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Journal articles on the topic 'Fish stock assessment – Mathematical models'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Schnute, Jon T., and Laura J. Richards. "Use and abuse of fishery models." Canadian Journal of Fisheries and Aquatic Sciences 58, no. 1 (2001): 10–17. http://dx.doi.org/10.1139/f00-150.

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Recent failures of important fish stocks give mathematical models a poor reputation as tools for fishery management. This paper examines the role of models in fish stock assessment and identifies reasons why they can fail. Starting with laws of arithmetic, models attempt to relate observed data to unknown quantities, such as the stock biomass and abundance. Typically, the number of unknowns greatly exceeds the number of observations, and models must impose hypothetical constraints to give useful estimates. We use the word "fishmetic" (rhymes with arithmetic) to represent uncertainty in the con

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2

Millar, Colin P., Ernesto Jardim, Finlay Scott, Giacomo Chato Osio, Iago Mosqueira, and Nekane Alzorriz. "Model averaging to streamline the stock assessment process." ICES Journal of Marine Science 72, no. 1 (2014): 93–98. http://dx.doi.org/10.1093/icesjms/fsu043.

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Abstract The current fish stock assessment process in Europe can be very resource- and time-intensive. The scientists involved require a very particular set of skills, acquired over their career, drawing from biology, ecology, statistics, mathematical modelling, oceanography, fishery policy, and computing. There is a particular focus on producing a single “best” stock assessment model, but as fishery science advances, there are clear needs to address a range of hypotheses and uncertainties, from large-scale issues such as climate change to specific ones, such as high observation error on young

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Orlowski, Andrzej. "Experimental verification of the acoustic characteristics of the clupeoid diel cycle in the Baltic." ICES Journal of Marine Science 62, no. 6 (2005): 1180–90. http://dx.doi.org/10.1016/j.icesjms.2005.02.013.

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Abstract This paper describes the results of a short-term experiment using measurements of sv from the diel, spatial, clupeoid distribution in the southern Baltic. The aim of the experiment was to verify fish-behaviour characteristics measured over the period from 1995 to 2001. It was also intended to estimate the dynamics of fish behaviour over one separate diel cycle. The studies were based on a 24 h continuous integration of fish echoes using an EY500 echosounder at 38 kHz. Measurements were carried out by RV “Baltica” travelling along the sides of a square of 4 nautical miles at a constant

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Xiao, Yongshun. "A general theory of fish stock assessment models." Ecological Modelling 128, no. 2-3 (2000): 165–80. http://dx.doi.org/10.1016/s0304-3800(00)00199-x.

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5

Vasilyev, D. A. "Diagnostics of the results of models application for fish stock assessment." Problems of fisheries 16, no. 4 (2015): 460–64. http://dx.doi.org/10.36038/0234-2774-2015-16-4-460-464.

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6

Albertsen, Christoffer Moesgaard, Anders Nielsen, and Uffe Høgsbro Thygesen. "Connecting single-stock assessment models through correlated survival." ICES Journal of Marine Science 75, no. 1 (2017): 235–44. http://dx.doi.org/10.1093/icesjms/fsx114.

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Abstract Fisheries management is mainly conducted via single-stock assessment models assuming that fish stocks do not interact, except through assumed natural mortalities. Currently, the main alternative is complex ecosystem models which require extensive data, are difficult to calibrate, and have long run times. We propose a simple alternative. In three case studies each with two stocks, we improve the single-stock models, as measured by Akaike information criterion, by adding correlation in the cohort survival. To limit the number of parameters, the correlations are parameterized through the

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7

Xiao, Yongshun. "Two simple approaches to use of production models in fish stock assessment." Fisheries Research 34, no. 1 (1998): 77–86. http://dx.doi.org/10.1016/s0165-7836(97)00064-7.

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8

Schnute, Jon T., and Ray Hilborn. "Analysis of Contradictory Data Sources in Fish Stock Assessment." Canadian Journal of Fisheries and Aquatic Sciences 50, no. 9 (1993): 1916–23. http://dx.doi.org/10.1139/f93-214.

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Fisheries stock assessments sometimes prove, in retrospect, to be wrong. Errors may be due to poor model assumptions or to data that do not reflect the biological process of interest. We develop a method that formally admits the possibility of such errors. Likelihood functions derived from this method indicate greater uncertainty in parameter values than conventional likelihoods, whose derivations presume that models correctly describe the observed data. The problem of uncertainty is particularly acute when more than one data source is available and different data sets provide contradictory pa

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9

Kuparinen, Anna, Samu Mäntyniemi, Jeffrey A. Hutchings, and Sakari Kuikka. "Increasing biological realism of fisheries stock assessment: towards hierarchical Bayesian methods." Environmental Reviews 20, no. 2 (2012): 135–51. http://dx.doi.org/10.1139/a2012-006.

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Excessively high rates of fishing mortality have led to rapid declines of several commercially important fish stocks. To harvest fish stocks sustainably, fisheries management requires accurate information about population dynamics, but the generation of this information, known as fisheries stock assessment, traditionally relies on conservative and rather narrowly data-driven modelling approaches. To improve the information available for fisheries management, there is a demand to increase the biological realism of stock-assessment practices and to better incorporate the available biological kno

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Deroba, J. J., D. S. Butterworth, R. D. Methot, et al. "Simulation testing the robustness of stock assessment models to error: some results from the ICES strategic initiative on stock assessment methods." ICES Journal of Marine Science 72, no. 1 (2014): 19–30. http://dx.doi.org/10.1093/icesjms/fst237.

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Abstract The World Conference on Stock Assessment Methods (July 2013) included a workshop on testing assessment methods through simulations. The exercise was made up of two steps applied to datasets from 14 representative fish stocks from around the world. Step 1 involved applying stock assessments to datasets with varying degrees of effort dedicated to optimizing fit. Step 2 was applied to a subset of the stocks and involved characteristics of given model fits being used to generate pseudo-data with error. These pseudo-data were then provided to assessment modellers and fits to the pseudo-dat

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Cadrin, Steven X., and Mark Dickey-Collas. "Stock assessment methods for sustainable fisheries." ICES Journal of Marine Science 72, no. 1 (2014): 1–6. http://dx.doi.org/10.1093/icesjms/fsu228.

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Abstract This special volume of the ICES Journal compiles contributions from the World Conference on Stock Assessment Methods for Sustainable Fisheries (July 2013, Boston, USA). The conference was the product of a strategic initiative on stock assessment methods that engaged many national and regional fishery management organizations to assure that scientists can apply the most appropriate methods when developing management advice. An inclusive workshop was designed to evaluate the performance of a variety of model categories by applying multiple models to selected case study data as well as s

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Saul, Steven, Elizabeth N. Brooks, and David Die. "How fisher behavior can bias stock assessment: insights from an agent-based modeling approach." Canadian Journal of Fisheries and Aquatic Sciences 77, no. 11 (2020): 1794–809. http://dx.doi.org/10.1139/cjfas-2019-0025.

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During stock assessment, fishery-dependent observations are often used to develop indices of abundance or biomass from catch per unit of effort (CPUE) and contribute catch at size or age information. However, fisher behavior, rather than scientific sampling protocols, determines the spatial and temporal locations of fishery-dependent observations. As a result, trends from fishery-dependent data may be a function of fishing activity rather than fish population changes. This study evaluates whether data collected from commercial fishing fleets in the Gulf of Mexico are representative of trends i

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Stewart, Ian J., and Steven J. D. Martell. "Reconciling stock assessment paradigms to better inform fisheries management." ICES Journal of Marine Science 72, no. 8 (2015): 2187–96. http://dx.doi.org/10.1093/icesjms/fsv061.

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Abstract For several decades, the fisheries stock assessment paradigms of virtual population analysis (VPA) and statistical catch-at-age (SCA) models have been routinely applied to major fish stocks, and their prevalence often dictated by historical continuity, local experience, and geographical differences in standard practices. Similarly, there is a growing split among models using short and long time-series. In one approach, only the recent time-series, where the data are relatively complete, and the assumptions about stationarity in population and sampling processes are relatively simple,

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Xiao, Yongshun. "Subtleties in, and practical problems with, the use of production models in fish stock assessment." Fisheries Research 33, no. 1-3 (1997): 17–36. http://dx.doi.org/10.1016/s0165-7836(97)00065-9.

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15

Jamnia, Abdul Rashid, Ahmad Ali Keikha, Mahmoud Ahmadpour, Abdoul Ahad Cissé, and Mohammad Rokouei. "Applying bayesian population assessment models to artisanal, multispecies fisheries in the Northern Mokran Sea, Iran." Nature Conservation 28 (August 13, 2018): 61–89. http://dx.doi.org/10.3897/natureconservation.28.25212.

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Small-scale fisheries substantially contribute to the reduction of poverty, local economies and food safety in many countries. However, limited and low-quality catches and effort data for small-scale fisheries complicate the stock assessment and management. Bayesian modelling has been advocated when assessing fisheries with limited data. Specifically, Bayesian models can incorporate information of the multiple sources, improve precision in the stock assessments and provide specific levels of uncertainty for estimating the relevant parameters. In this study, therefore, the state-space Bayesian

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Chen, D. G., and D. M. Ware. "A neural network model for forecasting fish stock recruitment." Canadian Journal of Fisheries and Aquatic Sciences 56, no. 12 (1999): 2385–96. http://dx.doi.org/10.1139/f99-178.

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A neural network model is developed to forecast the recruiting biomass of fish. The west coast of Vancouver Island, British Columbia, Pacific herring (Clupea pallasi) stock is selected as an example application based on data compiled from long-term ecosystem research and stock assessment programs. A fuzzy logic decision procedure was used to evaluate all possible neural networks. The output from the two "optimal" networks was compared with the output from a multiple regression analysis and a standard Ricker climate stock-recruitment model. The performance of the neural network models in reprod

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Correa, Giancarlo M., Lorenzo Ciannelli, Lewis A. K. Barnett, Stan Kotwicki, and Claudio Fuentes. "Improved estimation of age composition by accounting for spatiotemporal variability in somatic growth." Canadian Journal of Fisheries and Aquatic Sciences 77, no. 11 (2020): 1810–21. http://dx.doi.org/10.1139/cjfas-2020-0166.

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Age composition is defined as the proportion of a fish population belonging to each age class and is an informative input to stock assessment models. Variations in somatic growth rates may lead to larger errors in age composition estimates. To reduce this source of error, we compared the performance of four methods for estimating age compositions of a simulated fish population: two methods based on age–length keys (ALK, pooled and annual) and two model-based approaches (generalized additive models (GAMs) and continuation ratio logits (CRLs)). CRL was the most robust and precise method, followe

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GU, EN-GUO. "STOCK-HARVEST DYNAMICS IN MULTIAGENT FISHERIES." International Journal of Bifurcation and Chaos 21, no. 01 (2011): 363–72. http://dx.doi.org/10.1142/s0218127411028477.

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In this work, we build a two-dimensional dynamical fishery model in which the total harvest is obtained by a multiagent game with best reply strategy and naive expectations, i.e. each agent decides the harvest quantity by solving a profit maximization problem. Special attention is paid to the global dynamic analysis in the light of feasible domains (initial conditions giving non-negative trajectories converging to an equilibrium), which is related to the crisis of extinction. We also study the existence and stability of non-negative equilibria for models through mathematical analysis and numer

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Moustahfid, H., J. S. Link, W. J. Overholtz, and M. C. Tyrrell. "The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel." ICES Journal of Marine Science 66, no. 3 (2009): 445–54. http://dx.doi.org/10.1093/icesjms/fsn217.

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AbstractMoustahfid, H., Link, J. S., Overholtz, W. J., and Tyrrell, M. C. 2009. The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel. – ICES Journal of Marine Science, 66: 445–454. An age-structured assessment programme (ASAP) that explicitly incorporates predation mortality was applied to Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic. Predatory removals were modelled in the same manner as fishing mortality, with a comparable set of time-series, to produce estimates of predation mortalit

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20

Harley, Shelton J., and Ransom A. Myers. "Hierarchical Bayesian models of length-specific catchability of research trawl surveys." Canadian Journal of Fisheries and Aquatic Sciences 58, no. 8 (2001): 1569–84. http://dx.doi.org/10.1139/f01-097.

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To estimate absolute abundance from research trawl surveys, the catchability of the fish to the gear must be known or estimated. Using 47 data sets of length-specific catchability, we conducted a hierarchical Bayesian meta-analysis of length-specific catchability for a number of different species groups. It was found that the Bayesian estimates of catchability were seldom near or above 1 for any species or size. This suggests that any assumption that swept-area abundance estimates are in fact absolute abundance would likely underestimate the true abundance. Catchability was higher for haddock

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Walters, Carl J., and Ramón Bonfil. "Multispecies spatial assessment models for the British Columbia groundfish trawl fishery." Canadian Journal of Fisheries and Aquatic Sciences 56, no. 4 (1999): 601–28. http://dx.doi.org/10.1139/f98-205.

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A multispecies spatial model is proposed for evaluation of trawl management strategies and tested with data from British Columbia groundfish. Minimum stock sizes are estimated for 16 species using spatial catch per unit effort data; these data indicate that only small proportions of most stocks are exposed to fishing at any time and that exchange rates of fish between the grounds and other habitats are rapid. A gravity model for spatial effort allocation predicts substantial side effects of marine protected areas or discarding of particular species on nontarget species/grounds due to redistrib

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Correa, Giancarlo M., Carey R. McGilliard, Lorenzo Ciannelli, and Claudio Fuentes. "Spatial and temporal variability in somatic growth in fisheries stock assessment models: evaluating the consequences of misspecification." ICES Journal of Marine Science 78, no. 5 (2021): 1900–1908. http://dx.doi.org/10.1093/icesjms/fsab096.

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Abstract Distinct types of fish species experience variation in somatic growth rates over their life span; however, growth has historically been assumed to be invariant across time and space in integrated analysis-based stock assessment. A few previous studies have reported biased and imprecise assessment model outcomes when variability in somatic growth was ignored. In this study, we used a simulation-estimation framework to expand previous analyses and to examine the consequences of ignoring or incorporating spatial and temporal (year- and cohort-specific) variability in somatic growth in st

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Helu, S. Langitoto, David B. Sampson, and Yanshui Yin. "Application of statistical model selection criteria to the Stock Synthesis assessment program." Canadian Journal of Fisheries and Aquatic Sciences 57, no. 9 (2000): 1784–93. http://dx.doi.org/10.1139/f00-137.

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Statistical modeling involves building sufficiently complex models to represent the system being investigated. Overly complex models lead to imprecise parameter estimates, increase the subjective role of the modeler, and can distort the perceived characteristics of the system under investigation. One approach for controlling the tendency to increased complexity and subjectivity is to use model selection criteria that account for these factors. The effectiveness of two selection criteria was tested in an application with the stock assessment program known as Stock Synthesis. This program, which

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McGarvey, Richard, John E. Feenstra, and Qifeng Ye. "Modeling fish numbers dynamically by age and length: partitioning cohorts into "slices"." Canadian Journal of Fisheries and Aquatic Sciences 64, no. 9 (2007): 1157–73. http://dx.doi.org/10.1139/f07-080.

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Fishery processes of selectivity and recruitment to legal size vary with fish length and are mediated by fish growth. Yet most fishery models are age-based. To model length-dependent change within each cohort, fish numbers must vary dynamically with length as well as with age in the model population array. The fishery model formalism described here achieves this by a partition of the continuous length-at-age distribution. This method is computationally efficient and cleanly differentiates legal from sublegal fish. Fish numbers within each cohort are partitioned into length bins, called slices.

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Webster, Raymond A., William G. Clark, Bruce M. Leaman, and Joan E. Forsberg. "Pacific halibut on the move: a renewed understanding of adult migration from a coastwide tagging study." Canadian Journal of Fisheries and Aquatic Sciences 70, no. 4 (2013): 642–53. http://dx.doi.org/10.1139/cjfas-2012-0371.

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Results of a coastwide tagging study show that ontogenetic migration of Pacific halibut (Hippoglossus stenolepis) continues for larger fish, whereas in recent years the assumption had been that only smaller, younger fish migrated. In 2003–2004, a total of 67 000 Pacific halibut tagged with passive integrated transponder tags were released by the International Pacific Halibut Commission (IPHC) from Oregon to the Bering Sea. Portside scanning recovered over 3000 of these tags. Models were fitted that allowed commercial fishing mortality to be a function of fish length, year, and IPHC regulatory

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Berg, Casper W., and Anders Nielsen. "Accounting for correlated observations in an age-based state-space stock assessment model." ICES Journal of Marine Science 73, no. 7 (2016): 1788–97. http://dx.doi.org/10.1093/icesjms/fsw046.

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Abstract Fish stock assessment models often rely on size- or age-specific observations that are assumed to be statistically independent of each other. In reality, these observations are not raw observations, but rather they are estimates from a catch-standardization model or similar summary statistics based on observations from many fishing hauls and subsamples of the size and age composition of the data. Although aggregation mitigates the strong intra-haul correlation between sizes/ages that is usually found in haul-by-haul data, violations of the independence assumption can have a large impa

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Fournier, David A., and Ian J. Doonan. "A Length-Based Stock Assessment Method Utilizing a Generalized Delay-Difference Model." Canadian Journal of Fisheries and Aquatic Sciences 44, no. 2 (1987): 422–37. http://dx.doi.org/10.1139/f87-051.

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We present a length-based stock assessment method based on a generalization of the delay-difference methods of Deriso. Data inputs to the model include the estimated weight of the catch, the estimated fishing effort, the estimated mean weight of the catch, and the estimated central moments of the length distribution of the catch. The model's performance is demonstrated by applying it to data from a simulated exploited fish population exhibiting biomass-dependent catchability which would cause conventional catch–effort models to seriously underestimate the extent of stock depletion. The model w

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Winters, G. H., and J. P. Wheeler. "Interaction Between Stock Area, Stock Abundance, and Catchability Coefficient." Canadian Journal of Fisheries and Aquatic Sciences 42, no. 5 (1985): 989–98. http://dx.doi.org/10.1139/f85-124.

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The relationship between commercial catch-rates and population density upon which many stock assessment models depend assumes that stock area (A) is constant and independent of population abundance. Starting from a theoretical demonstration that the catchability coefficient (q) is inversely proportional to A, we establish the empirical basis of this relationship through comparisons of q and A of various Northwest Atlantic herring (Clupea harengus harengus) stocks and, in more detail, for Fortune Bay herring. For these stocks the relationship was of the form q = cA−b. For Atlantic herring stock

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Xu, Haikun, James T. Thorson, Richard D. Methot, and Ian G. Taylor. "A new semi-parametric method for autocorrelated age- and time-varying selectivity in age-structured assessment models." Canadian Journal of Fisheries and Aquatic Sciences 76, no. 2 (2019): 268–85. http://dx.doi.org/10.1139/cjfas-2017-0446.

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Selectivity is a key parameter in stock assessments that describes how fisheries interact with different ages and sizes of fish. It is usually confounded with other processes (e.g., natural mortality and recruitment) in stock assessments and the assumption of selectivity can strongly affect stock assessment outcome. Here, we introduce a new semi-parametric selectivity method, which we implement and test in Stock Synthesis. This selectivity method includes a parametric component and an autocorrelated nonparametric component consisting of deviations from the parametric component. We explore the

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Siskey, Matthew R., Michael G. Frisk, Robert M. Cerrato, and Karin E. Limburg. "Redefining spatial population structure of winter flounder (Pseudopleuronectes americanus): implications for stock assessment and management." Canadian Journal of Fisheries and Aquatic Sciences 77, no. 7 (2020): 1189–200. http://dx.doi.org/10.1139/cjfas-2019-0279.

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The southern New England – mid-Atlantic (SNE–MA) stock of winter flounder (Pseudopleuronectes americanus) collapsed in the 1990s without discernable recovery to date. Owing to the lack of recovery, consideration of population subcomponents, which are currently ignored in fisheries stock structure definitions, may be necessary for rebuilding. We used the otolith chemistry tracer manganese–calcium ratios (Mn/Ca) to estimate inshore- versus ocean-nursery contributions of 77.3%/22.7% in SNE–MA, 15.7%/84.3% in the Gulf of Maine (GOM), and 60.0%/40.0% in Georges Bank (GB). In addition, we used stron

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Kempf, Alexander, Jens Floeter, and Axel Temming. "Decadal changes in the North Sea food web between 1981 and 1991 — implications for fish stock assessment." Canadian Journal of Fisheries and Aquatic Sciences 63, no. 11 (2006): 2586–602. http://dx.doi.org/10.1139/f06-147.

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The North Sea ecosystem of the early 1980s differed substantially from that of the early 1990s. The current North Sea multispecies fisheries assessment models are parameterized by fish diet data sets that reflect both ecosystem states, as the stomachs were sampled in 1981 and 1991. In this study, multispecies virtual population analysis (MSVPA) was parameterized with either diet data set, leading to different model food webs, each representing the predator's diet selection behavior and spatiotemporal overlap with their prey in the two respective ecosystem states. The impact of these changes in

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Hinrichsen, Hans-Harald, Mark Dickey-Collas, Martin Huret, Myron A. Peck, and Frode B. Vikebø. "Evaluating the suitability of coupled biophysical models for fishery management." ICES Journal of Marine Science 68, no. 7 (2011): 1478–87. http://dx.doi.org/10.1093/icesjms/fsr056.

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Abstract Hinrichsen, H-H., Dickey-Collas, M., Huret, M., Peck, M. A., and Vikebø, F. B. 2011. Evaluating the suitability of coupled biophysical models for fishery management. – ICES Journal of Marine Science, 68: 1478–1487. The potential role of coupled biophysical models in enhancing the conservation, management, and recovery of fish stocks is assessed, with emphasis on anchovy, cod, herring, and sprat in European waters. The assessment indicates that coupled biophysical models are currently capable of simulating transport patterns, along with temperature and prey fields within marine ecosyst

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Francis, R. I. C. Chris. "Comment on “Differences in predicted catch composition between two widely used catch equation formulations”Appears in Can. J. Fish. Aquat. Sci. 66: 126–132." Canadian Journal of Fisheries and Aquatic Sciences 67, no. 4 (2010): 763–65. http://dx.doi.org/10.1139/f10-023.

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Branch (2009. Can. J. Fish. Aquat. Sci. 66: 126–132) described the two most common catch equation formulations in stock assessment models: the continuous (Baranov) one, which represents fishing mortality as an instantaneous rate, F, and the discrete one, in which it is represented as an exploitation rate, u. He claimed that the continuous formulation is preferable at high fishing mortality where a fish could encounter multiple sets of gear within a year. This claim is wrong for two reasons. First, it is based on the false supposition that the discrete catch equations require the assumption tha

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Carvalho, Felipe, Robert Ahrens, Debra Murie, et al. "Using pop-up satellite archival tags to inform selectivity in fisheries stock assessment models: a case study for the blue shark in the South Atlantic Ocean." ICES Journal of Marine Science 72, no. 6 (2015): 1715–30. http://dx.doi.org/10.1093/icesjms/fsv026.

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Abstract Selectivity has traditionally been well estimated internally in stock assessment models when length or age composition data are available. However, in stock assessment, temporal or spatial variation in fishery or stock structure can lead to misspecification of the selectivity pattern, which can contribute substantially to the uncertainty in stock assessment results. Consequently, generating auxiliary information to help stock assessment scientists avoid unrealistic specifications of selectivity patterns should be encouraged. Here, we combine data from pop-up satellite archival tags (P

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McGilliard, Carey R., André E. Punt, Richard D. Methot, and Ray Hilborn. "Accounting for marine reserves using spatial stock assessments." Canadian Journal of Fisheries and Aquatic Sciences 72, no. 2 (2015): 262–80. http://dx.doi.org/10.1139/cjfas-2013-0364.

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Some fish stock assessments are conducted in regions that contain no-take marine reserves (NTMRs). NTMRs are expected to lead to spatial heterogeneity in fish biomass by allowing a buildup of biomass inside their borders while fishing pressure occurs outside. Stock assessments do not typically account for spatial heterogeneity caused by NTMRs, which may lead to biased estimates of biomass. Simulation modeling is used to analyze the ability of several stock assessment configurations to estimate current biomass after the implementation of a single, large NTMR. Age-structured spatial operating mo

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Guay, J. C., D. Boisclair, M. Leclerc, and M. Lapointe. "Assessment of the transferability of biological habitat models for Atlantic salmon parr (Salmo salar)." Canadian Journal of Fisheries and Aquatic Sciences 60, no. 11 (2003): 1398–408. http://dx.doi.org/10.1139/f03-120.

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We assessed the transferability of the habitat suitability index (HSI) and the habitat probabilistic index (HPI) between two rivers. Transferability was measured by the ability of HSI and HPI models developed in the Sainte-Marguerite River to predict the distribution of Atlantic salmon parr (Salmo salar) in the Escoumins River. HSI and HPI were based on the pattern of utilization by fish of water depth, current velocity, and substrate size. HSI was developed using the preference curve approach, and HPI was developed using a multiple logistic regression. Predicted values of HSI and HPI in Escou

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Goethel, Daniel R., Christopher M. Legault, and Steven X. Cadrin. "Demonstration of a spatially explicit, tag-integrated stock assessment model with application to three interconnected stocks of yellowtail flounder off of New England." ICES Journal of Marine Science 72, no. 1 (2014): 164–77. http://dx.doi.org/10.1093/icesjms/fsu014.

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Abstract Ignoring population structure and connectivity in stock assessment models can introduce bias into important management metrics. Tag-integrated assessment models can account for spatially explicit population dynamics by modelling multiple population components, each with unique demographics, and estimating movement among them. A tagging submodel is included to calculate predicted tag recaptures, and observed tagging data are incorporated in the objective function to inform estimates of movement and mortality. We describe the tag-integrated assessment framework and demonstrate its use t

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Pepin, Pierre. "Reconsidering the impossible — linking environmental drivers to growth, mortality, and recruitment of fish." Canadian Journal of Fisheries and Aquatic Sciences 73, no. 2 (2016): 205–15. http://dx.doi.org/10.1139/cjfas-2015-0091.

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After a century of research into the drivers of early life (EL) growth and mortality, fisheries science has acquired limited capacity to predict future recruitment. A meta-analysis of stock assessment time series revealed that it may be difficult to identify stock– or environmental–recruitment drivers given limited variability in spawner biomass, recruitment, and survivorship in most populations. In nearly 50% of the stocks, there was limited information at low spawner biomass, limiting the reliability of fits to stock–recruitment models. Furthermore, variations in survivorship in 50% of year-

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Eide, Arne. "Substituting model-based indicators in Harvest Control Rules by observations using fuzzy logic methodology." ICES Journal of Marine Science 75, no. 3 (2017): 977–87. http://dx.doi.org/10.1093/icesjms/fsx227.

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Abstract Harvest Control Rules are predefined heuristic decision rules to provide quota advices for managed fisheries. Frequently statistical methods and biological assumptions expressed in mathematical models, are used to provide the Harvest Control Rules with initial information (indicators values). The aim of this article is to investigate a possible way forward of replacing these inputs by quantities of measurable observations, e.g. catch-at-age statistics. The article presents a method by which recruitment indexes and stock biomass indicators are obtained by non-parametric use of annual c

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Sguotti, Camilla, Saskia A. Otto, Xochitl Cormon, et al. "Non-linearity in stock–recruitment relationships of Atlantic cod: insights from a multi-model approach." ICES Journal of Marine Science 77, no. 4 (2019): 1492–502. http://dx.doi.org/10.1093/icesjms/fsz113.

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Abstract The stock–recruitment relationship is the basis of any stock prediction and thus fundamental for fishery management. Traditional parametric stock–recruitment models often poorly fit empirical data, nevertheless they are still the rule in fish stock assessment procedures. We here apply a multi-model approach to predict recruitment of 20 Atlantic cod (Gadus morhua) stocks as a function of adult biomass and environmental variables. We compare the traditional Ricker model with two non-parametric approaches: (i) the stochastic cusp model from catastrophe theory and (ii) multivariate simple

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Haltuch, Melissa A., and André E. Punt. "The promises and pitfalls of including decadal-scale climate forcing of recruitment in groundfish stock assessment." Canadian Journal of Fisheries and Aquatic Sciences 68, no. 5 (2011): 912–26. http://dx.doi.org/10.1139/f2011-030.

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Concurrent declines in demersal fish stock abundances and shifts in long-term average environmental conditions have been well documented in the Pacific. Management advice ignoring environmental forcing of recruitment may cause stocks to be over- or under-harvested, so it is important to consider including environmental forcing on recruitment in stock assessment models. Simulation testing is used to determine the statistical power of stock assessments to identify long-term, decadal-scale environmental forcing of recruitment and the ability to estimate management reference points when the durati

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O’Leary, Cecilia A., Timothy J. Miller, James T. Thorson, and Janet A. Nye. "Understanding historical summer flounder (Paralichthys dentatus) abundance patterns through the incorporation of oceanography-dependent vital rates in Bayesian hierarchical models." Canadian Journal of Fisheries and Aquatic Sciences 76, no. 8 (2019): 1275–94. http://dx.doi.org/10.1139/cjfas-2018-0092.

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Climate can impact fish population dynamics through changes in productivity and shifts in distribution, and both responses have been observed for many fish species. However, few studies have incorporated climate into population dynamics or stock assessment models. This study aimed to uncover how past variations in population vital rates and fishing pressure account for observed abundance variation in summer flounder (Paralichthys dentatus). The influences of the Gulf Stream Index, an index of climate variability in the Northwest Atlantic, on abundance were explored through natural mortality an

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He, Ji X., James R. Bence, Charles P. Madenjian, et al. "Coupling age-structured stock assessment and fish bioenergetics models: a system of time-varying models for quantifying piscivory patterns during the rapid trophic shift in the main basin of Lake Huron." Canadian Journal of Fisheries and Aquatic Sciences 72, no. 1 (2015): 7–23. http://dx.doi.org/10.1139/cjfas-2014-0161.

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We quantified piscivory patterns in the main basin of Lake Huron during 1984–2010 and found that the biomass transfer from prey fish to piscivores remained consistently high despite the rapid major trophic shift in the food webs. We coupled age-structured stock assessment models and fish bioenergetics models for lake trout (Salvelinus namaycush), Chinook salmon (Oncorhynchus tshawytscha), walleye (Sander vitreus), and lake whitefish (Coregonus clupeaformis). The model system also included time-varying parameters or variables of growth, length–mass relations, maturity schedules, energy density,

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BABCOCK, RUSSELL C., DANIEL P. EGLI, and COLIN G. ATTWOOD. "Incorporating behavioural variation in individual-based simulation models of marine reserve effectiveness." Environmental Conservation 39, no. 3 (2012): 282–94. http://dx.doi.org/10.1017/s0376892912000148.

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SUMMARYEffective spatial management of marine species requires informed planning, as well as ongoing assessment. For mobile species such as fish, knowledge of the scale and variation in movement is central to key planning decisions, such as the size and shape of marine reserves and the interpretation of the response of protected populations. For example, populations of species that require large areas of habitat may not show increases in abundance inside small reserves, but calculating optimal reserve size is complicated by individual variations in behaviour. Fish movements can be used to quan

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Rahikainen, Mika, and Sakari Kuikka. "Fleet dynamics of herring trawlerschange in gear size and implications for interpretation of catch per unit effort." Canadian Journal of Fisheries and Aquatic Sciences 59, no. 3 (2002): 531–41. http://dx.doi.org/10.1139/f02-030.

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Catch per unit effort (CPUE) is widely used as an index of stock abundance. It is as widely acknowledged that CPUE can be a misleading index of abundance owing to a multitude of factors including fish behavior, fishing fleet interaction, and the increase in catchability over time caused by improvement in fishing technology. Based on information concerning the size of herring trawls manufactured in Finland since the early 1980s, an increase in fishing power of the fleet was postulated. Because we lacked direct information about the size of trawls aboard, we applied a model to estimate the chang

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Harris, Julianne E., and Joseph E. Hightower. "An integrated tagging model to estimate mortality rates of Albemarle Sound – Roanoke River striped bass." Canadian Journal of Fisheries and Aquatic Sciences 74, no. 7 (2017): 1061–76. http://dx.doi.org/10.1139/cjfas-2016-0141.

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We developed an integrated tagging model to estimate mortality rates and run sizes of Albemarle Sound – Roanoke River striped bass (Morone saxatilis), including (i) a multistate component for telemetered fish with a high reward external tag; (ii) tag return components for fish with a low reward external or PIT tag; and (iii) catch-at-age data. Total annual instantaneous mortality was 1.08 for resident (458–899 mm total length, TL) and 0.45 for anadromous (≥900 mm TL) individuals. Annual instantaneous natural mortality was higher for resident (0.70) than for anadromous (0.21) fish due to high s

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Stewart, Ian J., and Owen S. Hamel. "Bootstrapping of sample sizes for length- or age-composition data used in stock assessments." Canadian Journal of Fisheries and Aquatic Sciences 71, no. 4 (2014): 581–88. http://dx.doi.org/10.1139/cjfas-2013-0289.

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Integrated stock assessment models derive estimates of management quantities by fitting to indices of abundance and length and age compositions. For composition data, where a multinomial likelihood is often applied, weights are determined by input sample sizes, which can be an important contributor to model results. We used a generic bootstrap method, verified through simulation, to calculate year-specific maximum realized sample sizes from the observation error inherent in fishery biological data. Applying this method to length-composition observations for 47 groundfish species collected duri

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Nadon, Marc O., and Jerald S. Ault. "A stepwise stochastic simulation approach to estimate life history parameters for data-poor fisheries." Canadian Journal of Fisheries and Aquatic Sciences 73, no. 12 (2016): 1874–84. http://dx.doi.org/10.1139/cjfas-2015-0303.

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Coastal fisheries are typically characterized by species-rich catch compositions and limited management resources, which typically leads to notably data-poor situations for stock assessment. Some parsimonious stock assessment approaches rely on cost-efficient size composition data, but these also require estimates of life history parameters associated with natural mortality, growth, and maturity. These parameters are unavailable for most exploited stocks. Here, we present a novel approach that uses a local estimate of maximum length and statistical relationships between key life history parame

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Schnute, Jon. "A General Fishery Model for a Size-Structured Fish Population." Canadian Journal of Fisheries and Aquatic Sciences 44, no. 5 (1987): 924–40. http://dx.doi.org/10.1139/f87-111.

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This paper describes a fishery model based on size, rather than age, as the fundamental population variable. The model's key ingredient is a density function related to number of fish within any given size range. A key assumption is that selectivity in the fishery is determined by size, not age, and that fish can reach recruitment size at various ages. The theory easily yields moment equations comparable with those obtained recently by Fournier and Doonan; for example, the general moment equation here is derived in a four-line proof. The paper gives detailed recommendations for tailoring the n

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Gudmundsson, Gudmundur, and Thorvaldur Gunnlaugsson. "Selection and estimation of sequential catch-at-age models." Canadian Journal of Fisheries and Aquatic Sciences 69, no. 11 (2012): 1760–72. http://dx.doi.org/10.1139/f2012-095.

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Fish stock assessment by catch-at-age and survey data is affected by many stochastic elements: measurement errors; sampling variations; natural variations in mortality, catchability and migrations; technological and social effects on fishing intensity and selectivity. Estimation of simulated models shows that the bias in estimation by linear approximation of the Kalman filter or automatic approximation of the marginal likelihood function is much smaller than the errors produced by the stochastic elements. In time series modelling, they are represented by residuals in the equations. Strong simp

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