higher than average probability of significant break points. While it is difficult to determine causation, the results suggest that long-term impacts such as habitat fragmentation may be influencing the species assemblage structure in the Georges Bank ecosystem. Further, we used slopes from the intraspecific A–O relationships to derive a measure of a species’ potential risk of hyperstability, where catch rates remain high as the population declines. Combining this measure of the risk of hyperstability with resilience to exploitation provided a means to rank species risk of decline due to both demographics and the interaction of the behaviors of the species and fishing fleets.©2011 The Ecological Society of America

TAMDRARI, H., M. CASTONGUAY, J.-C BRÊTHES, D. DUPLISEA, 2010. Density-independent and dependent habitat selection of Atlantic Cod (Gadus morhua) bases on geostatistical aggregation curves in the northern Gulf of St Lawrence. ICES J. Mar. Sci., 67(8): 1676-1686 .

Relationships were sought between local density and population abundance of Atlantic cod (Gadus morhua) in the northern Gulf of St Lawrence (Canada) over its entire area (4RS) and also within a subarea (4R) where the stock has concentrated since it collapsed during the early 1990s. Relationships were analysed using geostatistical aggregation curves computed within the two areas between years of contrasting abundance levels. The curves were interpreted in terms of four conceptual models of spatial dynamics: models D1 and D2, forced mainly by environmental heterogeneity, and models D3 and D4, in which individual behaviour is influenced by local density. Over the entire area, the cod population follows the D2 model for all years and age groups, and it is influenced by abiotic factors. Within the subarea, all four models applied, and the density-dependent basin model (D4) dominated from 2006 to 2008. The year 2006 seems to be pivotal because it coincides with the expansion of the cod population into its former area in the western Gulf (4S).©2010 International Council for the Exploration of the Sea. Published by Oxford Journals

DROUINEAU, H., S. MAHÉVAS, M. BERTIGNAC, D. DUPLISEA, 2010. A length-structured spatially explicit model for estimating hake growth and migration rates. ICES J. Mar. Sci., 67(8): 1697-1709 .

Despite an abundant literature, hake growth and migration remain poorly understood. A recent tagging campaign and an analysis of the growth increments on juvenile hake otoliths demonstrate that the growth rate has probably been largely underestimated. Migration rates have been studied through qualitative analysis of catch rate, but have not been confirmed by a more-quantitative analysis. Those biological uncertainties affect stock assessments and predictions by the uncertainty they bring to age–length keys and by hindering our ability to assess the impact of spatial management measures. Here, a spatially explicit length-structured model is developed to improve the biological knowledge of European hake (Merluccius merluccius), in terms specifically of migration and growth. The model belongs to the state–space class of models and is fitted by maximum likelihood on commercial landings, survey abundance indices, and tagging data. The estimated growth curve is close to estimates from tagging data, lending weight to the assumption of the species being fast-growing. Few migrations are long in distance, and there are none between the Bay of Biscay and the Celtic Sea. The model also demonstrates a high level of heterogeneity in the spatial distribution of spawning-stock biomass, with concentrations on the margins of the continental shelf.©2010 International Council for the Exploration of the Sea. Published by Oxford Journals

DUPLISEA, D.E., 2009. Precautionary reference point estimates for northern Gulf of St. Lawrence (3Pn4RS) Cod (Gadus morhua) and methods for their calculation ; Estimation des points de référence pour l'approche de précaution pour la morue (Gadus morhua) du nord du golfe du Saint-Laurent (3Pn4RS) et méthodes pour leur calcul. DFO, Canadian Science Advisory Secretariat, Research Document ; MPO, Secrétariat canadien de consultation scientifique, Document de recherche, 2009/097, 28 p .

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Six biomass limit reference points are estimated for northern Gulf of St. Lawrence (nGSL) cod. Five of these points are based on stock-recruit data while the sixth point is based purely on the concept of the minimum observed biomass from which there has been a recovery. In addition, two new methods for estimating reference points from stock-recruit data are introduced and estimated for nGSL cod. These new points should be evaluated on a variety of data sets, including simulated data and peer review before acceptance, though we introduce them here to place them in the context of other established methods. We conclude that for this stock, two of the six estimates can be considered credible for the stock using the 1974-2009 cohort reconstruction model output and place the biomass limit reference point at about 140,000 t spawning stock biomass (SSB) (this value was used in the 2009 assessment) We further suggest an upper stock reference point at about 200,000 t SSB which is a point above which there is little evidence of increased recruitment for an increase in SSB.

CHASSOT, E., D. DUPLISEA, M. HAMMILL, A. CASKENETTE, N. BOUSQUET, Y. LAMBERT, G. STENSON, 2009. Role of predation by harp seals Pagophilus groenlandicus in the collapse and non-recovery of northern Gulf of St. Lawrence cod Gadus morhua. Mar. Ecol. Prog. Ser., 379: 279-297 .

A statistical catch-at-age model was developed to assess the effects of predation by the northwest Atlantic harp seal population on northern Gulf of St. Lawrence cod by estimating the relative importance of different sources of mortality that affected the stock during a period of collapse and non-recovery. Cod recruitment at age 1 is modeled via a non-linear stock-recruitment relationship based on total egg production and accounts for changes in female length-at-maturity and cod condition. Natural mortality other than seal predation also depends on cod condition used as an integrative index of changes in environmental conditions. The linkage between seals and cod is modeled through a multi-age functional response that was derived from the reconstruction of the seal diet using morphometric relationships and stomach contents of more than 200 seals collected between 1998 and 2001. The model was fitted following a maximum likelihood estimation approach to a scientific survey abundance index (1984 to 2006). Model results show that the collapse of the northern Gulf of St. Lawrence cod stock was mainly due to the combination of high fishing mortality rates and poor environmental conditions in the early to mid-1990s contributing to the current state of recruitment overfishing. The increase in harp seal abundance during 1984 to 2006 was reflected by an increase in predation mortality for the young cod age-groups targeted by seals. Although current levels of predation mortality affect cod spawning biomass, the lack of recovery of the NGSL cod stock seems mainly due to the very poor recruitment.©2009 Inter-Research

BUNDY, A., G. CHOUINARD, D. DUPLISEA, G. JAMIESON, M. KOEN-ALONSO, M. KOOPS, J. RICE, L. RICHARD, 2008. National Workshop on Modelling Tools for Ecosystem Approaches to Management, 22-25 October 2007, Harbour Towers Hotel & Suites, Victoria, British Columbia, Canada ; Atelier national sur les outils de modelisation pour les approches de gestion ecosystemiques, du 22 au 25 octobre 2007, Harbour Towers Hotel & Suites, Victoria, Colombie-Britannique, Canada. DFO, Canadian Science Advisory Secretariat, Proceedings series, ; MPO, Secrétariat canadien de consultation scientifique, Série des comptes rendus, 2008/007, 98 p .

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A National workshop on modeling tools in support of ecosystem approaches to management was held in Victoria, BC, in October 22-25, 2007. Its main objectives were to discuss and evaluate different ecosystem modeling approaches and to explore their suitability in the Canadian and DFO context. Scientists from all regions, fisheries managers and international experts participated in the workshop. The workshop included an overview of the current use of ecosystem models in DFO, a series of presentations by ecosystem modelling experts of methods in use globally and in-depth discussions during breakout groups and plenary sessions. This report summarises the presentations and discussions, evaluates the questions that can be addressed by different ecosystem modelling approaches, highlights the essential role of ecosystem modeling for developing strategic advice and provides conclusions and recommendations to further develop ecosystem modelling and ecosystem approaches to management in DFO. It concludes with a summary of recommended actions, including suggestions of where efforts could be directed to provide strategic advice over the next one to two years.

DUPLISEA D.E., D. ROBERT, 2008. Prerecruit survival and recruitment of northern Gulf of St Lawrence Atlantic cod. ICES J. Mar. Sci., 65(6): 946-952 .

Recruitment (R) of exploited marine fish populations is usually modelled exclusively as a function of spawning-stock biomass (SSB). A problem arising when modelling over long time-series is that the nature of the R-SSB relationship is unlikely to be stationary. Changes are often interpreted as productivity regime shifts and are linked to alterations in prerecruit survival rate. We examine the role of environment and predation by fish and harp seals as factors affecting the R-SSB relationship in the northern Gulf of St Lawrence cod, by fitting linear models using combinations of covariates to explain cod prerecruit survival. The most parsimonious model (based on a Bayesian Information Criterion, BIC) included cod, mackerel, and temperature, whereas redfish and seals did not appear in any of the best-fit models. Recruitment models derived from this analysis could be used in operating models for management strategy evaluation simulations for northern Gulf cod, so one could develop harvest control rules that are robust to changes in recruitment productivity regimes.©2008 Canadian Crown & Oxford Journals

SHELTON, P.A., B. BEST, A. CASS, C. CYR, D. DUPLISEA, J. GIBSON, M. HAMMILL, S. KHWAJA, M.A. KOOPS, K.A. MARTIN, R. O'BOYLE, J.C. RICE, A. SINCLAIR, K. SMEDBOL, D.P. SWAIN, L.A. VÉLEZ-ESPINO, C.C. WOOD, 2007. Assessing recovery potential : long-term projections and their implications for socio-economic analysis ; Évaluation du potentiel de rétablissement : projections à long terme et répercussions sur l'analyse socio-économique. DFO, Canadian Science Advisory Secretariat, Research Document ; MPO, Secrétariat canadien de consultation scientifique, Document de recherche, 2007/045, 38 p .

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Recovery Potential Assessment (RPA) and associated socio-economic analysis are required to inform the decision on whether or not to list a species under the Species at Risk Act (SARA). RPA should also provide the basis for the Recovery Team to develop a Recovery Strategy and Action Plan after listing. While DFO has considerable experience in providing short-term scientific advice in support of fisheries management, approaches constituting best scientific practice and standards for long-term advice in support of listing decisions and recovery planning are still developing. Biological processes are best captured in a life-history model. This model needs to deal with both observation error and process error. Uncertainty associated with process error expands rapidly in projections beyond three years and methods have to take this into account. Bayesian state-space approaches provide a way of incorporating both observation and process error in the analysis. In most cases management strategy evaluation (MSE) of performance relative to a simulation of the biological process, assessment process and management process (operating model) may have the greatest potential given difficulties associated with making long-term quantitative projections. This approach could be expanded to include socioeconomic aspects. Scientific analysis can be completed as a first step and the results then passed to Policy and Economics to undertake socio-economic analysis. This twostep approach is considered to be less attractive than a fully integrated approach in which scientific and socio-economic analyses are undertaken and peer reviewed in a joint assessment. The current review was unable to fully develop the best-practice standard without further work. In order to make progress it is recommended that DFO management chose an upcoming high-profile RPA as a national case study to establish a best-practice standard for the preferred fully integrated biological/socio-economic approach that is described. The case study should include establishing independent socio-economic and scientific peer review, and public communication of expert advice on recovery potential and cost-benefit of alternative recovery options, independent of the political process of determining SARA listing.

SOLOW, A.R., D.E. DUPLISEA, 2007. Testing for compensation in a multi-species community. Ecosystems, 10(6): 1034-1038 .

The dynamics of a community are said to be compensatory if aggregate biomass is less variable over time than the biomass of the individual components of the system. In broad terms, the presence of compensation reflects interactions between components that tend to stabilize the overall community. A common quantitative measure used to detect compensation is the ratio of the temporal variance of total biomass to the sum of the biomass variances of the components, with a ratio less than 1 indicative of compensation. The purpose of this note is to describe a test for compensation when the variance ratio is estimated from biomass time series data. The test involves a bootstrap procedure that accounts for serial correlation in biomass. Failure to account for positive serial correlation can lead to spurious detection of compensation. The test is illustrated using biomass data for fish stocks on Georges Bank.©2007 Springer Science+Business Media, LLC

CHASSOT, E., A. CASKENETTE, D. DUPLISEA, M. HAMMILL, H. BOURDAGES, Y. LAMBERT, G. STENSON, 2007. A model of predation by harp seals (Phoca groenlandica) on the northern Gulf of St. Lawrence stock of Atlantic cod (Gadus morhua) ; Un modèle de prédation des phoques du Groenland (Phoca groenlandica) sur le stock de morue (Gadus morhua) du nord du golfe du Saint-Laurent. DFO, Canadian Science Advisory Secretariat, Research Document ; MPO, Secrétariat canadien de consultation scientifique, Document de recherche, 2007/066, 56 p .

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A dynamic model was developed to examine harp seal predation on Atlantic cod in the northern Gulf of St. Lawrence. The model describes the energetic requirements of the seal population by accounting for sex, age-structure and seal growth. The linkage between seals and cod is modeled through a functional response (FR) that was derived from the reconstruction of the seal diet using morphometric relationships and a large database of seal stomach contents. The FR then allows us to quantify the impact of seal predation on the cod population, based on age-structure attack rates and accounting for changes in cod size-at-age with time. Cod recruitment (age 1) is modeled via a linear stock-recruitment relationship based on total egg production that accounts for changes in female length at maturity and cod condition. Natural mortality other than seal predation also depends on cod condition used as an integrative index of changes in environmental conditions. The model was fitted following a maximum likelihood estimation approach to a consistent time-series of abundance indices taking into account changes in DFO research vessels over the last 23 years (1984-2006). Results were consistent with the most recent DFO stock assessment of the northern Gulf of St. Lawrence cod stock, explaining the history of the stock. Predation mortality, despite an increase in the mid-1990s, was a minor proportion of total mortality for ages targeted by harp seals, i.e. ages 1-4. Total cod biomass removed by seals showed higher interannual variability and greater decrease in the early 2000s than for modeling approaches based on a constant ratio diet. The type of FR–II or III– has a strong impact on the biomass removed, especially when the cod abundance is low. Sensitivity analyses were performed to assess the robustness of the results. The next step will be to project the model in to the future to evaluate repercussions of predation mortality rates on cod recovery.

SHELTON, P.A., A.F. SINCLAIR, G.A. CHOUINARD, R. MOHN, D.E. DUPLISEA, 2006. Fishing under low productivity conditions is further delaying recovery of northwest Atlantic cod (Gadus morhua). Can. J. Fish. Aquat. Sci., 63(2): 235-238 .

Excessive and unsustainable fishing mortality was the predominant factor in the depletion of Northwest Atlantic cod (Gadus morhua) stocks. However, despite imposition of severe catch restrictions for over a decade, stocks have mostly failed to recover at predicted rates. A number of explanations have been considered. Our analysis of demographic characteristics of 12 of these stocks indicates that recent productivity over the northern portion of the range is much lower than 20 years previous when several stocks recovered from less severe declines. Main contributing factors are, in rank order, increased natural mortality, decreased body growth, and in a few cases, reduced recruitment rates. Continued fishing in directed and bycatch fisheries is also an important factor. Under current conditions, we estimate negative or very low (<2 % per year) average growth rates in eight stocks. If fishing ceases, growth rates of >:5 % would be expected in six stocks, with >10 % in four of these. Although productivity is low, we conclude that fishing mortality is further delaying recovery.

DUPLISEA, D.E., M. CASTONGUAY, 2006. Comparison and utility of different size-based metrics of fish communities for detecting fishery impacts. Can. J. Fish. Aquat. Sci., 63: 810-820 .

The use of fish community indicators based on size spectra has become popular in the development of an ecosystem approach to fisheries. Size spectrum theory arose from basic ecological work on energy flow, predator-prey interactions, and biomass standing stock and was later applied to fish communities as length-frequency analysis. A multitude of size spectrum indicators have resulted, but it is not clear if they all present similar information. Here we develop a simple framework describing what four size spectra indicators suggest about fish communities, their likely response to fisheries exploitation, their ecological interpretation, and some of their biases. We examined indicators for scientific survey data from six exploited North Atlantic fish communities for the information that they reveal about each community. Each indicator revealed different information and had different biases. Combining indicators for the most impacted system (owing to fisheries and environmental change), the eastern Scotian Shelf, revealed a pattern analogous to Holling’s ecological cycle of exploitation, conservation, release, and reorganisation. If this analogy is generally valid, then it suggests that collapsed fish communities are more susceptible to chance events, and recovery is not directly reversible and may not be recoverable (to previous known state) at all if the system moves to an alternative cycle.

HIDDINGS, J.G., S. JENNINGS, M.J. KAISER, A.M. QUEIROS, D.E. DUPLISEA, G.J. PIET, 2006. Cumulative impacts of seabed trawl disturbance on benthic biomass, production, and species richness in different habitats. Can. J. Fish. Aquat. Sci., 63: 721-736 .

Bottom trawling causes widespread disturbance of sediments in shelf seas and can have a negative impact on benthic fauna. We conducted a large-scale assessment of bottom trawl fishing of benthic fauna in different habitats, using a theoretical, size-based model that included habitat features. Species richness was estimated based on a generalized body mass versus species richness relationship. The model was validated by sampling 33 stations subject to a range of trawling intensities in four shallow, soft sediment areas in the North Sea. Both the model and the field data demonstrated that trawling reduced biomass, production, and species richness. The impacts of trawling were greatest in areas with low levels of natural disturbance, while the impact of trawling was small in areas with high rates of natural disturbance. For the North Sea, the model showed that the bottom trawl fleet reduced benthic biomass and production by 56&nsbp;% and 21&nsbp;%, respectively, compared with an unfished situation. Because of the many simplifications and assumptions required to synthesize these data, additional work is required to refine the model and evaluate applicability in other geographic areas. Our model enables managers to understand the consequences of altering the distribution of fishing activities on benthic production and hence on food web processes

DUPLISEA, D.E., 2005. Running the gauntlet: the predation environment of small fish in the northern Gulf of St Lawrence, Canada. ICES J. Mar. Sci., 62(3): 412-416 .

Predation size spectra were constructed for the northern Gulf of St Lawrence, covering prey size ranges that include pre-recruit cod. Predation by fish and harp seals was modelled with a log-normally distributed predator-prey size ratio along with a relationship between predator body size and the energy required. Fish concentrate predation on prey of weight 0.5-2 g, whereas harp seals prefer prey of 60-125 g. It is speculated that predation caused by harp seals on pre-recruits could be a major factor limiting cod recruitment in the system. The northern Gulf of St Lawrence is a cold boreal system with a large predatory seal population, and cod recruit older than elsewhere. Therefore, cod recruitment may be more strongly affected by predation in the northern Gulf of St Lawrence than in warmer systems such as the North Sea, where recruitment is strongly influenced by temperature.©2004 Elsevier Ltd on behalf of International Council for the Exploration of the Sea

PINNEGAR, J.K., J.L. BLANCHARD, S. MACKINSON, R.D. SCOTT, D.E. DUPLISEA, 2005. Aggregation and removal of weak-links in food-web models: system stability and recovery from disturbance. Ecol. Model., 184(2-4): 229-248 .

Modelling is perceived as being one of the only tools available to address the new agenda of ecosystem management. However, little is currently understood with regard to the influence of model structure and configuration on predictions and hence management recommendations. In the present study we used a detailed Ecopath with Ecosim (EwE) model of the Barents Sea to test the impacts of food-web aggregation and the removal of weak linkages. Aggregation of a 41-compartment food-web to 27 and 16 compartment systems, greatly affected system properties (e.g. connectance, system omnivory, ascendancy), and also influenced dynamic stability. Highly aggregated models recovered more quickly following disturbances (a pulse of increased fishing pressure) compared to the original disaggregated model. Models aggregated with emphasis placed on particular parts of the food-web (fish, marine-mammals or invertebrates) exhibited marked differences in system indices, despite having the same number of compartments. Models in which invertebrates and basal materials (primary producers and detritus) were heavily aggregated proved particularly resilient to system disturbances. Models focusing on marine-mammals (but in which all other groups were heavily aggregated) also proved very resilient to disturbance, partly due to the slow turnover rates and low biomasses of these top-predatory consumers compared to all other functional groups in the model. Thus, the psychology and decisions of scientists constructing the model can greatly affect its performance and predictions. The Pareto c index is proposed, as a useful measure of skewness towards weak trophic links in food-web models. The 41-compartment 'control' model exhibited the highest Pareto c value, and hence was most skewed. Removal of weak links from the food-web, either by eliminating fluxes below a certain threshold or by random-sampling the diet-composition matrix, resulted in models with much lower connectance and Pareto c values. Such models were inherently less stable than the 41-compartment 'control' model. Recovery to within 10 % of starting values took longer when links had been removed, and the magnitude of fluctuations following a disturbance was also increased. Our findings infer a clear contradiction. Aggregated models possessed fewer weak links but recovered from a disturbance more quickly than disaggregated models (i.e., they were more stable). By contrast, food-webs from which weak links were specifically removed were the least stable of all the models tested. Thus whether weak links are removed through 'lumping' or 'chopping' seems to have very different system consequences.©2004 Elsevier B.V.

DUPLISEA, D.E., F. BLANCHARD, 2005. Relating species and community dynamics in an heavily exploited marine fish community. Ecosystems, 8(8): 899-910 .

DUPLISEA, D.E., S. JENNINGS, K.J. WARR, T.A. DINMORE, 2003. Erratum : A size-based model of the impacts of bottom trawling on benthic community structure. Can. J. Fish. Aquat. Sci., 60: 1306 .

DINMORE, T.A., D.E. DUPLISEA, B.D. RACKHAM, D.L. MAXWELL, S. JENNINGS, 2003. Impact of a large-scale area closure on patterns of fishing disturbance and the consequences for benthic communities. ICES J. Mar. Sci., 60: 371-380 .

DUPLISEA, D.E., S. JENNINGS, K.J. WARR, T.A. DINMORE, 2002. A size-based model of the impacts of bottom trawling on benthic community structure. Can. J. Fish. Aquat. Sci., 59: 1785-1795 .

Bottom trawling causes widespread disturbance to the sediments in shallow-shelf seas. The resultant mortality of benthic fauna is strongly size dependent. We empirically demonstrate that beam trawling frequency in the central North Sea had a greater effect on fauna size distribution in a soft sediment benthic community than variables such as sediment particle size and water depth. Accordingly, we simulated the impacts of trawling disturbance on benthos using a model consisting of 37 organism size classes between 1 µg and 140 g wet weight. The model produced a production-biomass versus size relationship consistent with published studies and allowed us to predict the impacts of trawling frequency on benthos size distributions. Outputs were consistent with empirical data; however, at high yet realistic trawling frequencies, the model predicted an extirpation of most macrofauna. Empirical data show that macrofauna persist in many heavily trawled regions; therefore, we suggest that trawling by real fisheries is sufficiently heterogeneous to provide spatial refuges less impacted by trawling. If correct, our analyses suggest that fishery management measures that do not reduce total effort but do lead to effort displacement and spatial homogenization (e.g., temporarily closed areas) may have adverse effects on the systemic persistence of intermediate- and large-sized macrofauna.

DUPLISEA, D.E., S. JENNINGS, S.J. MALCOM, R. PARKER, B. SIVYER, 2001. Modeling potential impacts of bottom trawl fisheries on soft sediment biogeochemistry in the North Sea. Geochem. Trans., 14: 1-6 .