386 results on '"André E. Punt"'
Search Results
2. Estimating Bycatch Mortality for Marine Mammals: Concepts and Best Practices
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Jeffrey E. Moore, Dennis Heinemann, Tessa B. Francis, Philip S. Hammond, Kristy J. Long, André E. Punt, Randall R. Reeves, Maritza Sepúlveda, Guðjón Már Sigurðsson, Margaret C. Siple, Gísli A. Víkingsson, Paul R. Wade, Rob Williams, and Alexandre N. Zerbini
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Potential Biological Removal (PBR) ,seafood import provisions ,stock assessment ,marine mammal ,estimation ,bycatch ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Fisheries bycatch is the greatest current source of human-caused deaths of marine mammals worldwide, with severe impacts on the health and viability of many populations. Recent regulations enacted in the United States under the Fish and Fish Product Import Provisions of its Marine Mammal Protection Act require nations with fisheries exporting fish and fish products to the United States (hereafter, “export fisheries”) to have or establish marine mammal protection standards that are comparable in effectiveness to the standards for United States commercial fisheries. In many cases, this will require estimating marine mammal bycatch in those fisheries. Bycatch estimation is conceptually straightforward but can be difficult in practice, especially if resources (funding) are limiting or for fisheries consisting of many, small vessels with geographically-dispersed landing sites. This paper describes best practices for estimating bycatch mortality, which is an important ingredient of bycatch assessment and mitigation. We discuss a general bycatch estimator and how to obtain its requisite bycatch-rate and fisheries-effort data. Scientific observer programs provide the most robust bycatch estimates and consequently are discussed at length, including characteristics such as study design, data collection, statistical analysis, and common sources of estimation bias. We also discuss alternative approaches and data types, such as those based on self-reporting and electronic vessel-monitoring systems. This guide is intended to be useful to managers and scientists in countries having or establishing programs aimed at managing marine mammal bycatch, especially those conducting first-time assessments of fisheries impacts on marine mammal populations.
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- 2021
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3. Best Practices for Assessing and Managing Bycatch of Marine Mammals
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Paul R. Wade, Kristy J. Long, Tessa B. Francis, André E. Punt, Philip S. Hammond, Dennis Heinemann, Jeffrey E. Moore, Randall R. Reeves, Maritza Sepúlveda, Genoa Sullaway, Guðjón Már Sigurðsson, Margaret C. Siple, Gísli A. Víkingsson, Rob Williams, and Alexandre N. Zerbini
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bycatch ,management ,assessment ,marine mammal ,framework ,MMPA import rule ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Bycatch in marine fisheries is the leading source of human-caused mortality for marine mammals, has contributed to substantial declines of many marine mammal populations and species, and the extinction of at least one. Schemes for evaluating marine mammal bycatch largely rely on estimates of abundance and bycatch, which are needed for calculating biological reference points and for determining conservation status. However, obtaining these estimates is resource intensive and takes careful long-term planning. The need for assessments of marine mammal bycatch in fisheries is expected to increase worldwide due to the recently implemented Import Provisions of the United States Marine Mammal Protection Act. Managers and other stakeholders need reliable, standardized methods for collecting data to estimate abundance and bycatch rates. In some cases, managers will be starting with little or no data and no system in place to collect data. We outline a comprehensive framework for managing bycatch of marine mammals. We describe and provide guidance on (1) planning for an assessment of bycatch, (2) collecting appropriate data (e.g., abundance and bycatch estimates), (3) assessing bycatch and calculating reference points, and (4) using the results of the assessment to guide marine mammal bycatch reduction. We also provide a brief overview of available mitigation techniques to reduce marine mammal bycatch in various fisheries. This paper provides information for scientists and resource managers in the hope that it will lead to new or improved programs for assessing marine mammal bycatch, establishing best practices, and enhancing marine mammal conservation globally.
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- 2021
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4. Estimating the Abundance of Marine Mammal Populations
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Philip S. Hammond, Tessa B. Francis, Dennis Heinemann, Kristy J. Long, Jeffrey E. Moore, André E. Punt, Randall R. Reeves, Maritza Sepúlveda, Guðjón Már Sigurðsson, Margaret C. Siple, Gísli Víkingsson, Paul R. Wade, Rob Williams, and Alexandre N. Zerbini
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abundance ,cetaceans ,pinnipeds ,sirenians ,population size ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Motivated by the need to estimate the abundance of marine mammal populations to inform conservation assessments, especially relating to fishery bycatch, this paper provides background on abundance estimation and reviews the various methods available for pinnipeds, cetaceans and sirenians. We first give an “entry-level” introduction to abundance estimation, including fundamental concepts and the importance of recognizing sources of bias and obtaining a measure of precision. Each of the primary methods available to estimate abundance of marine mammals is then described, including data collection and analysis, common challenges in implementation, and the assumptions made, violation of which can lead to bias. The main method for estimating pinniped abundance is extrapolation of counts of animals (pups or all-ages) on land or ice to the whole population. Cetacean and sirenian abundance is primarily estimated from transect surveys conducted from ships, small boats or aircraft. If individuals of a species can be recognized from natural markings, mark-recapture analysis of photo-identification data can be used to estimate the number of animals using the study area. Throughout, we cite example studies that illustrate the methods described. To estimate the abundance of a marine mammal population, key issues include: defining the population to be estimated, considering candidate methods based on strengths and weaknesses in relation to a range of logistical and practical issues, being aware of the resources required to collect and analyze the data, and understanding the assumptions made. We conclude with a discussion of some practical issues, given the various challenges that arise during implementation.
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- 2021
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5. Bottom–Up Impacts of Forecasted Climate Change on the Eastern Bering Sea Food Web
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George A. Whitehouse, Kerim Y. Aydin, Anne B. Hollowed, Kirstin K. Holsman, Wei Cheng, Amanda Faig, Alan C. Haynie, Albert J. Hermann, Kelly A. Kearney, André E. Punt, and Timothy E. Essington
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Bering Sea ,climate change ,fisheries ,food web ,Rpath ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Recent observations of record low winter sea-ice coverage and warming water temperatures in the eastern Bering Sea have signaled the potential impacts of climate change on this ecosystem, which have implications for commercial fisheries production. We investigate the impacts of forecasted climate change on the eastern Bering Sea food web through the end of the century under medium- and high-emissions climate scenarios in combination with a selection of fisheries management strategies by conducting simulations using a dynamic food web model. The outputs from three global earth system models run under two greenhouse gas emission scenarios were dynamically downscaled using a regional ocean and biogeochemical model to project ecosystem dynamics at the base of the food web. Four fishing scenarios were explored: status quo, no fishing, and two scenarios that alternatively assume increased fishing emphasis on either gadids or flatfishes. Annual fishery quotas were dynamically simulated by combining harvest control rules based on model-simulated stock biomass, while incorporating social and economic tradeoffs induced by the Bering Sea’s combined groundfish harvest cap. There was little predicted difference between the status quo and no fishing scenario for most managed groundfish species biomasses at the end of the century, regardless of emission scenario. Under the status quo fishing scenario, biomass projections for most species and functional groups across trophic levels showed a slow but steady decline toward the end of the century, and most groups were near or below recent historical (1991–2017) biomass levels by 2080. The bottom–up effects of declines in biomass at lower trophic levels as forecasted by the climate-enhanced lower trophic level modeling, drove the biomass trends at higher trophic levels. By 2080, the biomass projections for species and trophic guilds showed very little difference between emission scenarios. Our method for climate-enhanced food web projections can support fisheries managers by informing strategic guidance on the long-term impacts of ecosystem productivity shifts driven by climate change on commercial species and the food web, and how those impacts may interact with different fisheries management scenarios.
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- 2021
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6. Recruitment variation disrupts the stability of alternative life histories in an exploited salmon population
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Lukas B. DeFilippo, Daniel E. Schindler, Jan Ohlberger, Kevin L. Schaberg, Matt Birch Foster, Darin Ruhl, and André E. Punt
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alternative reproductive tactic ,Bayesian state‐space ,cohort mismatch ,fisheries‐induced evolution ,frequency‐dependent selection ,jack ,Evolution ,QH359-425 - Abstract
Abstract Males of many fish species exhibit alternative reproductive tactics, which can influence the maturation schedules, fishery productivity, and resilience to harvest of exploited populations. While alternative mating phenotypes can persist in stable equilibria through frequency‐dependent selection, shifts in tactic frequencies have been observed and can have substantial consequences for fisheries. Here, we examine the dynamics of precocious sneaker males called “jacks” in a population of sockeye salmon (Oncorhynchus nerka) from Frazer Lake, Alaska. Jacks, which are of little commercial value due to their small body sizes, have recently been observed at unusually high levels in this stock, degrading the value of regional fisheries. To inform future strategies for managing the prevalence of jacks, we used long‐term monitoring data to identify what regulates the frequencies of alternative male phenotypes in the population over time. Expression of the jack life history could not be explained by environmental factors expected to influence juvenile body condition and maturation probability. Instead, we found a strong positive association between the proportion of individuals maturing as jacks within a cohort and the prevalence of jacks among the males that sired that cohort. Moreover, due to differences in age‐at‐maturity between male phenotypes, and large interannual variability in recruitment strength, jacks from strong year‐classes often spawn among older males from the weaker recruitments of earlier cohorts. Through such “cohort mismatches,” which are amplified by size‐selective harvest on older males, jacks frequently achieve substantial representation in the breeding population, and likely high total fertilizations. The repeated occurrence of these cohort mismatches appears to disrupt the stabilizing influence of frequency‐dependent selection, allowing the prevalence of jacks to exceed what might be expected under equilibrium conditions. These results emphasize that the dynamics of alternative life histories can profoundly influence fishery performance and should be explicitly considered in the management of exploited populations.
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- 2019
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7. Ensemble Projections of Future Climate Change Impacts on the Eastern Bering Sea Food Web Using a Multispecies Size Spectrum Model
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Jonathan C. P. Reum, Julia L. Blanchard, Kirstin K. Holsman, Kerim Aydin, Anne B. Hollowed, Albert J. Hermann, Wei Cheng, Amanda Faig, Alan C. Haynie, and André E. Punt
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uncertainty partitioning ,predictive ecology ,Arrhenius factor ,body size ,size-based food web ,cumulative effects ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Characterization of uncertainty (variance) in ecosystem projections under climate change is still rare despite its importance for informing decision-making and prioritizing research. We developed an ensemble modeling framework to evaluate the relative importance of different uncertainty sources for food web projections of the eastern Bering Sea (EBS). Specifically, dynamically downscaled projections from Earth System Models (ESM) under different greenhouse gas emission scenarios (GHG) were used to force a multispecies size spectrum model (MSSM) of the EBS food web. In addition to ESM and GHG uncertainty, we incorporated uncertainty from different plausible fisheries management scenarios reflecting shifts in the total allowable catch of flatfish and gadids and different assumptions regarding temperature-dependencies on biological rates in the MSSM. Relative to historical averages (1994–2014), end-of-century (2080–2100 average) ensemble projections of community spawner stock biomass, catches, and mean body size (±standard deviation) decreased by 36% (±21%), 61% (±27%), and 38% (±25%), respectively. Long-term trends were, on average, also negative for the majority of species, but the level of trend consistency between ensemble projections was low for most species. Projection uncertainty for model outputs from ∼2020 to 2040 was driven by inter-annual climate variability for 85% of species and the community as a whole. Thereafter, structural uncertainty (different ESMs, temperature-dependency assumptions) dominated projection uncertainty. Fishery management and GHG emissions scenarios contributed little (
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- 2020
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8. Estimating economic-based target reference points for key species in multi-species multi-métier fisheries
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Sean Pascoe, André E. Punt, Trevor Hutton, Paul Burch, Pia Bessell-Browne, and L. Richard Little
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Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Abstract
Consideration of economic outcomes is commonplace in most fisheries management systems globally, although only a few jurisdictions have adopted an economic objective as the primary target for fisheries management. Such an objective has been adopted for Australia's federally managed fisheries, with maximum economic yield (MEY) identified as the primary management objective. Correspondingly, target reference points defined in terms of biomass (i.e., BMEY) are used in harvest control rules. In the absence of explicit BMEY estimates, proxy estimates based on maximum sustainable yield (i.e., BMSY) are used. Identifying BMEY in multi-species fisheries is complicated as most stock assessments are undertaken at the individual species level, but economic activity occurs across species. This is further complicated when different fishing activities using different fishing gears and targeting practices (i.e., métiers) are present in a fishery. We employ an age-structured bioeconomic model to estimate BMEY for key species in a multi-species, multi-métier fishery. We find that optimal biomass levels are substantially higher than those assumed under the current proxy-based system, and that the economic targets are sensitive to prices and fishing costs, both of which change over time.
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- 2023
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9. mmrefpoints: Projecting long-term marine mammal abundance with bycatch.
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Margaret C. Siple, André E. Punt, Tessa B. Francis, Philip S. Hammond, Dennis Heinemann, Kristy J. Long, Jeffrey Moore, Maritza Sepúlveda, Randall R. Reeves, Guðjón Már Sigurðsson, Gísli Víkingsson, Paul R. Wade, Rob Williams, and Alexandre N. Zerbini
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- 2022
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10. The estimated impact of changes to otolith field-sampling and ageing effort on stock assessment inputs, outputs, and catch advice
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Matthew R. Siskey, André E. Punt, Peter-John F. Hulson, Meaghan D. Bryan, James N. Ianelli, and James T. Thorson
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Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Abstract
Generating accurate data for stock assessments is resource-demanding, necessitating periodic evaluation of survey sampling designs and potential impacts on stock assessments. We developed a framework for bootstrapped resampling of survey age data and calculation of input sample sizes as a function of among-bootstrap variance in age compositions. Data from this bootstrap estimator were then used to evaluate the influence of alternative sampling rates and methods on uncertainty in estimates of the overfishing limit (OFL) calculated using stock assessment models. For dusky rockfish ( Sebastes variabilis) and Pacific ocean perch ( Sebastes alutus), a 10% decrease in the number of tows sampled upon led to a predicted 5%–6% increase in the CV of OFL (log–log slope = −0.576 to −0.486), which was greater than the 0%–2% increase from a 10% decrease in otoliths-per-tow (log–log slope = −0.238 to −0.029). Application of this approach across all stocks monitored in the survey of interest is required to identify which stocks ( i) benefit the most from increased sampling of ageing structures or ( ii) cost the least in terms of OFL uncertainty owing to reduced sampling.
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- 2023
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11. Oceans of plenty? Challenges, advancements, and future directions for the provision of evidence-based fisheries management advice
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Daniel R. Goethel, Kristen L. Omori, André E. Punt, Patrick D. Lynch, Aaron M. Berger, Carryn L. de Moor, Éva E. Plagányi, Jason M. Cope, Natalie A. Dowling, Richard McGarvey, Ann L. Preece, James T. Thorson, Milani Chaloupka, Sarah Gaichas, Eric Gilman, Sybrand A. Hesp, Catherine Longo, Nan Yao, and Richard D. Methot
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Aquatic Science - Abstract
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 synthesize current challenges, recent advances, and interdisciplinary developments in biological fisheries models (i.e., data-limited, stock assessment, spatial, ecosystem, and climate), management strategy evaluation, and the scientific advice that bridges the science-policy interface. Our review demonstrates that proliferation of interdisciplinary research teams and enhanced data collection protocols have enabled increased integration of spatiotemporal, ecosystem, and socioeconomic dimensions in many fisheries models. However, not all management systems have the resources to implement model-based advice, while protocols for sharing confidential data are lacking and impeding research advances. We recommend that management and modeling frameworks continue to adopt participatory co-management approaches that emphasize wider inclusion of local knowledge and stakeholder input to fill knowledge gaps and promote information sharing. Moreover, fisheries management, by which we mean the end-to-end process of data collection, scientific analysis, and implementation of evidence-informed management actions, must integrate improved communication, engagement, and capacity building, while incorporating feedback loops at each stage. Increasing application of management strategy evaluation is viewed as a critical unifying component, which will bridge fisheries modeling disciplines, aid management decision-making, and better incorporate the array of stakeholders, thereby leading to a more proactive, pragmatic, transparent, and inclusive management framework-ensuring better informed decisions in an uncertain world.The online version contains supplementary material available at 10.1007/s11160-022-09726-7.
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- 2022
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12. Nutrient allocation to eggs in female Argentinus shortfin squid, Illex argentinus using fatty acids as nutrient indicator
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Na Zang, Dongming Lin, André E. Punt, and xinjun chen
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Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics - Abstract
Fatty acids play a critical role in embryonic development of cephalopods. However, little information is available on the allocation of fatty acids to eggs during oogenesis, limiting our understanding regarding how these animals maximize reproductive performance in terms of energy and nutrient use. We explored the nutrients for egg production during maturation for Argentine shortfin squid (Illex argentinus (Castellanos, 1960)) by comparing the fatty acid profiles between the ovary and eggs in the oviducts. We detected 30 fatty acids in the ovary and eggs, of which 19 constituted more than 0.2% of the total fatty acid content. The overall fatty acids in the ovary varied significantly among maturity stages, while the eggs had a consistent amount of total fatty acids and relative amount of individual fatty acids. There were consequently significant differences in the fatty acid profiles between the ovary and eggs by maturity stage and in total. Additionally, eggs had more saturated fatty acids but less polyunsaturated fatty acids than the ovary. Cumulatively, our results reveal that this squid produces eggs with consistent levels of nutrients virtually regardless of how the nutrient profile of the ovary varies during maturation, providing insight into the egg production process relation to nutrient allocation.
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- 2023
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13. Understanding transboundary stocks’ availability by combining multiple fisheries-independent surveys and oceanographic conditions in spatiotemporal models
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Cecilia A O'Leary, Lukas B DeFilippo, James T Thorson, Stan Kotwicki, Gerald R Hoff, Vladimir V Kulik, James N Ianelli, and André E Punt
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Ecology ,Aquatic Science ,Oceanography ,Ecology, Evolution, Behavior and Systematics - Abstract
Shifts in the distribution of groundfish species as oceans warm can complicate management efforts if species distributions expand beyond the extent of existing scientific surveys, changing the proportion of groundfish available to any one survey each year. We developed the first-ever model-based biomass estimates for three Bering Sea groundfishes (walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus), and Alaska plaice (Pleuronectes quadrituberculatus)) by combining fishery-independent bottom trawl data from the U.S. and Russia in a spatiotemporal framework using Vector Autoregressive Spatio-Temporal (VAST) models. We estimated a fishing-power correction to calibrate disparate data sets and the effect of an annual oceanographic index to explain variation in groundfish spatiotemporal density. Groundfish densities shifted northward relative to historical densities, and high-density areas spanned the international border, particularly in years warmer than the long-term average. In the final year of comprehensive survey data (2017), 49%, 65%, 47% of biomass was in the western and northern Bering Sea for pollock, cod, and plaice, respectively, suggesting that availability of groundfish to the more regular eastern Bering Sea survey is declining. We conclude that international partnerships to combine past data and coordinate future data collection are necessary to track fish as they shift beyond historical survey areas.
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- 2022
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14. Oceanographic drivers of legal-sized male Dungeness crab in the California Current System
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Ridouan Bani, André E. Punt, Daniel S. Holland, Nick Tolimieri, Kate Richerson, Melissa A. Haltuch, Nathan J. Mantua, and Kiva L. Oken
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We investigate environmental drivers of pre-season abundance of US West Coast legal-sized male Dungeness crab (Cancer magister), with the goal of developing an environmental index that can be used to forecast crab abundance in advance of the fishery. A conceptual life history approach is used to generate life-stage-specific and spatio-temporally-specific mechanistic hypotheses regarding oceanographic variables that influence survival at each life stage. Linear models are fit using the logarithms of pre-season abundance estimates of the coastal population of legal-sized male Dungeness crab as the dependent variable and environmental drivers from outputs developed using a regional oceanographic model for the California Current System as the independent environmental variables. Using different model selection methods, we show that the so-called ‘best’ models differ substantially among model selection approaches, illustrating the need to carefully choose performance metrics for model selection. Since our goal was to forecast crab abundance, we selected the ‘best’ model using a cross-validation metric that accounts for the time-series nature of the data. The resulting ‘best’ models suggest that the mechanisms that drive preseason abundance differ among regions widely recognized for spatially and seasonally varying dominant physical processes. We found that the processes determining pre-season abundance of legal-sized male Dungeness crab could be identified with sufficient precision to enable a predictive skill, suggesting that the predictions may be useful for management purposes. Moreover, we found that transport (within and between regions), as well as temperature were likely drivers of pre-season abundance, highlighting that future studies should focus on multiple processes.
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- 2023
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15. Rapid age estimation of longnose skate (
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Timothy E. Essington, Irina M. Benson, Thomas E. Helser, André E. Punt, Morgan B. Arrington, and Mary Elizabeth Matta
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Multivariate statistics ,Ecology ,biology ,Near-infrared spectroscopy ,External validation ,Aquatic Science ,Oceanography ,biology.organism_classification ,Raja rhina ,Age estimation ,Statistics ,Skate ,Southern Hemisphere ,Ecology, Evolution, Behavior and Systematics - Abstract
There is a paucity of age data for chondrichthyan fishes owing, in large part, to limitations in traditional age estimation methods. Fourier transform near-infrared (FT-NIR) spectroscopy has shown promise as an alternative, more efficient method for acquiring age data from chondrichthyans. However, studies are limited to sharks in the southern hemisphere. We explored FT-NIR spectroscopy to predict age for a batoid species in the northern hemisphere. The longnose skate (Raja rhina) is one of a small number of batoids for which annual band periodicity in vertebral centra has been validated, allowing for traditional age estimation and making it an ideal candidate for this study. We fit a multivariate partial least-square predictive model between FT-NIR spectra collected from vertebral centra and traditional age estimates, and tested model predictive skill by using external validation. Using FT-NIR spectroscopy, we were able to predict age for longnose skates between the ages of 1 and 14 years with precision and bias near equal to those of traditional methods in less than a quarter of the time. These results support potential for FT-NIR spectroscopy to increase the amount of age data available for assessments used to inform the conservation and management of this sensitive group of species.
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- 2021
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16. Implementing the precautionary approach into fisheries management: Biomass reference points and uncertainty buffers
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Adrian Hordyk, Casper Willestofte Berg, Tobias Mildenberger, J. Rasmus Nielsen, Chantel R. Wetzel, Alexandros Kokkalis, André E. Punt, and Nis Sand Jacobsen
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business.industry ,media_common.quotation_subject ,Environmental resource management ,Biomass ,Management, Monitoring, Policy and Law ,Aquatic Science ,Oceanography ,Uncertainty ,Scientific uncertainty ,Management procedures ,Environmental science ,Fisheries management ,Harvest control rules (HRCs) ,business ,Risk assessment ,Ecology, Evolution, Behavior and Systematics ,Management strategy evaluation (MSE) ,media_common - Abstract
The precautionary approach to fisheries management advocates for risk-averse management strategies that include biological reference points and account for scientific uncertainty (i.e. process, model and observation uncertainty). In this regard, two approaches have been recommended: (a) biomass reference points to safeguard against low stock biomass, and (b) uncertainty buffers that reduce the catch limit as a function of the scientific uncertainty. This study compares the effectiveness of these two precautionary approaches in recovering over-exploited fish stocks. We evaluate the performance of more than 80 harvest control rules (HCRs) within a stochastic management strategy evaluation (MSE) framework for three stocks with contrasting life-history parameters and under various levels of scientific uncertainty. The results show that both approaches reduce the risk of overfishing at the expense of expected yield. This risk-yield trade-off strongly depends on the HCRs, life-history parameters of the species, as well as the level of the scientific uncertainty. Nevertheless, some combinations of biomass threshold and limit reference points as well as uncertainty buffers lead to a more favourable risk-yield trade-off than other rules. This study elucidates the multiple factors affecting the effectiveness of management strategies and highlights key features of HCRs for precautionary fisheries management.
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- 2021
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17. Multiple‐model stock assessment frameworks for precautionary management and conservation on fishery‐targeted coastal dolphin populations off Japan
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Yu Kanaji, Hiroshi Okamura, Trevor A. Branch, André E. Punt, and Hikari Maeda
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Fishery ,Geography ,Stock assessment ,Ecology ,Production model - Published
- 2021
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18. Estimating spatiotemporal availability of transboundary fishes to fishery‐independent surveys
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Stan Kotwicki, James N. Ianelli, Jason Conner, James T. Thorson, Vladimir Kulik, Robert R. Lauth, André E. Punt, Gerald R. Hoff, Cecilia A. O'Leary, and Daniel G. Nichol
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Fishery ,Ecology ,Environmental science ,Groundfish - Published
- 2021
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19. Incorporating vertical distribution in index standardization accounts for spatiotemporal availability to acoustic and bottom trawl gear for semi-pelagic species
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André E. Punt, James N. Ianelli, Stan Kotwicki, James T. Thorson, Cole C. Monnahan, and N. Lauffenburger
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0106 biological sciences ,Index (economics) ,Ecology ,Standardization ,business.industry ,010604 marine biology & hydrobiology ,Distribution (economics) ,Pelagic zone ,Aquatic Science ,Oceanography ,010603 evolutionary biology ,01 natural sciences ,business ,Ecology, Evolution, Behavior and Systematics ,Mathematics - Abstract
Abundance indices from scientific surveys are key stock assessment inputs, but when the availability of fish varies in space and time, the estimated indices and associated uncertainties do not accurately reflect changes in population abundance. For example, indices for many semi-pelagic species rely on acoustic and bottom trawl gear that differ in water column coverage, and so spatiotemporal trends in fish vertical distribution affect the availability of fish to each gear type. The gears together cover the whole water column, and so in principle allow estimation of more accurate, combined indices of the whole population. Here, we extend previous methods and develop a vertically integrated index, which accounts for spatiotemporal correlation and works with data unbalanced spatially or unpaired from distinct surveys. Using eastern Bering Sea walleye pollock (Gadus chalcogrammus) as an example, we identified clear spatial and temporal patterns in vertical distribution and gear availability from 2007 to 2018. Estimated acoustic annual vertical availability ranged from 0.339 to 0.888 among years, and from 0.588 to 0.911 for the bottom trawl survey. Our results highlight the importance of accounting for the spatiotemporal and vertical distribution of semi-pelagic fish to estimate more accurate indices, and provide important context for gear availability.
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- 2021
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20. Can we manage marine mammal bycatch effectively in low‐data environments?
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Paul R. Wade, Kristy J. Long, Gísli A. Víkingsson, Tessa B. Francis, Guðjón Már Sigurðsson, Margaret C. Siple, Alexandre N. Zerbini, Rob Williams, Randall R. Reeves, Philip S. Hammond, Jeffrey E. Moore, Dennis Heinemann, André E. Punt, Maritza Sepúlveda, University of St Andrews. Sea Mammal Research Unit, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Centre for Research into Ecological & Environmental Modelling, and University of St Andrews. School of Biology
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Ecology ,QH301 Biology ,DAS ,Marine mammal ,Fishery ,Bycatch ,QH301 ,Bycatch limits ,SDG 3 - Good Health and Well-being ,Environmental science ,Fishery interactions ,Potential Biological Removal ,SDG 14 - Life Below Water ,Mortality ,Low data - Abstract
Funding: Support for this project was provided by the Lenfest Ocean Program. 1. Determining acceptable rates of human‐caused mortality in low‐data situations is a concern for many taxa world‐wide. An established approach for determining acceptable levels of human‐caused mortality of marine mammals and other species of conservation concern is the Potential Biological Removal (PBR) framework, but PBR requires near‐unbiased estimates of absolute abundance, constraining its use in systems with limited data. 2. We develop three alternative methods for identifying acceptable levels of human‐caused mortality for long‐lived, slowly reproducing species, using indices of relative abundance combined with estimates of bycatch mortality in fisheries, and evaluate these methods using simulations similar to those used to develop PBR. 3. Across a variety of scenarios, the parameters of the three methods can be tuned to achieve conservation performance similar to that of PBR in scenarios that represent nearly ideal conditions. However, these methods produce lower and more variable bycatch mortality limits, depend upon reasonably accurate estimates of bycatch mortality and are more sensitive to uncertainties. 4. Synthesis and applications. Here we develop three alternative methods that expand the toolbox of approaches available for use in determining marine mammal conservation reference points for human‐caused mortality when it is not possible to apply the more standard, data‐hungry PBR approach. These approaches may be useful in supporting the establishment of new bycatch management programmes, or until estimates of absolute abundance become available. Publisher PDF
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- 2021
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21. Development of harvest control rules for hard-to-age crab stocks: the example of the golden king crab (Lithodes aequispinus) in the eastern Aleutian Islands in Alaska
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Shareef M. Siddeek, Benjamin Daly, André E. Punt, Steve Martell, Jie Zheng, and Mark Sticher
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Aquatic Science - Published
- 2020
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22. Review of the assessment of two stocks of Antarctic minke whales (eastern Indian Ocean and western South Pacific)
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Kenji Konishi, Takashi Hakamada, Tsutomu Tamura, Koji Matsuoka, Genta Yasunaga, Takeharu Bando, Hiroto Murase, Debra L. Palka, Hiroshi Okamura, André E. Punt, Hidehiro Kato, Toshihide Kitakado, Tatsuya Isoda, and Luis A. Pastene
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Systematics ,education.field_of_study ,biology ,Population ,Circumpolar star ,Aquatic Science ,Spatial distribution ,biology.organism_classification ,Fishery ,Geography ,Marine debris ,Animal Science and Zoology ,Whaling ,Minke whale ,education ,Ecology, Evolution, Behavior and Systematics ,Stock (geology) - Abstract
An in-depth assessment of an eastern Indian stock (I-stock) and a western South Pacific stock (P-stock) of Antarctic minke whales distributed between 35°E and 145°W was carried out by the Scientific Committee of the International Whaling Commission (IWC/SC) from 2001 to 2014 using data mainly collected from 1985 to 2004. This paper is a synthesis and summary of the outcomes of that assessment, although research on this species has been ongoing since 2014. The assessment integrates information from a wide range of topics including systematics, survey methods, direct catches, population structure, abundance, spatial distribution, biological information, population dynamics, species interactions, pollutants and interactions with marine debris. At least two stocks (I-stock and P-stock) are found between 35°E–145°W, with a soft boundary between 100°E and 165°E. Two sets of agreed circumpolar estimates of abundance from IWC assessment cruises (termed ‘CPII’ – 1985/86–1990/91, and ‘CPIII’ – 1991/92–2003/04) were obtained; a null hypothesis of no change in overall abundance between CPII and CPIII was not rejected. The results of a Statistical Catch-at-Age Analysis (SCAA) applied to the two stocks revealed that (1) abundance increased from 1930 until the mid-1970s, anddeclined over the period from the mid-1970s until the late-1980s and (2) trends in abundance over the most recent 20 years were relatively flat for the I-stock but decreasing for the P-stock. Although the primary focus at the start of this assessment was to try to understand abundance trends during the 1985–2004 period, it expanded to increasing knowledge on the life history of this species. The assessment also advanced many aspects of analytical methods.
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- 2020
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23. Robustness of potential biological removal to monitoring, environmental, and management uncertainties
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Guðjón Már Sigurðsson, Gísli A. Víkingsson, André E. Punt, Rob Williams, Dennis Heinemann, Kristy J. Long, Randall R. Reeves, Alexandre N. Zerbini, Jeffrey E. Moore, Tessa B. Francis, Maritza Sepúlveda, P.S. Hammond, Margaret C. Siple, Paul R. Wade, University of St Andrews. Scottish Oceans Institute, University of St Andrews. School of Biology, University of St Andrews. Sea Mammal Research Unit, University of St Andrews. Centre for Research into Ecological & Environmental Modelling, and University of St Andrews. Marine Alliance for Science & Technology Scotland
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0106 biological sciences ,QH301 Biology ,Conservation ,Marine mammal ,Aquatic Science ,Oceanography ,010603 evolutionary biology ,01 natural sciences ,QH301 ,MSE ,SDG 3 - Good Health and Well-being ,Robustness (computer science) ,QA Mathematics ,SDG 14 - Life Below Water ,QA ,Potential biological removal ,Ecology, Evolution, Behavior and Systematics ,GC ,Ecology ,010604 marine biology & hydrobiology ,Uncertainty ,DAS ,Reliability engineering ,Geography ,Bycatch ,GC Oceanography ,Simulation - Abstract
Support for this project was provided by the Lenfest Ocean Program. The potential biological removal (PBR) formula used to determine a reference point for human-caused mortality of marine mammals in the United States has been shown to be robust to several sources of uncertainty. This study investigates the consequences of the quality of monitoring on PBR performance. It also explores stochastic and demographic uncertainty, catastrophic events, sublethal effects of interactions with fishing gear, and the situation of a marine mammal population subject to bycatch in two fisheries, only one of which is managed. Results are presented for two pinniped and two cetacean life histories. Bias in abundance estimates and whether there is a linear relationship between abundance estimates and true abundance most influence conservation performance. Catastrophic events and trends in natural mortality have larger effects than environmental stochasticity. Managing only one of two fisheries with significant bycatch leads, as expected, to a lower probability of achieving conservation management goals, and better outcomes would be achieved if bycatch in all fisheries were managed. The results are qualitatively the same for the four life histories, but estimates of the probability of population recovery differ. Publisher PDF
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- 2020
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24. Evaluating management strategies for marine mammal populations: an example for multiple species and multiple fishing sectors in Iceland
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Guðjón Már Sigurðsson, Paul R. Wade, Rob Williams, Philip S. Hammond, Tessa B. Francis, Jeffrey E. Moore, Margaret C. Siple, Kristy J. Long, Gísli A. Víkingsson, Alexandre N. Zerbini, Sandra Magdalena Granquist, André E. Punt, Dennis Heinemann, Randall R. Reeves, and Maritza Sepúlveda
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0106 biological sciences ,Fishery ,Management strategy ,Geography ,Marine mammal ,010604 marine biology & hydrobiology ,Fishing ,Fisheries management ,Aquatic Science ,Multiple species ,010603 evolutionary biology ,01 natural sciences ,Ecology, Evolution, Behavior and Systematics - Abstract
A management strategy evaluation (MSE) is used to estimate success at achieving conservation goals for marine mammals while also aiming to minimize impacts on commercial fisheries. It is intended to improve understanding of US import rules that require countries exporting fish and fish products to the USA to adhere to marine mammal bycatch standards “comparable” to those used by the USA. The MSE framework is applied, for illustrative purposes, to export fisheries in Iceland that impact harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), and grey seals (Halichoerus grypus). Several management strategies are evaluated. The harbor porpoise population is estimated to be close to or above its maximum net productivity level (MNPL) and, according to the model, will continue to increase even if current levels of human-caused mortality are unchanged. In contrast, the grey seal and harbor seal populations are below MNPL, and bycatch mortality in the lumpfish (Cyclopterus lumpus) fishery will need to be reduced to allow them to recover to MNPL.
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- 2020
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25. The breeding strategy of female jumbo squid Dosidicus gigas: energy acquisition and allocation
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Han Fei, André E. Punt, Zhu Kai, Xinjun Chen, and Dongming Lin
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Male ,0106 biological sciences ,Food intake ,Ecosystem ecology ,media_common.quotation_subject ,Ovary (botany) ,Zoology ,lcsh:Medicine ,01 natural sciences ,Article ,biology.animal ,Animals ,Some Energy ,Mantle (mollusc) ,lcsh:Science ,media_common ,Marine biology ,chemistry.chemical_classification ,Squid ,Multidisciplinary ,biology ,Reproduction ,010604 marine biology & hydrobiology ,Fatty Acids ,Ovary ,lcsh:R ,Decapodiformes ,Fatty acid ,Feeding Behavior ,04 agricultural and veterinary sciences ,Animal behaviour ,Gastrointestinal Tract ,chemistry ,Turnover ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Female ,lcsh:Q ,Energy Metabolism - Abstract
Reproductive investment generally involves a trade-off between somatic growth and energy allocation for reproduction. Previous studies have inferred that jumbo squid Dosidicus gigas support growth during maturation through continuous feeding (an “income” source). However, our recent work suggests possible remobilization of soma during maturation (a “capital” source). We used fatty acids as biochemical indicators to investigate energy acquisition and allocation to reproduction for female D. gigas. We compared the fatty acid profiles of the ovary to those of the mantle muscle (slow turnover rate tissue, representing an energy reserve) and the digestive gland (fast turnover rate organ, reflecting recent consumption). For each tissue, the overall fatty acids among maturity stages overlapped and were similar. The changes with maturation in fatty acid composition in the ovary consistently resembled those of the digestive gland, with the similarity of fatty acids in the mantle muscle and the ovary increasing during maturation, indicating some energy reserves were utilized. Additionally, squid maintained body condition during maturation regardless of increasing investment in reproduction and a decline in feeding intensity. Cumulatively, D. gigas adopt a mixed income-capital breeding strategy in that energy for reproduction is mainly derived from direct food intake, but there is limited somatic reserve remobilization.
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- 2020
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26. Simulation testing a new multi-stage process to measure the effect of increased sampling effort on effective sample size for age and length data
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Peter-John F. Hulson, James T. Thorson, André E. Punt, Meaghan Bryan, and Haikun Xu
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0106 biological sciences ,Measure (data warehouse) ,Ecology ,010604 marine biology & hydrobiology ,Process (computing) ,Sampling (statistics) ,Aquatic Science ,Effective sample size ,Oceanography ,010603 evolutionary biology ,01 natural sciences ,Multi stage ,Statistics ,Environmental science ,Ecology, Evolution, Behavior and Systematics ,Simulation testing - Abstract
Ocean management involves monitoring data that are used in biological models, where estimates inform policy choices. However, few science organizations publish results from a recurring, quantitative process to optimize effort spent measuring fish age. We propose that science organizations could predict the likely consequences of changing age-reading effort using four independent and species-specific analyses. Specifically we predict the impact of changing age collections on the variance of expanded age-composition data (“input sample size”, Analysis 1), likely changes in the variance of residuals relative to stock-assessment age-composition estimates (“effective sample size”, Analysis 2), subsequent changes in the variance of stock status estimates (Analysis 3), and likely impacts on management performance (Analysis 4). We propose a bootstrap estimator to conduct Analysis 1 and derive a novel analytic estimator for Analysis 2 when age-composition data are weighted using a Dirichlet-multinomial likelihood. We then provide two simulation studies to evaluate these proposed estimators and show that the bootstrap estimator for Analysis 1 underestimates the likely benefit of increased age reads while the analytic estimator for Analysis 2 is unbiased given a plausible mechanism for model misspecification. We conclude by proposing a formal process to evaluate changes in survey efforts for stock assessment.
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- 2020
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27. Natural mortality: Theory, estimation and application in fishery stock assessment models
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Owen S. Hamel, James N. Ianelli, Mark N. Maunder, and André E. Punt
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Aquatic Science - Published
- 2023
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28. Those who fail to learn from history are condemned to repeat it: A perspective on current stock assessment good practices and the consequences of not following them
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André E. Punt
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Aquatic Science - Published
- 2023
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29. Information flow among fishing vessels modelled using a Bayesian network.
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L. Richard Little, Sakari Kuikka, André E. Punt, Francis Pantus, Campbell R. Davies, and Bruce D. Mapstone
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- 2004
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30. Implications of the maximum modelled age on the estimation of natural mortality when using a meta-analytic prior: The example of eastern Australian orange roughy (Hoplostethus atlanticus)
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Paul Burch, Sandra Curin-Osorio, Pia Bessell-Browne, Geoffrey N. Tuck, Malcolm Haddon, Nils C. Krueck, and André E. Punt
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Aquatic Science - Published
- 2023
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31. A review of estimation methods for natural mortality and their performance in the context of fishery stock assessment
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Mark N. Maunder, Owen S. Hamel, Hui-Hua Lee, Kevin R. Piner, Jason M. Cope, André E. Punt, James N. Ianelli, Claudio Castillo-Jordán, Maia S. Kapur, and Richard D. Methot
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Aquatic Science - Published
- 2023
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32. Identifying spawner biomass per‐recruit reference points from life‐history parameters
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Shijie Zhou, Yeming Lei, Roy Deng, André E. Punt, and Simon D. Hoyle
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Biomass (ecology) ,Geography ,Productivity (ecology) ,Agroforestry ,Management, Monitoring, Policy and Law ,Aquatic Science ,Life history ,Oceanography ,Resilience (network) ,FishBase ,Ecology, Evolution, Behavior and Systematics - Published
- 2020
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33. A novel spatiotemporal stock assessment framework to better address fine‐scale species distributions: Development and simulation testing
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André E. Punt, James T. Thorson, Jie Cao, and Cody S. Szuwalski
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Geography ,Stock assessment ,Scale (ratio) ,Management, Monitoring, Policy and Law ,Aquatic Science ,Oceanography ,Industrial engineering ,Ecology, Evolution, Behavior and Systematics ,Simulation testing - Published
- 2019
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34. Leveraging scientific uncertainty in fisheries management for estimating among-assessment variation in overfishing limits
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Kristin M. Privitera-Johnson and André E. Punt
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0106 biological sciences ,Ecology ,Overfishing ,business.industry ,010604 marine biology & hydrobiology ,media_common.quotation_subject ,Environmental resource management ,04 agricultural and veterinary sciences ,Aquatic Science ,Oceanography ,01 natural sciences ,Uncertainty ,Variation (linguistics) ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Environmental science ,Fisheries management ,business ,Ecology, Evolution, Behavior and Systematics ,media_common - Abstract
Fisheries management systems can utilize probability-based harvest control rules to incorporate scientific uncertainty and manager risk tolerance when setting catch limits. A precautionary buffer that scales with scientific uncertainty is used to calculate the acceptable biological catch from the overfishing limit (OFL) for US West Coast groundfish and coastal pelagic species. A previous analysis formed the basis for estimating scientific uncertainty as the among-assessment variation in estimates of historical spawning biomass time-series. This “historical biomass” approach may underestimate scientific uncertainty, because the OFL is a function of estimated exploitable biomass and fishing mortality. We developed a new approach that bases the calculation of scientific uncertainty on projected spawning biomass (SSB) and OFLs, accounting for uncertainty in recruitment and among-assessment variation. OFL projections yielded a higher estimate of uncertainty than SSB (0.502 vs. 0.413 for 25-year projections and 0.562 vs. 0.384 for a 1-year projection, assuming a deterministic stock-recruitment relationship). Assuming a stochastic stock-recruitment relationship produced smaller estimates of uncertainty (0.436, 25-year OFL projections; 0.452, 1-year OFL projections; 0.360, 25-year SSB projections; 0.318, 1-year SSB projections). The projection-based approach presented herein is applicable across stocks and regions that conduct assessments with sufficient and consistent outputs for calculating an OFL.
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- 2019
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35. There is no best method for constructing size-transition matrices for size-structured stock assessments
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André E. Punt and Lee Cronin-Fine
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0106 biological sciences ,Stock assessment ,Ecology ,010604 marine biology & hydrobiology ,04 agricultural and veterinary sciences ,Aquatic Science ,Oceanography ,01 natural sciences ,040102 fisheries ,Econometrics ,0401 agriculture, forestry, and fisheries ,Transition matrices ,Ecology, Evolution, Behavior and Systematics ,Mathematics - Abstract
Stock assessment methods for many invertebrate stocks, including crab stocks in the Bering Sea of Alaska, rely on size-structured population dynamics models. A key component of these models is the size-transition matrix, which specifies the probability of growing from one size-class to another after a certain period of time. Size-transition matrices can be defined using three parameters, the growth rate (k), asymptotic size (L∞), and variability in the size increment. Most assessments use mark-recapture data to estimate these parameters and assume that all individuals follow the same growth curve, but this can lead to biased estimates of growth parameters. We compared three approaches: the traditional approach, the platoon method, and a numerical integration method that allows k, L∞, or both to vary among individuals, under a variety of scenarios using simulated data based on golden king crabs (Lithodes aequispinus) in the Aleutian Islands region of Alaska. No estimation method performed best for all scenarios. The number of size-classes in the size-transition matrix and how the data are generated heavily dictate performance. However, we recommend the numerical integration method that allows L∞ to vary among individuals and smaller size-class widths.
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- 2019
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36. Attending to spatial social–ecological sensitivities to improve trade‐off analysis in natural resource management
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Tessa B. Francis, André E. Punt, Russ Jones, Phillip S. Levin, Lynn C. Lee, John Woodruff, Steve Reifenstuhl, Jennifer J. Silver, Harvey Kitka, Jaclyn S. Cleary, Alec D. MacCall, Jörn Schmidt, Daniel K. Okamoto, Jim A. McIsaac, Thomas F. Thornton, Rüdiger Voss, Melissa R. Poe, Andrew O. Shelton, Sherri C. Dressell, and Derek Armitage
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Trade offs ,Metapopulation ,Business ,Management, Monitoring, Policy and Law ,Aquatic Science ,Natural resource management ,Oceanography ,Trade-off ,Environmental planning ,Ecology, Evolution, Behavior and Systematics ,Spatial planning - Published
- 2019
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37. Recruitment: Theory, estimation, and application in fishery stock assessment models
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Mark N. Maunder, Elizabeth A. Babcock, Rishi Sharma, Clay E. Porch, and André E. Punt
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Fishery ,Estimation ,Stock assessment ,Geography ,Aquatic Science - Published
- 2019
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38. Extending integrated stock assessment models to use non-depensatory three-parameter stock-recruitment relationships
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Jason M. Cope and André E. Punt
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0106 biological sciences ,Beverton–Holt model ,education.field_of_study ,Stock assessment ,Ecology ,010604 marine biology & hydrobiology ,Maximum sustainable yield ,Population size ,Population ,04 agricultural and veterinary sciences ,Aquatic Science ,01 natural sciences ,Depensation ,040102 fisheries ,Econometrics ,0401 agriculture, forestry, and fisheries ,Environmental science ,Groundfish ,education ,Stock (geology) - Abstract
Stock assessments based on the integrated paradigm often include an underlying stock-recruitment relationship. This, along with estimates of fishery selectivity and biological parameters, allows the biomass and fishing mortality associated with Maximum Sustainable Yield (BMSY and FMSY respectively) to be calculated. However, the estimates of these quantities may differ from the proxies assumed in the harvest control rules that are used to provide management advice. Moreover, the estimated values for BMSY and FMSY are related functionally in population dynamics models based on 2-parameter stock-recruitment relationships such as the commonly used Beverton-Holt or Ricker relationships. Use of 2-parameter stock-recruitment relationships (SRRs) consequently restricts the ability to fully quantify the uncertainty associated with estimating BMSY and FMSY because 2-parameter SRRs restrict the potential range of values for BMSY/B0. In principle, BMSY/B0 and FMSY can be more independent if the stock-recruitment relationship is more general than these 2-parameter SRRs. This paper outlines eleven potential 3-parameter stock-recruitment relationships and evaluates them in terms of whether they are able to match a wide range of specifications for BMSY (expressed relative to unfished spawning stock biomass, B0) and FMSY (expressed relative to natural mortality, M). Of the eleven 3-parameter stock-recruitment relationships considered, the Ricker-Power stock-recruitment relationship is found to best satisfy the characteristics of (a) being able to mimic a wide range of BMSY/B0 and FMSY/M values, (b) not to lead to negative recruitment for biomasses between 0 and B0, and (c) not to lead to increasing recruitment while approaching the limit of zero population size. Bayesian assessments of three example groundfish species off the US west coast (aurora rockfish, petrale sole, and cabezon) are conducted using Simple Stock Synthesis based on the Beverton-Holt and Ricker-Power stock-recruitment relationships to illustrate some of the impacts of allowing for a 3-parameter stock-recruitment relationship.
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- 2019
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39. Modelling recruitment in a spatial context: A review of current approaches, simulation evaluation of options, and suggestions for best practices
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André E. Punt
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0106 biological sciences ,Spatial contextual awareness ,education.field_of_study ,biology ,business.industry ,010604 marine biology & hydrobiology ,Best practice ,Population ,Environmental resource management ,Subsistence agriculture ,04 agricultural and veterinary sciences ,Aquatic Science ,Fish stock ,biology.organism_classification ,01 natural sciences ,Spatial heterogeneity ,Canary rockfish ,Geography ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,education ,business ,Recreation - Abstract
Many, if not most, stocks of fish and invertebrates subject to commercial, recreational or subsistence harvesting exhibit some degree of spatial heterogeneity. This can be due to a lack of complete movement within a single biological population or due to the assessed region consisting of multiple sub-stocks. In principle, assessments for stocks for which the assumption of homogeneity is violated should be based on population dynamics models that are spatially-explicit. There are, however, relatively few stocks for which multi-stock/multi-area assessments are conducted. However, the number of assessments in which space is explicitly represented in the population dynamics model has been increasing in recent years and such models are available for fish stocks such as New Zealand hoki and canary rockfish off the US west coast, as well as invertebrates such as the rock lobsters off southern Australia and New Zealand. A challenge within such spatially-explicit assessments pertains to how recruitment and movement are modelled. This paper reviews assessments for fish and invertebrate stocks that are based on spatially-explicit models, identifying the challenges associated with modelling recruitment caused by increased model and parameter estimation complexity, and the available solutions. A set of illustrative simulations are undertaken to evaluate the consequences of different assumptions regarding spatial recruitment and movement, and hence develop some recommendations for best practice guidelines.
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- 2019
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40. Connectivity between spawning and nursery areas for Pacific cod (Gadus macrocephalus) in the Gulf of Alaska
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Georgina A. Gibson, Sarah Hinckley, Miriam J. Doyle, William T. Stockhausen, Carolina Parada, Albert J. Hermann, Kenneth O. Coyle, Carol Ladd, André E. Punt, Thomas P. Hurst, and Benjamin J. Laurel
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0106 biological sciences ,geography ,geography.geographical_feature_category ,010504 meteorology & atmospheric sciences ,biology ,010604 marine biology & hydrobiology ,Pacific cod ,Model system ,Oceanography ,biology.organism_classification ,01 natural sciences ,Early life ,symbols.namesake ,Ocean gyre ,symbols ,Biological dispersal ,Gadus ,Sound (geography) ,Lagrangian ,0105 earth and related environmental sciences - Abstract
We present the results of a study of the connectivity between Pacific cod spawning and nursery areas, and settlement of Pacific cod in the Gulf of Alaska. This work was conducted to address the hypothesis that spatial and temporal patterns of recruitment are related to variability in connectivity between spawning and nursery areas. To examine this hypothesis, we developed a Lagrangian, biophysical, individual-based model of Pacific cod early life history and dispersal using the Dispersal Model for Early Life Stages (DisMELS) framework. This model is driven by currents and scalars such as temperature from a version of the Regional Oceanographic Model System (ROMS) developed for the Gulf of Alaska. Results of our study show connectivity patterns predicted by the model that agree with our understanding (based on genetic analyses) that there is a high degree of localized retention in Pacific cod. The results indicate that the Shumagin Islands and Prince William Sound regions may serve as important collectors of Pacific cod recruits from upstream spawning areas. We also find correlations between individual-based model outputs and several large-scale climate indicators that appear to show settlement in several important nursery areas, and recruitment overall, are positively affected by slower gyre circulation in the Gulf of Alaska. We hypothesize that this is due to enhancement of retention, settlement in the Shumagin Island region, and reduction of transport of young cod out of the Gulf of Alaska to the southwest.
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- 2019
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41. Integrating Governance and Quantitative Evaluation of Resource Management Strategies to Improve Social and Ecological Outcomes
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Andrew O. Shelton, Ian P. Davies, Thomas F. Thornton, Sherri C. Dressel, Rudi Voss, Lynn C. Lee, Alec D. MacCall, Tessa B. Francis, Derek Armitage, Phillip S. Levin, Harvey Kitka, Jaclyn S. Cleary, André E. Punt, John Woodruff, Jörn Schmidt, Daniel K. Okamoto, Jennifer J. Silver, Jim A. McIsaac, Steve Reifenstuhl, Melissa R. Poe, and Russ Jones
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,010604 marine biology & hydrobiology ,Corporate governance ,Resource management ,Business ,General Agricultural and Biological Sciences ,01 natural sciences ,Environmental planning ,0105 earth and related environmental sciences - Abstract
In this article, we examine how governance can be more effectively integrated with quantitative evaluation methods in applied resource management. Governance refers to how societies organize to make decisions in ways that influence management choices (e.g., harvest allocation), such as levels of participation, the inclusion of different types of knowledge, and legitimacy of processes that lead to decisions. Using a fisheries example, we show that a failure to consider the governance context for quantitative evaluation of alternative management strategies may lead to unexpected consequences or break points in decision-making, bias estimates of risk and returns from management choices, and mask the potential for undesirable social and ecological outcomes.
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- 2019
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42. A multi-model approach to understanding the role of Pacific sardine in the California Current food web
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Timothy E. Essington, Nathan G. Taylor, Enrique N. Curchitser, Kirstin K. Holsman, Salvador E. Lluch-Cota, Alec D. MacCall, Laura E. Koehn, André E. Punt, William J. Sydeman, Kelli F. Johnson, Tessa B. Francis, Isaac C. Kaplan, Phillip S. Levin, and Felipe Hurtado-Ferro
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,Ecology ,010604 marine biology & hydrobiology ,Sardine ,Aquatic Science ,01 natural sciences ,Food web ,Fishery ,Geography ,Ecosystem model ,Forage fish ,Current (fluid) ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Published
- 2019
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43. Spatio-temporal variability in trophic ecology of jumbo squid (Dosidicus gigas) in the southeastern Pacific: Insights from isotopic signatures in beaks
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Chunxia Gao, Guanyu Hu, Xinjun Chen, Bai Li, André E. Punt, Yong Chen, and Robert Boenish
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0106 biological sciences ,Squid ,δ13C ,Range (biology) ,Ecology ,010604 marine biology & hydrobiology ,Foraging ,04 agricultural and veterinary sciences ,δ15N ,Aquatic Science ,Biology ,01 natural sciences ,Latitude ,biology.animal ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Marine ecosystem ,Trophic level - Abstract
Jumbo squid (Dosidicus gigas) plays an important role in marine ecosystems throughout the eastern Pacific, but the knowledge of its feeding and migration patterns is limited. In this study, we measured stable isotopic values (δ13C and δ15N) from the edge of lower beak lateral wall to investigate spatio-temporal and trophic ecology of jumbo squid in the southeastern Pacific. The effects of latitude, mantle length and distance to the shelf break (DSB) on isotopic values in normal years (2013 and 2014) and an El Nino year (2015) were evaluated with a generalized additive model. Differences in response curves between the normal and El Nino years revealed a shift of migratory strategy. Compared with normal years, the predicted range of the horizontal migration of jumbo squid became smaller in the El Nino year. The analysis characterized significant differences in the isotopic niche between years and areas. The isotopic niche in the El Nino year was narrower than those in normal years. Our results suggest that the migration and foraging ecology of jumbo squid are substantially influenced by mesoscale oceanic oscillations. The spatio-temporal variability of trophic patterns indicates that substantial migration and foraging plasticity facilitate jumbo squid with a high capability to adapt to environmental volatility.
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- 2019
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44. Implications of a climate-induced recruitment shift in the stock assessment of Patagonian grenadier (Macruronus magellanicus) in Chile
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Geoffrey N. Tuck, André E. Punt, Sally E. Wayte, Claudio Castillo-Jordán, Stewart Frusher, and Sean R. Tracey
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0106 biological sciences ,Stock assessment ,Operating model ,010604 marine biology & hydrobiology ,04 agricultural and veterinary sciences ,Aquatic Science ,01 natural sciences ,Demersal zone ,Fishery ,Management strategy ,Geography ,040102 fisheries ,Macruronus magellanicus ,0401 agriculture, forestry, and fisheries ,Ecosystem ,Sustainable yield ,Stock (geology) - Abstract
Patagonian grenadier (Macruronus magellanicus) is the most abundant demersal fisheries resource off Chilean Patagonia, and also is a key fisheries species off the south of Argentina and off the Falkland Islands. A Stock Synthesis assessment shows that this stock has declined in abundance off Chile, which has been attributed to a major change in recruitment strength, and subsequent production, after 1999. An assessment is conducted in which the change in recruitment is modelled as a shift in the stock-recruitment relationship. Management Strategy Evaluation is then used to examine the consequences of a mismatch between the assumptions related to recruitment in the assessment used to set the annual total allowable catch (TAC), and those in the operating model that represents the actual situation being managed. A management strategy that does not consider a shift in recruitment resulted in average TAC values of approximately 125,000 t, substantially larger than the sustainable yield of 45,000 t when there is a recruitment shift. A management strategy based on ignoring the shift in recruitment would thus lead to unsustainable catches, with major impacts on the ecosystem as well as the industry and coastal communities reliant on the fishery, if there was an actual shift in recruitment. Management of the fishery has not accounted for a recruitment shift, and annual landings have been consistently lower than the estimated annual TACs. The 2014 landings are similar to the long term TAC estimated by the assessment models under the Shift operating model. The history of the Patagonian grenadier fishery demonstrates the benefits of taking a precautionary approach that accounts for changes in fish productivity (whether climate-driven or otherwise). However, there can be considerable delays before a shift is observed in recruitment estimates or assessment model mis-specification is detected. The need for alternative approaches for providing more timely recruitment information is discussed.
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- 2019
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45. The effects of population synchrony, life history, and access constraints on benefits from fishing portfolios
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Daniel S. Holland, Kiva L. Oken, and André E. Punt
- Subjects
0106 biological sciences ,Conservation of Natural Resources ,Resource (biology) ,Natural resource economics ,Population Dynamics ,Fishing ,Population ,Fisheries ,Context (language use) ,010603 evolutionary biology ,01 natural sciences ,Salmon ,Natural Resources ,Animals ,Humans ,Revenue ,education ,Ecosystem ,education.field_of_study ,Ecology ,010604 marine biology & hydrobiology ,Natural resource ,Portfolio ,Groundfish ,Business - Abstract
Natural resources often exhibit large interannual fluctuations in productivity driven by shifting environmental conditions, and this translates to high variability in the revenue resource users earn. However, users can dampen this variability by harvesting a portfolio of resources. In the context of fisheries, this means targeting multiple populations, though the ability to actually build diverse fishing portfolios is often constrained by the costs and availability of fishing permits. These constraints are generally intended to prevent overcapitalization of the fleet and ensure populations are fished sustainably. As linked human-natural systems, both ecological and fishing dynamics influence the specific advantages and disadvantages of increasing the diversity of fishing portfolios. Specifically, a portfolio of synchronous populations with similar responses to environmental drivers should reduce revenue variability less than a portfolio of asynchronous populations with opposite responses. We built a bioeconomic model based on the Dungeness crab (Metacarcinus magister), Chinook salmon (Oncorhynchus tshawytscha), and groundfish fisheries in the California Current, and used it to explore the influence of population synchrony and permit access on income patterns. As expected, synchronous populations reduced revenue variability less than asynchronous populations, but only for portfolios including crab and salmon. Synchrony with the longer-lived groundfish population was not important because environmentally driven changes in groundfish recruitment were mediated by growth and natural mortality over the full population age structure, and overall biomass was relatively stable across years. Thus, building a portfolio of diverse life histories can buffer against the impacts of poor environmental conditions over short time scales. Increasing access to all permits generally led to increased revenue stability and decreased inequality of the fleet, but also resulted in less revenue earned by an individual from a given portfolio because more vessels shared the available biomass. This means managers are faced with a trade-off between the average revenue individuals earn and the risk those individuals accept. These results illustrate the importance of considering connections between social and ecological dynamics when evaluating management options that constrain or facilitate fishers' ability to diversify their fishing.
- Published
- 2021
- Full Text
- View/download PDF
46. A framework for assessing harvest strategy choice when considering multiple interacting fisheries and a changing environment: The example of eastern Bering Sea crab stocks
- Author
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André E. Punt, Michael G. Dalton, Benjamin Daly, Tyler Jackson, W. Christopher Long, William T. Stockhausen, Cody Szuwalski, and Jie Zheng
- Subjects
Aquatic Science - Published
- 2022
- Full Text
- View/download PDF
47. An ensemble approach to understand predation mortality for groundfish in the Gulf of Alaska
- Author
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Grant D. Adams, Kirstin K. Holsman, Steven J. Barbeaux, Martin W. Dorn, James N. Ianelli, Ingrid Spies, Ian J. Stewart, and André E. Punt
- Subjects
Aquatic Science - Published
- 2022
- Full Text
- View/download PDF
48. Implications of climate change on the Bering Sea and other cold water systems
- Author
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Anne Babcock Hollowed, Alan C. Haynie, Albert J. Hermann, Kirstin K. Holsman, André E. Punt, and Cody S. Szuwalski
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Oceanography - Published
- 2022
- Full Text
- View/download PDF
49. Shifting trends: Detecting changes in cetacean population dynamics in shifting habitat
- Author
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Charlotte Boyd and André E. Punt
- Subjects
Population Dynamics ,Binomials ,Marine and Aquatic Sciences ,Transportation ,Surveys ,Polynomials ,Abundance (ecology) ,skin and connective tissue diseases ,Wildlife conservation ,Mammals ,education.field_of_study ,Multidisciplinary ,Ecology ,Population size ,Eukaryota ,Habitats ,Geography ,Habitat ,Fecundity ,Research Design ,Vertebrates ,Physical Sciences ,Engineering and Technology ,Medicine ,Algorithms ,Research Article ,Conservation of Natural Resources ,Population Size ,Climate Change ,Science ,Population ,Climate change ,Context (language use) ,Marine Biology ,Research and Analysis Methods ,Models, Biological ,Population Metrics ,Population growth ,Animals ,education ,Marine Mammals ,Ecosystem ,Population Density ,Survey Research ,Population Biology ,Ecology and Environmental Sciences ,Organisms ,Whales ,Biology and Life Sciences ,Transect Surveys ,Boats ,Blue Whales ,Algebra ,Amniotes ,Earth Sciences ,Physical geography ,Cetacea ,sense organs ,Zoology ,Mathematics - Abstract
The ability to monitor population dynamics and detect major changes in population trend is essential for wildlife conservation and management. However, this is often challenging for cetaceans as surveys typically cover only a portion of a population’s range and conventional stock assessment methods cannot then distinguish whether apparent changes in abundance reflect real changes in population size or shifts in distribution. We developed and tested methods for estimating population size and trend and detecting changes in population trend in the context of shifting habitat by integrating additional data into distance-sampling analysis. Previous research has shown that incorporating habitat information can improve population size estimates for highly mobile species with dynamic spatial distributions. Here, using simulated datasets representative of a large whale population, we demonstrate that incorporating individual mark-recapture data can increase the accuracy and precision of trend estimation and the power to distinguish whether apparent changes in abundance reflect changes in population trend or distribution shifts. We recommend that similar simulation studies are conducted for specific cetacean populations to assess the potential for detecting changes in population dynamics given available data. This approach is especially important wherever population change may be confounded with long-term change in distribution patterns associated with regime shifts or climate change.
- Published
- 2021
50. Deep learning methods applied to electronic monitoring data: Automated catch event detection for longline fishing
- Author
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Geoffrey N. Tuck, André E. Punt, Maoying Qiao, Dadong Wang, L. Richard Little, Mike Gerner, and Beyan, C
- Subjects
0106 biological sciences ,Ecology ,Computer science ,business.industry ,010604 marine biology & hydrobiology ,Event (relativity) ,Deep learning ,Real-time computing ,Fisheries ,deep learning ,02 engineering and technology ,Aquatic Science ,Oceanography ,artificial intelligence ,01 natural sciences ,Longline fishing ,machine learning ,fisheries management ,Monitoring data ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Artificial intelligence ,business ,artificial neural networks ,Ecology, Evolution, Behavior and Systematics - Abstract
Electronic monitoring (EM) systems have become functional and cost-effective tools for the conservation and sustainable harvesting of marine resources. EM is an alternative to on-board observers, which produces video segments that can subsequently be reviewed by analysts. It is currently used in a range of fisheries. There are two major challenges to the widespread adoption of EM. One is the large storage requirement for the video footage recorded and the other is the long time required by analysts to review the video footage. We propose an automated catch event detection framework to address these challenges. Our solution, based on deep learning techniques, automatically extracts video segments of catch events, which substantially reduces storage space and review time by analysts. Here, we demonstrate the framework using video footage from three longline fishing trips. The system recalled nearly 100% of the catch events across all trips.
- Published
- 2021
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