
Richard D. MethotNational Oceanic and Atmospheric Administration | NOAA
Richard D. Methot
PhD
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Publications (111)
Marine fishes are heterogeneously distributed across their ranges according to population dynamics governed by complex spatiotemporal relationships between ontogenetic habitat usage, species interactions, environmental variability, and harvest patterns. However, few stock assessments incorporate spatial population structure in the determination of...
Spatial models enable understanding potential redistribution of marine resources associated with ecosystem drivers and climate change. Stock assessment platforms can incorporate spatial processes, but have not been widely implemented or simulation tested. To address this research gap, an international simulation experiment was organized. The study...
Multispecies models have existed in a fisheries context since at least the 1970s, but despite much exploration, advancement, and consideration of multispecies models, there remain limited examples of their operational use in fishery management. Given that species and fleet interactions are inherently multispecies problems and the push towards ecosy...
Natural mortality (M) is one of the most influential parameters in fisheries stock assessment and management. It relates directly to stock productivity and reference points used for fisheries management advice. Unfortunately, M is also very difficult to estimate, and hence very uncertain. Representing the uncertainty in M and how this influences es...
Marine population modeling, which underpins the scientific advice to support fisheries interventions, is an active research field with recent advancements to address modern challenges (e.g., climate change) and enduring issues (e.g., data limitations). Based on discussions during the ‘Land of Plenty’ session at the 2021 World Fisheries Congress, we...
The ICES Workshop on ICES reference points (WKREF1) was tasked to provide a thorough review of the ICES reference points system as a basis to re-evaluate the process for estimating,
updating and communicating reference points in the context of the ICES advice. As part of the preparation leading to WKREF1 a large database of the most recent assessm...
Shortspine thornyhead Sebastolobus alascanus are widely distributed along the eastern Pacific coast and are assessed as a demographically homogeneous stock off the coasts of California, Oregon and Washington. The validity of this assumption has been questioned because data suggest complex ontogenetic movements. Otolith microchemistry applied to imm...
Specification of how selectivity (the combination of availability and vulnerability) is modelled in integrated stock assessments is key to avoiding bias in estimates of quantities of management interest. Many “rules of thumb” are common in the community but these have yet to be rigorously tested. This paper uses simulation to compare 12 approaches...
Fish populations with spatial structure inherently violate the assumption of a single well-mixed stock, necessitating the use of spatially-structured population dynamics models. Accounting for spatial structure accurately and easily is a major goal for the next generation of stock assessment software development. Reference points (e.g., limit or ta...
Integrated analysis has increasingly been the preferred approach for conducting stock assessments and providing the basis for management advice for fish and invertebrate stocks around the world. Many decisions are required when developing integrated stock assessments. For example, the analyst needs to decide whether the model fits the data, if the...
Many fisheries and marine science organizations are working to determine how to meet their missions in the midst of the COVID-19 outbreak. As such, it seems prudent to exchange ideas, share knowledge, and initiate a discussion among us. As the scientific leadership team for NOAA Fisheries, we wanted to offer some perspectives. Others are also evalu...
Revisions to the National Standard 1 (NS1) guidelines published in 2016 included two
provisions that added flexibility in the process of specifying annual catch limits (ACLs). One
provision allowed the unused portion of an ACL to be carried over to the following year. A
second provision allowed changes in catch limits to be phased in over a period...
The Workshop on guidelines and methods for the evaluation of rebuilding plans (WKREBUILD) chaired by Vanessa Trijoulet (Denmark) and Martin Pastoors (Netherlands) met from 24 to 28 February 2020. The workshop attracted 27 participants from the US, Canada, Europe and FAO.
Integrated analysis (or integrated population modelling) methods have become the preferred approach for conducting stock assessments, and providing the basis for management advice for fish and invertebrate stocks since the publication of a seminal paper by Fournier and Archibald in 1982. Methods to assess fish stocks based on single-species, single...
How to properly weight composition data is an important ongoing research topic for fisheries stock assessments, and multiple methods for weighting composition data have been developed. Although several studies indicated that properly accounting for time-varying selectivity can reduce estimation biases in population biomass and management-related qu...
In the United States, implementation of strong legislative mandates and investments in scientific programmes have supported sustainable fisheries management for seafood production, marine ecosystems, and maritime communities and economies. Changing climate and ocean conditions present new and growing challenges that affect the ability to manage fis...
The northern Gulf of Mexico (GoM) is an ecologically and economically productive system that supports some of the largest volume and most valuable fisheries in the United States. The benefit of these fisheries to society and to the surrounding Gulf communities has varied historically, commensurate with the fish population sizes and the economic act...
Fisheries management is most effective when based on scientific estimates of sustainable fishing rates. While some simple approaches allow estimation of harvest limits, more data-intensive stock assessments are generally required to evaluate the stock’s biomass and fishing rates relative to sustainable levels. Here we evaluate how stock characteris...
Marginal probability of a stock in category k being assessed as a function of time (P(Tk ≤ t) = Fk(t) = exp(−λk
tτ)), for stocks of various taxonomic orders, class, regions and habitats.
For taxonomic variables, only the six levels with the most stocks represented in our dataset are shown. Marginal probabilities were evaluated at the mean of (cente...
Dataset used for analyses.
The full dataset used for all analyses presented in the manuscript.
(XLSX)
Validation of assessment classifications.
(PDF)
Marginal probability of a stock being assessed after 50 years as a function of mean ex-vessel price (US.kg-1) and maximum landings prior to assessment.
Marginal probabilities were evaluated at the mean of remaining continuous covariates. The dataset used for analysis is overlayed with assessed stocks as dark grey points and unassessed stocks in lig...
Comparison of finite population standard deviation (i.e., variance attributed to each variable) for random effects in the Weibull survival model.
Circles show posterior medians, thick bars show inter-quartile ranges of the posteriors, and thin lines show 95% confidence intervals.
(PDF)
Model fit of the Weibull survival model, based on Cox-Snell residuals calculated at the posterior mean of the linear predictor.
For a perfect fit all data points would lie on the y = x (green) line.
(PDF)
Model estimates and predictions.
Summaries of estimated posterior distributions for fixed effects, regional random effects, habitat random effects, and taxonomic class random effects in the time-to-event model with fishery management plan (FMP) variable. Circles show posterior medians, thick bars show inter-quartile ranges of the posteriors, and th...
Paramter estimates.
(PDF)
Assignment of year of first stock assessment.
(PDF)
Appropriateness of the Weibull event-time model for the time-to-assessment dataset.
If the Weibull applies, the time from first landings (or from first quantitative stock assessment in 1960 if a stock was landed before 1960) to the year of first assessment should fall on a line with slope τ (the Weibull shape parameter) between log(-log(S^(t))), wh...
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-pa...
Spatial patterns due to age-specific movement have been a source of unmodelled process error. Modeling movement in spatially explicit stock assessments is feasible, but hampered by a paucity of data from appropriate tagging studies. This study uses simulation analyses to evaluate alternative model structures that either explicitly or implicitly acc...
Populations of small pelagic fish are strongly influenced by climate. The inability of managers to anticipate environment-driven fluctuations in stock productivity or distribution can lead to overfishing and stock collapses, inflexible management regulations inducing shifts in the functional response to human predators, lost opportunities to harves...
The addition of juveniles to marine populations (termed “recruitment”) is highly variable due to variability in the survival of fish through larval and juvenile stages. Recruitment estimates are often large or small for several years in a row (termed “autocorrelated” recruitment). Autocorrelated recruitment can be due to numerous factors, but typic...
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 opt...
Modern stock assessment models can make use of a wide variety of data types, but measures of catch and relative abundance remain crucial to the estimates of the population abundance. Additional data types, such as the age or size composition of the catch, are useful for estimation of the age structure of the population. However, inappropriate data...
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, whic...
Stock assessment models estimate the dynamics of a single species in response to a time series of catch and an indicator of the trend in stock abundance over time. More complete assessments also include size/age composition data which provides direct information on the level of total mortality being experienced by the stock. Where there are suffici...
Since the Reauthorization of the Magnuson-Stevens Act in 2006, the NOAA Fisheries stock assessment enterprise has been critical to providing fishery managers with scientific information to set annual catch limits to rebuild fish stocks and prevent overfishing. Over the past decade, NOAA Fisheries has successfully implemented a number of measurable...
Biological processes such as fishery selectivity, natural mortality, and somatic growth can vary over time, but it is challenging
to estimate the magnitude of time-variation of demographic parameters in population dynamics models, particularly when using
penalized-likelihood estimation approaches. Random-effect approaches can estimate the variance,...
Assessments of marine fish and shellfish provide the information needed to set annual catch limits that prevent overfishing and provide for a sustainable fishery. For the near 500 managed stocks in U.S. Fishery Management Plans, over 100 stocks get updated assessments each year in order to adjust annual catch limits. An important assessment data co...
Understanding the relationship between abundance of spawners and subsequent recruitment is one of the central issues in fisheries stock assessment. We developed a new, pre-recruit survival based stock–recruitment model that enables explicit modeling of survival between embryos and age 0 recruits, and allows the description of a wide range of pre-re...
100 years after Rosa Lee (1912) showed that higher mortality on faster growing fish can alter length-at-age distributions in fish populations, we present a computationally-efficient and parsimonious method for modeling size-selective mortality within a commonly-used assessment model, Stock Synthesis. Stock Synthesis allows the normal distribution o...
a b s t r a c t Stock synthesis (SS) is a statistical age-structured population modeling framework that has been applied in a wide variety of fish assessments globally. The framework is highly scalable from data-weak sit-uations where it operates as an age-structured production model, to complex situations where it can flexibly incorporate multiple...
Methot, R. D., Tromble, G. R., Lambert, D. M., and Greene, K. E. 2014. Implementing a science-based system for preventing overfishing and guiding sustainable fisheries in the United States. – ICES Journal of Marine Science, 71: 183–194.
Fisheries management in the United States is primarily governed by the Magnuson–Stevens Fishery Conservation and...
Steepness of the stock–recruitment relationship is one of the most uncertain and critical quantities in fishery stock assessment and management. Steepness is defined as the fraction of recruitment from a virgin population obtained when the spawners are at 20% of the virgin level. Steepness directly relates to productivity and yield and is an import...
Integrated analysis models provide a tool to estimate fish abundance, recruitment, and fishing mortality from a wide variety of data. The flexibility of integrated analysis models allows them to be applied over extended time periods spanning historical decades with little information from which to estimate the annual signal of recruitment variabili...
Recent developments in the models used in wildlife and fisheries science have allowed the inclusion of a wider range of data than previously. However, the diagnostics of such complex models have not kept pace. We describe a new diagnostic technique based on simulation analysis. Model misspecification was identified through simulation methods that c...
The Magnuson-Stevens Act (MSA) provides the foundation for management of marine fisheries in the US. In 2007, the MSA was amended to contain a provision that required establishment of Annual Catch Limits (ACLs) in all fisheries at a level “such that overfishing does not occur”. Further, these ACLs are required to be accompanied by accountability me...
Two processes may explain observations of fewer large fish than expected in assessment models: dome-shaped selectivity in which the large fish escape capture, or higher mortality on faster growing fish that become selected at an earlier age. Simulation methods are used to explore the confounding between these two processes. The simulation model inc...
Assessment of marine fisheries in the U.S. strives to quantify the probability that a specified future catch limit will prevent overfishing. This probabilistic approach has been most recently elucidated in the work by Prager and Shertzer (NAJFM, 2010). While the population and fishery forecast model to apply such methods can be done subsequent to c...
The NOAA Fisheries Service (NMFS) provides high-quality science information on marine fish population abundance and fishery exploitation rates to enable conservation and sustainable management. Stock assessments produce the information necessary to determine a stock’s status relative to pre-determined limits and goals for abundance and exploitation...
The swept-area estimates of biomass from the triennial groundfish trawl surveys on the shelf of the U.S. West Coast are believed to seriously underestimate rockfish (Scorpaenidae) stock biomasses. The bulk catchability (Q), defined to be the ratio between swept-area biomass and actual biomass, is herein modeled using a Bayesian age-structured meta-...
Annual preseason abundance for the central and northern California Dungeness crab (Cancer magister) fisheries is estimated from the decline in catch per unit of effort (CPUE) within each fishing season. The results support the common assumption that a large fraction of the available, legal size, male crabs are harvested each year; however, we noted...
Knowledge of the dynamic response of fishing effort to abundance is essential to a complete understanding of the cycles in catch in the northern California Dungeness crab fishery. In this fishery there is a lagged response of harvest rate to changes in abundance that is caused either by a time lag in fishermen entering and leaving the fishery follo...
Natural mortality (M) is one of the most influential and difficult to estimate number of losses in fisheries stock assessment and management. Typically, natural mortality is estimated using indirect methods, such as correlation with measurable life history factors and rarely relies on direct data such as tagging studies. In contemporary stock asses...
DiCosimo, J., Methot, R. D., and Ormseth, O. A. 2010. Use of annual catch limits to avoid stock depletion in the Bering Sea and Aleutian Islands management area (Northeast Pacific). – ICES Journal of Marine Science, 67: 1861–1865.
In total, 41 fish stocks in US ocean waters continue to be fished at unsustainable levels, and 46 fish stocks are overf...
Schirripa, M. J., Goodyear, C. P., and Methot, R. M. 2009. Testing different methods of incorporating climate data into the assessment of US West Coast sablefish. – ICES Journal of Marine Science, 66: 1605–1613.
The objective of this investigation was to evaluate different methods of including environmental variability directly into stock assessmen...
Fishery stock assessment models connect ecosystem data to quantitative fishery management. Control rules that calculate annual
catch limits and targets from stock assessment results are a common component of US Fishery Management Plans. Ideally, the
outcome of such control rules are updated annually on the basis of stock assessment forecasts to tra...
The Research Article Impacts of biodiversity loss on ocean ecosystem services By B. Worm et al. (3 Nov. 2006, p. [787][1]) projects that 100 of seafood-producing species stocks will collapse by 2048. The projection is inaccurate and overly pessimistic.
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CREDIT: DIGITAL VISION/
Marine protected areas (MPAs) have been increasingly proposed, evaluated and implemented as management tools for achieving both fisheries and conservation objectives in aquatic ecosystems. However, there is a challenge associated with the application of MPAs in marine resource management with respect to the consequences to traditional systems of mo...
Discarding of target species can be substantial in some fisheries. For fisheries managed using Total Allowable Catches, such as Australia's Southern and Eastern Scalefish and Shark Fishery (SESSF), discarding of target species can occur for reasons related to the size of the fish caught, markets, and the amount of quota held by individual quota hol...
A generalized linear mixed model (GLMM) that treats year and spatial cell as fixed effects while treating vessel as a random effect is used to examine fishing power among chartered industry-based vessels and a research trawler, the FRV Miller Freeman, for bottom trawl surveys on the upper continental slope of U.S. West coast. A Bernoulli distributi...
Fishery stock assessments are designed to estimate the current status of fished marine resources relative to target and limit reference levels and to provide advice on the implications of future harvest rates and other management actions. Most fisheries stock assessments are based on the assumption that the fishery or the fish population is distrib...
Summary The rebuilding analysis for canary rockfish was first conducted in 2000 based on the 1999 stock assessment. This document updates the analysis based upon the 2002 assessment. The target spawning stock biomass is 40% of the unfished spawning stock biomass (Bzero). The method to calculate Bzero is improved to incorporate more historical infor...
The swept-area estimates of biomass from the triennial groundfish trawl surveys on the shelf of the U.S. West Coast are believed to seriously underestimate rockfish (Scorpaenidae) stock biomasses. The bulk catchability (Q), defined to be the ratio between swept-area biomass and actual biomass, is herein modeled using a Bayesian age-structured meta-...
Pacific hake (Merluccius productus), also known as Pacific whiting, is the most abundant commercial fish species off the US west coast of California, Oregon and Washington and has supported a fishery averaging 170000 tonnes since 1966. The life history and biology of this population has been studied extensively. Bailey et al. (1982) and the collect...