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Atlantic bluefin tuna (Thunnus thynnus) are a large, highly migratory fish distributed throughout the North Atlantic Ocean and adjacent seas currently managed as two discrete stocks: western and eastern. Both stocks forage in the North Atlantic, and a high degree of intermixing occurs, which combined with limited single-stock survey data makes it difficult to assess the abundance and status of individual populations. In this study, we used movement patterns from a multidecadal tagging dataset to create monthly distribution maps for these two major stocks. We then used these maps to separate the overall catch records into stock-specific catch (catch per unit effort, CPUE) time series. We identified an increase in the past two decades in the proportion of catch estimated to come from the eastern stock, attributable to a decrease in CPUE in regions dominated by the western stock, relative to other regions. The stock-specific catch series can be used to improve the accuracy of stock assessments and inform spatial management.

Impacts of Karenia brevis red tide blooms have been an increasing cause of concern for fisheries management in the Gulf of Mexico (Gulf). The 2019 Gulf red grouper (Epinephelus morio) stock assessment was confronted with the challenges of quantifying and parameterizing red tides during both historical and projection time periods. Red tide mortality was estimated for each age class in the model solely in 2005 and 2014 during severe events. Given the considerable uncertainty surrounding the 2018 red tide and its substantial implications on the status of the population, several projection scenarios were evaluated. Under the assumption of no 2018 red tide mortality, near-term catches were projected to nearly double, a predicted outcome that appeared to be in contrast with recent record low catches and fishing industry perceptions of major stock depletion. In the event that the 2018 red tide caused mortality, but was not accounted for in projections, the recommended catch levels would lead to high probabilities of overfishing and potentially stock collapse. Collectively, these results highlight how consideration of uncertainty in projections can help avoid unintended consequences.

This review documents the current state of knowledge and gaps therein, as determined through a survey of published research on relevant topics, regarding the potential impacts of offshore oil production platforms (OPP) on the biology of highly migratory fish species (HMS) which include tunas, swordfish, billfishes, and oceanic sharks. There is a limited amount of published research directly related to HMS and OPPs. This may be due to the relatively recent offshore expansion of the industry and of studies. Most studies have focused on structure-associated species such as rockfishes and snappers. Within the U.S. exclusive economic zone, the most probable areas of interaction between HMS and OPPs occur in the Gulf of Mexico. This report focuses primarily upon this region, while noting that HMS roam the majority of the world’s oceans and may interact with petroleum infrastructure in many other locations. With such large stock boundaries it is unlikely that HMS interactions with OPPs will have a significant impact at the stock level, however, there could be impacts at local or regional levels.

Management strategy evaluation (MSE) is a simulation-based approach to examine the efficacy of management options in achieving fishery-, ecosystem-, and socioeconomic-related objectives while integrating over system uncertainties. As a form of structured decision analysis, MSE is amenable to stakeholder involvement, which can reduce implementation barriers associated with nontransparent decision-making procedures. Based on analysis of three MSE processes (Atlantic tunas (Thunnus spp.), Atlantic herring (Clupea harengus), and eastern oysters (Crassostrea virginica)), we provide suggestions for improving stakeholder engagement in MSE. By assembling a workgroup and modeling team with diverse backgrounds, including professional facilitators, communication liaisons, and social scientists, dialogue can be improved and an atmosphere of mutual learning fostered. Communication further benefits from clearly defining roles, responsibilities, and terms of engagement for all involved; explicitly and transparently identifying goals and objectives of the MSE before modeling has begun; and, when appropriate, revisiting goals and objectives throughout the MSE process. Although MSEs are not without limitations, the participatory modeling framework, wherein stakeholders are actively engaged at each stage of MSE development, provides a useful mechanism to support fisheries management.

Management strategy evaluation (MSE) is an increasingly popular tool for developing, testing, and implementing fisheries management regimes, oftentimes utilizing participatory modeling. This special issue, “Under pressure: addressing fisheries challenges with Management Strategy Evaluation”, includes eleven articles highlighting cutting edge MSE approaches and perspectives on improving stakeholder engagement. The special issue is the culmination of a two-session MSE symposium held during the 147th American Fisheries Society Annual Meeting in Tampa, Florida. We summarize the themes from the symposium and special issue articles. Contributions demonstrated that important strides have been made in quantifying and exploring risk (by including more sophisticated multispecies and socioeconomic components), developing and testing data-limited harvest control rules, acknowledging and diagnosing limitations of MSE (e.g., identifying exceptional circumstances), and dealing with issues of stakeholder engagement and dimensionality (e.g., determining appropriate representation, communication techniques, and participation levels). Although MSE is a not a panacea for marine policy and resource utilization issues, it is a useful tool for implementing co-management regimes that should become increasingly robust as the multidisciplinary nature of MSE processes continues to expand.

Globally, tunas are among the most valuable fish stocks, but are also inherently difficult to monitor and assess. Samples of larvae of Western Atlantic bluefin tuna Thunnus thynnus (Linnaeus, 1758) from standardized annual surveys in the northern Gulf of Mexico provide a potential source of “offspring” for close-kin mark-recapture (CKMR) estimates of abundance. However, the spatial patchiness and highly skewed numbers of larvae per tow suggest sampled larvae may come from a small number of parents, compromising the precision of CKMR. We used high throughput genomic profiling to study sibship within and among larval tows from the 2016 standardized Gulf-wide survey compared to targeted sampling carried out in 2017. Full- and half-siblings were found within both years, with 12% of 156 samples in 2016 and 56% of 317 samples in 2017 having at least one sibling. There were also two pairs of cross cohort half-siblings. Targeted sampling increased the number of larvae collected per sampling event but resulted in a higher proportion of siblings. The combined effective sample size across both years was about 75% of the nominal size, indicating that Gulf of Mexico larval collections could be a suitable source of juveniles for CKMR in Western Atlantic bluefin tuna.

Specifying annual catch limits for artisanal fisheries, low economic value stocks, or bycatch species is problematic due to data limitations. Many empirical management procedures (MPs) have been developed that provide catch advice based on achieving a stable catch or a historical target (i.e., instead of maximum sustainable yield). However, a thorough comparison of derived yield streams between empirical MPs and stock assessment models has not been explored. We first evaluate trade-offs in conservation and yield metrics for data-limited approaches through management strategy evaluation (MSE) of seven data-rich reef fish species in the Gulf of Mexico. We then apply data-limited approaches for each species and compare how catch advice differs from current age-based assessment models. MSEs identified empirical MPs (e.g., using relative abundance) as a compromise between data requirements and the ability to consistently achieve management objectives (e.g., prevent overfishing). Catch advice differed greatly among data-limited approaches and current assessments, likely due to data inputs and assumptions. Adaptive MPs become clearly viable options that can achieve management objectives while incorporating auxiliary data beyond catch-only approaches.

Effective sustainable management of marine fisheries requires that assessed management units (that is, fish stocks) correspond to biological populations. This issue has long been discussed in the context of Atlantic bluefin tuna (ABFT, Thunnus thynnus) management, which currently considers two unmixed stocks but does not take into account how individuals born in each of the two main spawning grounds (Gulf of Mexico and Mediterranean Sea) mix in feeding aggregations throughout the Atlantic Ocean. Using thousands of genome-wide molecular markers obtained from larvae and young of the year collected at the species’ main spawning grounds, we provide what is, to the best of our knowledge, the first direct genetic evidence for “natal homing” in ABFT. This has facilitated the development of an accurate, cost-effective, and non-invasive tool for tracing the genetic origin of ABFT that allows for the assignment of catches to their population of origin, which is crucial for ensuring that ABFT management is based on biologically meaningful stock units rather than simply on catch location., Sí

Many stock assessments heavily rely on indices of relative abundance derived from fisheries-dependent catch-per-unit-effort (CPUE) data. Therefore, it is critical to evaluate different CPUE standardization methods under varying scenarios of data generating processes. Here, we evaluated nine CPUE standardization methods offering contrasting treatments of spatio-temporal variation, ranging from the basic generalized linear model (GLM) method not integrating a year-area interaction term to a sophisticated method using the spatio-temporal modeling platform VAST. We compared the performance of these methods against simulated data constructed to mimic the processes generating fisheries-dependent information for Atlantic blue marlin (Makaira nigricans), a common bycatch population in pelagic longline fisheries. Data were generated using a longline data simulator for different population trajectories (increasing, decreasing, and static). These data were further subsampled to mimic an observer program where trips rather than sets form the sampling frame, with or without a bias towards trips with low catch rates, which might occur if the presence of an observer alters fishing behavior to avoid bycatch. The spatio-temporal modeling platform VAST achieved the best performance in simulation, namely generally had one of the lowest biases, one of the lowest mean absolute errors (MAEs), and 50% confidence interval coverage closest to 50%. Generalized additive models accounting for spatial autocorrelation at a broad spatial scale (one of the lowest MAEs and one of the lowest biases) and, to a lesser extent, non-spatial delta-lognormal GLMs including a year-area interaction as a random effect (one of the lowest MAEs and one of the best confidence interval coverages) also performed adequately. The VAST method provided the most comprehensive and consistent treatment of spatio-temporal variation, in contrast with methods that simply weight predictions by large spatial areas, where it is critical, but difficult, to get the a priori spatial stratification correct before weighting. Next, we applied the CPUE standardization methods to real data collected by the National Marine Fisheries Service Pelagic Observer Program. The indices of relative abundance predicted from real observer data were relatively similar across CPUE standardization methods for the period 1998–2017 and suggested that the blue marlin population of the Atlantic declined over the period 1998–2004 and was relatively stable afterwards. As spatio-temporal variation related to environmental changes or depletion becomes increasingly necessary to consider, greater use of spatio-temporal models for standardizing fisheries-dependent CPUE data will likely be warranted.

Age–length key (ALK) methods generally perform well when length samples and age samples are representative of the underlying population. It is unclear how well these methods perform when lengths are representative but age samples are sparse (i.e. age samples are small or missing in many years, and some length groups do not have any age observations). With western Atlantic bluefin tuna, the available age data are sparse and have been, for the most part, collected opportunistically. We evaluated two methods capable of accommodating sparse age data: a novel hybrid ALK (combining forward ALKs and cohort slicing) and the combined forward-inverse ALK. Our goal was to determine if the methods performed better than cohort slicing, which has traditionally been used to obtain catch-at-age for Atlantic bluefin tuna, given the data limitations outlined above. Simulation results indicated that the combined forward-inverse ALK performed much better than the other methods. When applied to western Atlantic bluefin tuna data, the combined forward-inverse ALK approach was able to track cohorts and identified an inconsistency in the ageing of some samples.

The timing and extent of international crossings by billfishes, tunas, and sharks in the Cuba-Mexico-United States (U.S.) triangle was investigated using electronic tagging data from eight species that resulted in >22,000 tracking days. Transnational movements of these highly mobile marine predators were pronounced with varying levels of bi- or tri-national population connectivity displayed by each species. Billfishes and tunas moved throughout the Gulf of Mexico and all species investigated (blue marlin, white marlin, Atlantic bluefin tuna, yellowfin tuna) frequently crossed international boundaries and entered the territorial waters of Cuba and/or Mexico. Certain sharks (tiger shark, scalloped hammerhead) displayed prolonged periods of residency in U.S. waters with more limited displacements, while whale sharks and to a lesser degree shortfin mako moved through multiple jurisdictions. The spatial extent of associated movements was generally associated with their differential use of coastal and open ocean pelagic ecosystems. Species with the majority of daily positions in oceanic waters off the continental shelf showed the greatest tendency for transnational movements and typically traveled farther from initial tagging locations. Several species converged on a common seasonal movement pattern between territorial waters of the U.S. (summer) and Mexico (winter).

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 evaluating the impacts of COVID-19 but from the perspective of addressing tactical, day-to-day concerns of restarting operations for various marine and fisheries-oriented organizations. Thus, it seemed appropriate to us to explore the potential challenges posed by COVID-19 and to purposefully ascertain whether there are strategic opportunities for improving how we conduct our operations. We need to find ways to mitigate the effects of COVID-19 on our mission and also to glean information from our responses while in the midst of the crisis. We offer some recommendations to that end and offer these thoughts not as having solved every problem, but to learn from each other, compare across organizations, and engage in dialogue within our discipline to advance much-needed changes.

Mapping the spatial distributions of fish populations is an integral component of ecosystem-based fisheries management (EBFM). Particularly for red grouper ( Epinephelus morio ) and gag grouper (“gag”; Mycteroperca microlepis ), two economically important species, the lack of mapping due to data limitations (i.e., inconsistent capture in research surveys) has left a critical gap in the science needed to assess how ecosystem processes and EBFM measures in the Gulf of Mexico (GOM) impact their population dynamics. We combined multiple fisheries-dependent and fisheries-independent data sources to map the long-term spatial distributions of older juveniles and adults of red and gag groupers in the U.S. GOM, using spatio-temporal binomial generalized linear mixed models (GLMMs). Spatio-temporal binomial GLMMs rely on the idea that probability of encounter at a given site is more similar to probability of encounter at nearby sites than to probability of encounter at geographically remote locations; this tenet allows one to estimate a smoothed surface depicting how probability of encounter varies spatially. Our spatio-temporal binomial GLMMs do not integrate environmental covariates, yet they account for the effects of year and research survey. The distribution maps produced from the predictions of the spatio-temporal binomial GLMMs aligned with the current understanding of the long-term ontogenetic spatial distributions of red and gag groupers in the U.S. GOM. Red grouper was predicted to be encountered throughout the West Florida Shelf (WFS), primarily at depths ranging from 20 to 60 m. Both older juvenile and adult female gags were predicted to be encountered from Apalachicola, Florida, to the region northwest of Tampa, Florida, along the 20 m depth contour, especially in Apalachee Bay. The probability of encounter of adult female gag was also high in the Florida Middle Grounds and in deeper (>40 m) areas of the WFS. The probability of encounter of adult male gag was highest along the edge of the WFS, both inside recognized spawning grounds (including the Madison-Swanson marine protected area) and outside, i.e., below 27°N (including Pulley Ridge). The distribution maps produced are valuable for understanding the ecology of grouper species and can be used as a basis for further analyses. Our spatio-temporal binomial GLMM framework will serve many important EBFM projects, including the construction of reliable distribution maps in bulk for spatially explicit ecosystem models of the GOM, which will improve spatial distributions and species spatial overlaps in spatially explicit ecosystem models and, therefore, the trophic interactions predicted by these models.

A series of estimates of the total mortality rate (Z) can be obtained by using the Beverton–Holt nonequilibrium-based approach of Gedamke and Hoenig (2006) on observations of population mean length over time (ML model). In contrast, only relative mortality rates (not absolute values) can be obtained from a time series of catch rates. We derived the transitional behavior of the catch rate following a change in total mortality in the population. From this derivation, we developed a new method to estimate Z that utilizes both mean lengths and catch rates (MLCR model). Both the ML model and the MLCR model assume constant recruitment in the population. We used a simulation study to test performance when recruitment is variable. Simulations over various scenarios of Z and recruitment variability showed that there may be correlated residuals in the mean lengths and catch rates arising from fluctuations in recruitment. However, the root mean square errors of the Z estimates and the change point (i.e., the...

The article examines factors related to the decline and rebuilding of billfish stocks in the Atlantic and Indian oceans. Longline effort has declined over the last 10–15 years in both oceans. This decline in fishing pressure has led to the recovery of some stocks, but some species that are caught incidentally in industrial longline fisheries remain overexploited. Using a simple moving average technique on fishing mortality trajectories, we estimated a threshold effort size of 240 million hooks for the Atlantic Ocean and 364 million hooks for the Indian Ocean where stocks start experiencing overfishing. In addition, we highlight differences in the economic characteristics of the major fleets catching billfish in the two oceans and discuss how this may be associated with differences in management, enforcement, and stock rebuilding.

Catastrophic disturbances to marine environments, such as the Deepwater Horizon oil spill in the northern Gulf of Mexico (GoM), emphasize the need to approach fisheries management and restoration from an ecosystem perspective. To evaluate the ecosystem dynamics within the GoM, we developed a mass-balanced Ecopath model (“nGoM Ecopath”) which integrated ecosystem stressors, indirect effects of fishing (e.g. bycatch), and predator-prey dynamics. A meta-analysis of diet composition filled critical gaps in higher trophic level predator-prey linkages, such as predation on economically important groupers (Serranidae). Compared to previous Ecopath models of the GoM, nGoM Ecopath displayed higher ecosystem complexity including higher connectivity amongst trophic groups and increased omnivory. Mixed trophic impact analysis revealed species including snappers, groupers, pelagic coastal piscivores, oceanic piscivores, cephalopods, and dolphins as critical top-down predators. Bottom-up effects were identified for juvenile groupers and mackerels, which benefited from high production of invertebrates and small fishes. Network analysis revealed detrimental effects of red tides on sharks, skates and rays, and demersal coastal invertebrate feeders such as black drum, as well as adult red and gag grouper. Pelagic coastal piscivores (e.g. jacks (Carangidae)), snappers (Lutjanidae), and mobile epifauna (e.g. lobsters) imposed the largest influence on ecosystem structure as keystone predators. The nGoM Ecopath model using the dynamic module Ecosim can help guide restoration efforts through the evaluation of multispecies responses to management actions and identification of ecosystem trade-offs.

In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, patchy “hot spots” at a variety of depths along the Alabama coast and the west Florida shelf. Red Snapper biomass and fecundity estimates were higher for the northwestern GOM than for the northeastern GOM, as the latter area contained mostly smaller, younger individuals. The existence of similar surveys on petroleum platforms and artificial reefs also enabled us to calculate their relative contribution to Red Snapper distribution compared with that of natural habitats. We estimated that for the youngest age-classes, catch rates were approximately 20 times higher on artificial structures than on natural reefs. Despite the high catch rates observed on artificial structures, they represent only a small fraction of the total area in the northern GOM; thus, we estimated that they held less than 14% of Red Snapper abundance. Because artificial structures—particularly petroleum platforms—attract mostly the youngest individuals, their contribution was even lower in terms of total population biomass (7.8%) or spawning potential (6.4%). Our estimates of Red Snapper relative abundance, biomass, and spawning potential can be used to design spatial management strategies or as inputs to spatial modeling techniques. Received January 1, 2016; accepted October 28, 2016

Environmental variability changes the distribution, migratory patterns, and susceptibility to various fishing gears for highly migratory marine fish. These changes become especially problematic when they affect the indices of abundance (such as those based on catch-per-unit-effort: CPUE) used to assess the status of fish stocks. The use of simulated CPUE data sets with known values of underlying population trends has been recommended by ICCAT (International Commission for the Conservation of Atlantic Tunas) to test the robustness of CPUE standardization methods. A longline CPUE data simulator was developed to meet this objective and simulate fisheries data from a population with distinct habitat preferences. The simulation was used to test several statistical hypotheses regarding best practices for index standardization aimed at accurate estimation of population trends. Effort data from the US pelagic longline fleet was paired with a volume-weighted habitat suitability model for blue marlin (Makaira nigricans) to derive a simulated time series of blue marlin catch and effort from 1986 to 2015 with four different underlying population trends. The simulated CPUE data were provided to stock assessment scientists to determine if the underlying population abundance trend could accurately be detected with different methods of CPUE standardization that did or did not incorporate environmental data. While the analysts’ approach to the data and the modeling structure differed, the underlying population trends were captured, some more successfully than others. In general, the inclusion of environmental and habitat variables aided the standardization process. However, differences in approaches highlight the importance of how explanatory variables are categorized and the criteria for including those variables. A set of lessons learned from this study was developed as recommendations for best practices for CPUE standardization. FCT IF/00253/2014 info:eu-repo/semantics/publishedVersion

The Gulf of Mexico (GOM) is the primary spawning ground for western Atlantic bluefin tuna (Thunnus thynnus). In this work, information reported by previous studies about the preferred environmental conditions for the occurrence of bluefin tuna larvae in the GOM is integrated into a dimensionless index, the BFT_Index. This index is used to evaluate the spatial and temporal variability of areas with favorable environmental conditions for larvae within the GOM during 1993–2011. The main findings of this work are that: (i) the proposed index successfully captures the spatial and temporal variability in the in situ occurrence of bluefin tuna larvae; (ii) areas with favorable environmental conditions for larvae in the GOM exhibit year-to-year spatial and temporal variability linked with mesoscale ocean features and sea surface temperature; and (iii) comparison of the BFT_Index-derived variability with recruitment of age-0 fish estimated from recent stock assessment indicates that changes in environmental conditions may drive a relevant component (~58%) of the recruitment variability. The comparison with the recruitment dataset further revealed the existence of key regions linked with recruitment in the central/northern GOM, and that the Loop Current may function as a trap for larvae, possibly leading to low survival rates. Above (below) average conditions for occurrence of larvae in the GOM during spring were observed in 2000, 2001, 2002, 2006–2008, and 2011 (1994, 1996, 1998, 1999, 2003 and 2010). Results reported here have potential applications to assessment of bluefin tuna.

Recreational fishers discard millions of red snapper (Lutjanus campechanus) annually in the northern Gulf of Mexico (nGOM), resulting in significant foregone yield. We conducted simulation modeling to evaluate the potential for hook-size regulations to improve efficiency in the recreational red snapper fishery. First, we imposed a suite of candidate parameter sets, informed by recent empirical studies, within the 2015 red snapper assessment model to estimate contact-selectivity of recreational fleets in the northeastern or northwestern GOM. We then evaluated potential hook-size regulations by imposing a suite of candidate parameter sets on future contact-selectivity of each recreational fleet, conditional on likelihood-based estimates from the first simulation exercise. In the assessment model, maximum likelihood values improved when strongly domed contact-selectivity curves with peak size approximating the current minimum length limit were imposed in either the eastern or western recreational fleet. Simulation results indicate mandating large hook sizes could modestly increase retained catch for the eastern recreational fleet while dramatically reducing the number of red snapper discarded by either fleet. Realized benefits of hook-size regulations will depend upon future fisher retention behavior, such as the intensity of live high-grading, discard mortality reduction practices, such as venting and the use of descender devices, and changes to current management regulations.

Increasing water temperatures due to climate change will likely have significant impacts on distributions and life histories of Atlantic tunas. In this study, we combined predictive habitat models with a downscaled climate model to examine potential impacts on adults and larvae of Atlantic bluefin tuna ( Thunnus thynnus ) and skipjack tuna ( Katsuwonus pelamis ) in the Intra-Americas Sea (IAS). An additional downscaled model covering the 20th century was used to compare habitat fluctuations from natural variability to predicted future changes under two climate change scenarios: Representative Concentration Pathway (RCP) 4.5 (medium–low) and RCP 8.5 (high). Results showed marked temperature-induced habitat losses for both adult and larval bluefin tuna on their northern Gulf of Mexico spawning grounds. In contrast, habitat suitability for skipjack tuna increased as temperatures warmed. Model error was highest for the two skipjack tuna models, particularly at higher temperatures. This work suggests that influences of climate change on highly migratory Atlantic tuna species are likely to be substantial, but strongly species-specific. While impacts on fish populations remain uncertain, these changes in habitat suitability will likely alter the spatial and temporal availability of species to fishing fleets, and challenge equilibrium assumptions of environmental stability, upon which fisheries management benchmarks are based.

We develop and test spatial population dynamics models that estimate age-dependent offshore movement of fish populations from spatial fishery data. Spatially aggregated population dynamics models produced biased estimates of maximum sustainable yield (MSY) reference points when spatial dynamics were simulated. Spatial population dynamics models provided relatively unbiased estimates of MSY reference points regardless of whether spatial dynamics were simulated. We demonstrate that by using conventional fishery data that are disaggregated spatially, it is possible to estimate movement with age and obtain more accurate estimates of management reference points. The new spatial models were fitted to data for Gulf of Mexico red grouper (Epinephelus morio) and gag grouper (Mycteroperca microlepis) to estimate spatial distribution and offshore movement with age. Offshore ontogeny was estimated to be stronger for gag grouper than red grouper and predicted a larger fraction of older gag grouper in deeper waters.

Geostatistical prediction can address two difficult issues in interpreting fishery-dependent catch per unit effort (CPUE): the lack of a sampling design and the need to fill spatial gaps. In this paper we demonstrate the spatial weighting properties of geostatistics for treating data collected without a sampling design or with a selection bias, two basic traits of fishery-dependent data. We then examine the bias and precision of geostatistical prediction of CPUE based on fishery-dependent data through simulation. We create data sets with known variograms, sample them with a preference for sites with high abundance, and then estimate variograms and CPUE as the geostatistical mean relative abundance. The variograms obtained from the simulated fishery samples correctly estimated the range but underestimated the sill, and the geostatistical mean substantially improved the estimation of CPUE over the arithmetic mean. Though the geostatistical mean still overestimated the true value, the error was prima...

Fishery-dependent catch per unit effort (CPUE) comprises critical input for many stock assessments. Construction of CPUE indices usually employs some method of data standardization. However, conventional methods based on linear models do not effectively deal with the fact that samples are collected with a selection bias or with the problem of filling spatial gaps. Geostatistical interpolation methods can ameliorate some of the biases caused by both of these problems while remaining complementary to traditional linear model-based CPUE standardization. In this paper we present geostatistical estimates of sea scallop Placopecten magellanicus CPUE from tows recorded by onboard observers during an opening of Georges Bank Closed Area II in 1999. By selecting tows for which there was little prior effort (on the basis of accumulated effort measured by vessel monitoring systems), we obtained tows that reflected initial abundance as closely as possible. These tows were used to obtain a variogram which was u...

Conflicting trends in indices of abundance for North Atlantic swordfish starting in the mid-to late 1990s, in the form of fleet specific catch-per-unit-effort (CPUE), suggest the possibility of a spatial shift in abundance to follow areas of preferred temperature. The observed changes in the direction of the CPUEs correspond with changes in trends in the summer Atlantic Multidecadal Oscillation (AMO), a long term mode of variability of North Atlantic sea surface temperature. To test the hypothesis of a relation between the CPUE and the AMO, the CPUEs were made spatially explicit by re-estimating using an “areas-as-fleets” approach. These new CPUEs were then used to create alternative stock histories. The residuals of the fit were then regressed against the summer AMO. Significant, and opposite, relations were found in the regressions between eastern and western Atlantic areas. When the AMO was in a warm phase, the CPUEs in the western (eastern) areas were higher (lower) than predicted by the assessment model fit. Given the observed temperature tolerance limits of swordfish, it is possible that either their preferred habitat, prey species, or both have shifted spatial distributions resulting in conflicting CPUE indices. Because the available CPUE time series only overlaps with one change in the sign of the AMO (~1995), it is not clear whether this is a directional or cyclical trend. Given the relatively localized nature of many of the fishing fleets, and the difficulty of separating fleet effects from changes in oceanography we feel that it is critical to create CPUE indices by combining data across similar fleets that fish in similar areas. This approach allowed us to evaluate area-specific catch rates which provided the power to detect basin-wide responses to changing oceanography, a critical step for providing robust management advice in a changing climate., SI

1 Mississippi Laboratories Southeast Fisheries Science Center National Marine Fisheries Service, NOAA 3209 Frederic Street Pascagoula, Mississippi 39567-4112 2 Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 Eighth Avenue SE Saint Petersburg, Florida 33701-5020 3 Sustainable Fisheries Division Southeast Fisheries Science Center National Marine Fisheries Service, NOAA 75 Virginia Beach Drive Miami, Florida 33149-1003

Understanding the spatial distribution of a species is an important precondition to successfully managing marine populations. For reef fishes, this is of particular importance due to the patchy nature of reef communities. This study estimated the spatial distribution of five reef fish species on the West Florida Shelf: gag grouper ( Mycteroperca microlepis ), mutton snapper ( Lutjanus analis) , red grouper ( Epinephelus morio ), red snapper ( Lutjanus campechanus ), and vermilion snapper ( Rhomboplites aurorubens ). Estimation was done by combining large-scale fishery-dependent catch per unit of fishing effort with small scale fishery-independent video survey observation. Catch per unit of fishing effort was obtained from vessel logbook data while video observations of reef fish presence–absence and relative abundance were made by stratified random sampling on known reef and hard-bottom habitat in the Gulf of Mexico. Relative abundance estimates showed different abundance patterns for the five species depending on depth and geographical area. Variogram modeling suggested that gag grouper, mutton snapper, and red grouper were spatially autocorrelated on reef or hard-bottom habitats at short ranges of between 0.87 and 0.95 km, while red and vermilion snapper were found to be randomly distributed. Range estimates for gag grouper, mutton snapper and red grouper were supported by variograms of depth soundings in the Gulf which produced range estimates of between 1.56 and 6.34 km. Combining the relative estimates of abundance from catch per unit of effort with the spatial autocorrelation parameters from video surveys allowed us to provide stochastic fish abundance estimates at scales of about 2 km 2 .

Virtual population analysis requires information on the fishing mortality rate (or abundance) for one age group from each cohort. In many cases available data are insufficient to estimate these rates for every age group and structural assumptions must be imposed to reduce the number of effective parameters. Past assessments of western Atlantic bluefin tuna (Thunnus thynnus ) have reduced the number of parameters by assuming pre-specified values for the ratios of the fishing mortality rates on adjacent age groups. More recent bluefin tuna assessments have estimated terminal fishing mortality rates (F ) on each age with a constraint that restricts change from one year to the next. We explore the implications of these methods of estimating terminal-year F through retrospective analyses of the 2006 bluefin tuna assessment and through stochastic simulations. The use of pre-specified ratios for F created strong retrospective biases and may have led to overly optimistic projections. Constraining annual changes in the terminal-year F appeared to mute retrospective patterns and resulted in abundance projections less prone to spurious initial leaps. Simulation results indicate that the constraint improves estimation, particularly with moderate to low interannual changes in selectivity.

The Gulf Menhaden Brevoortia patronus is frequently cited as playing a predominant role in the trophic structure and function of the northern Gulf of Mexico (GOM) marine ecosystem, yet much work remains in quantifying its ecological importance. We performed a meta-analysis of diet studies to quantify the trophic role of Gulf Menhaden within this ecosystem. Of the 568 references consulted, 136 identified predator–prey interactions involving Gulf Menhaden, menhaden Brevoortia spp., or unidentified clupeid prey items. Overall, 79 species were reported to consume menhaden, and no significant difference was detected between the Atlantic Ocean and the GOM in the mean occurrence of Brevoortia spp. in predator stomachs. We employed a probabilistic approach using maximum likelihood estimation to quantify trophic interactions within the northern GOM, with a focus on the trophic role of Gulf Menhaden. The estimated contribution of identifiable menhaden to the diets of all predators generally ranged between 2% and 3%; the largest dietary contribution was identified for Blacktip Sharks Carcharhinus limbatus (8%), and lower estimates (Scomberomorus cavalla, juvenile Spanish Mackerel Scomberomorus maculatus, adult Spanish Mackerel, Red Drum Sciaenops ocellatus, and Blacktip Sharks. The quantification of trophic linkages and key predators identified herein will be fundamental to future modeling efforts focused on the northern GOM ecosystem. Received March 24, 2015; accepted September 3, 2015

Although many uncertainties surround the status of western atlantic sailfish, Istiophorus platypterus (shaw, 1792), stock size (b) is considered below and fishing mortality rate (F) above the targets that would allow maximum sustainable yield (MSY). One means of improving status is to implement live-release policies and to employ circle hooks to increase release survival. In the present study, we examined the efficacy of a switch to circle hooks to achieve population-level BMSY and FMSY targets. First, we evaluated the scope that exists to employ circle hooks and adopt live-release policies. Second, we decremented recent landings by the reductions that could be achieved through live release and increase in survival between circle hooks and traditional J-hooks. Third, we projected these landings in the bayesian surplus production model. Assuming that landings in the non-release fleets remain constant, the current percentages of circle hooks (approximately 25%) and live release (approximately 25%) could reduce landings by 7%-8%. This measure alone would have less than a one percentage point increase in probability of improving status. With maximum practicable live release of around 50%, because many fleets market sailfish, and 100% circle hook use, landings could be reduced by 13%-23%. This would only have a 0.42-1.36 and 0.45-2.56 percentage point increase in the probability of meeting biomass and fishing mortality targets, respectively. While circle hooks can be a useful tool to convert landed fish to live releases, they are unlikely to meet current targets for western atlantic sailfish unless combined with other management that would reduce overall landings.

We examine the impact on pelagic fish hooking survival rates (defined as the proportion of fish alive upon gear retrieval) of the rapid switch from J-hooks to circle hooks that was required of the us pelagic longline fishery operating in the atlantic ocean and gulf of mexico after august 2004. Our focus was on 12 fish taxa that are commonly caught as bycatch or retained for the market, and for which individual disposition (live or dead) information was available from 1992 to 2010. To test the hypothesis of no change in survival before vs after the circle hook rule went into effect, we utilized a repeated measures logistic regression approach which accounted for variation in several operational, environmental, and biological covariates, including bait, fishery target, fishing zone, soak duration, water temperature, maximum fishing depth, and fish size (length). For white marlin and albacore, results were mixed, with both increases and decreases in hooking survival varying by fishing zone. For blue shark and lancetfish, no significant differences in hooking survival were detected between the pre- and post-circle hook rule time periods. However, for the remaining eight taxa (swordfish, yellowfin tuna, dolphinfish, bigeye tuna, escolar, silky shark, blue marlin, and sailfish), significant increases in survival were evident. Our results are generally consistent with previous experimental and fishery observer longline studies which suggested circle hook use has the potential to increase hooking survival. Results imply that the 2004 circle hook rule has provided increased opportunities for: (1) live release for several bycatch species; and (2) improved quality (and perhaps prices) of targeted and incidentally-caught taxa that are retained for the market.

A presumed conservation benefit of circle hooks is that they reduce catchability (q) and therefore bycatch of non-target species. While these changes may benefit a fish stock, they are difficult to incorporate in a stock assessment context, particularly for models that rely on fishery-dependent data, because few experiments exist that quantify the effects of circle hooks for a given species over appropriately large spatial scales. Consequently, to develop management advice, it may be necessary to model assumed changes in q within the adopted stock assessment model framework. Here we present a case study of bigeye tuna (Thunnus obesus lowe, 1839), a highly migratory species managed by the international commission for the conservation of atlantic tunas (iccat), and explore the management implications of changes in q within a multi-fleet, age-structured assessment context. This study demonstrates that changes in q on the order of ±30% are sufficient to cause notable differences in the magnitude of common management reference points estimated by stock assessment models. Relative to a base model that assumed a constant q, models that incorporated a theoretical reduction in q produced higher estimates of spawning stock biomass and maximum sustainable yield, and lower estimates of fishing mortality while a theoretical increase in q had the opposite effect. The magnitude of the change was dependent on the number of fisheries affected. We conclude that carefully designed studies are essential to quantify the effects of a proposed gear change and to inform the appropriate parameterization of stock assessment models.

Rainbow parrotfish Scarus guacamaia is a coral-reef herbivore that requires both mangrove and coral-reef habitat to complete its life cycle. This species is listed as 'vulnerable' by the International Union for Conservation of Nature. The present study used a long-term visual sur- vey of mangrove fishes to develop a predictive habitat model for juvenile S. guacamaia. The fac- tors tested were temperature, dissolved oxygen, salinity, average depth, distance from offshore channel openings, temperature variation (ΔT), and salinity variation (ΔS). The average depth, dis- tance from offshore channel openings, ΔT, and ΔS emerged as significant within the model evalu- ations. The results suggested that high variation in salinity reduces mangrove habitat suitability for this species. Salinity variation along many of south Florida's coastal bays is largely driven by water management-related freshwater canal discharges. Everglades restoration efforts seek to reduce ΔS along south Florida's mainland shoreline; thus, if successful, restoration may also confer benefits to Scarus guacamaia through the subsequent expansion of suitable mangrove habitat.

The curve used until recently by the International Commission for the Conservation of Atlantic Tunas (ICCAT) to represent the growth of western Atlantic bluefin tuna, Thunnus thynnus, was estimated using tagging information and modal sizes that corresponded primarily to very young fish (ages 1–3, primarily). The estimated maximum average size from this curve is very large (382 cm), which could be a result of the scarcity of large bluefin in the data used. Recently, scientists have developed techniques for reading ages from bluefin ear bones (otoliths); the accuracy of the age readings has been validated with bomb radiocarbon dating. These age readings are primarily for large bluefin (ages 5 and older), and indicate slower growth and older ages than was previously assumed. However, an analysis of these data resulted in growth curves that predicted very small mean sizes for the youngest age group, which could be a result of the lack of small fish in the data used. In this study, we combine the otolith-based age readings with the size frequency distributions of small (ages 1–3) bluefin caught by purse seiners in the 1970s where the age groups are distinctly statistically as well as visible to the eye. We analyzed the two datasets jointly using a maximum likelihood approach and assumed that variability in length-at-age increases with age. The resulting growth curve predicts sizes at young and old ages that are very consistent with observed data such as the maximum sizes observed in the catch and the modal sizes for very young bluefin. The resulting curve is also very similar to the curve used by ICCAT for eastern Atlantic and Mediterranean bluefin.

The relationship between pelagic fish and ocean temperature is cited in many studies, the majority of which investigate correlations of pelagic species and sea surface temperatures (SST). While appropriate for surface-associated species, this may not be accurate for deep-diving fishes. A different way to examine this relationship is to model spatial autocorrelation of fish species and temperatures at an appropriate range of depths. Spatial autocorrelation, the distance at which data are interdependent, is a potential descriptor of the patch size of an organism. Here we modeled spa- tial autocorrelation for 5 pelagic species that inhabit different depths in the Gulf of Mexico: dolphin- fish Coryphaena hippurus, wahoo Acanthocybium solandri, yellowfin tuna Thunnus albacares, swordfish Xiphias gladius, and bigeye tuna Thunnus obesus. Additionally, we modeled spatial auto- correlation for ocean temperatures at the surface, at 200, and 400 m. We hypothesized that autocor- relation distances will be greater for deeper water temperatures and for species that live at deeper depths due to greater homogeneity of deep waters over greater spatial ranges. Results show average distances of autocorrelation on the order of 55 to 60 km for wahoo and dolphinfish, 90 km for yel- lowfin tuna, and 135 to 145 km for swordfish and bigeye tuna; the same data for temperature were 75, 135, and 300 km for SST, and at 200 and 400 m depth, respectively. Autocorrelation distances of dolphinfish, wahoo, and yellowfin were correlated with that of of SST, while the autocorrelation dis- tance of swordfish and bigeye were correlated with that of temperatures at 200 m. Results suggest that autocorrelation distances may be useful as a proxy for habitat delineation.

Most evidence for ontogenetic migration of fishes from mangroves to coral reefs has been based on cross-sectional studies of

Walter, J. F. III, Hoenig, J. M., and Gedamke, T. 2007. Correcting for effective area fished in fishery-dependent depletion estimates of abundance and capture efficiency. – ICES Journal of Marine Science 64: 000–000. Depletion methods are widely used to estimate capture efficiency and abundance. However, they are highly dependent on the depletion area assumed. In open-ocean depletion studies, it is difficult to determine the true area of depletion. Satellite vessel monitoring systems (VMS) offer the potential to determine the area effectively fished. Observer-collected catch-and-effort data from the 1999 Atlantic sea scallop fishery in Georges Bank Closed Area II were used to obtain spatially-explicit DeLury depletion estimates of dredge efficiency and abundance, with corrections for fished area made using VMS data. Non-area-corrected efficiency estimates often had theoretically impossible values, indicating that the naïvely assumed fished area was likely too big. Fine-scale spatial analyses on individual depletion cells confirmed this result. Corrected-area efficiency estimates exhibited reduced variability and more plausible efficiencies, with 70% of 289 individual depletion estimates falling between 20% and 55%, with a mean of 46%. Abundance estimates from individual depletion studies matched maps of abundance from a preseason survey. Results indicated a total abundance of ∼17 million pounds of scallop meat weight in the fished area, of which 6 million pounds were landed, providing an overall exploitation rate of 35%.

In marine invertebrate populations natural mortality events tend to be episodic in nature. The impact of these episodic mortality events can be estimated from the decline in catch rate of live animals over time obtained through successive population sampling. However, the high variability of catch rates makes them relatively insensitive indicators of mortality. For bivalve mollusks another means to estimate mortality is to assess the change in abundance of recently dead animals, called clappers, which are gaping shells still hinged together. We present a change in ratio estimator and its associated variance of the proportion of animals dying due to an episodic mortality event. This estimator is more sensitive to mortality events and may be preferable to a traditional estimator based upon changes in catch rates of live animals. When applied to a scallop population in Narragansett Bay, RI, the change in ratio estimator indicated that a 72% reduction in the population occurred after an intense mortality event associated with an epizootic of a rickettsia-like organism.

A requirement for geostatistical prediction is estimation of the variogram from the data. Often low sample size is a major impediment to elucidating a variogram even for a highly autocorrelated spatial process. This paper presents a methodology for improving variogram estimation when samples exist from multiple years or regions sharing a similar process for generating spatial autocorrelation. Such samples may come from annual monitoring programs for natural resources or from multiple geologic regions. As each set of samples contains some information on the spatial autocorrelation, combining information through the construction of a combined variogram cloud and binning to obtain a common variogram improves the estimation of the variogram. In both simulations and in real datasets of oyster abundance the method proposed here reduces the likelihood of failing to obtain a variogram from a set of samples and improves the efficiency of variogram estimation. In practice, the benefits obtained by estimating an otherwise elusive variogram generally outweigh the costs of using a slightly incorrect variogram model if different sampling stanzas are combined when they do not share the same spatial autocorrelation. Copyright © 2007 John Wiley & Sons, Ltd.

The recent increase in the Atlantic coast population of striped bass, Morone saxatilis (Walbaum), prompted managers to re-evaluate their predatory impact. Published and unpublished diet data for striped bass on the Atlantic Coast of North America were examined for geographical, ontogenetic and seasonal patterns in the diet and to assess diet for this species. Diets of young-of-the-year (YOY) striped bass were similar across the Upper Atlantic (UPATL), Chesapeake and Delaware Bays (CBDEL) and North Carolina (NCARO) areas of the Atlantic coast where either fish or mysid shrimp dominate the diet. For age one and older striped bass, cluster analysis partitioned diets based on predominance of either Atlantic menhaden, Brevoortia tyrannus (Latrobe), characteristic of striped bass from the CBDEL and NCARO regions, or non-menhaden fishes or invertebrates, characteristic of fish from the UPATL, in the diet. The predominance of invertebrates in the diets of striped bass in the UPATL region can be attributed to the absence of several important species groups in Northern waters, particularly sciaenid fishes, and to the sporadic occurrences of Atlantic menhaden to UPATL waters. In all regions, across most seasons and in most size classes of striped bass, the clupeiod fishes; menhaden, anchovies (Anchoa spp.) and river herrings (Alosa spp,) and Atlantic herring, Clupea harengus L., dominated the diets of striped bass above the first year of life.

The compiled data for this study represents the first Atlantic and Mediterranean-wide effort to pool all available biometric data for Atlantic bluefin tuna (Thunnus thynnus) with the collaboration of many countries and scientific groups. Biometric relationships were based on an extensive sampling (over 140,000 fish sampled), covering most of the fishing areas for this species in the North Atlantic Ocean and Mediterranean Sea. Sensitivity analyses were carried out to evaluate the representativeness of sampling and explore the most adequate procedure to fit the weight-length relationship (WLR). The selected model for the WLRs by stock included standardized data series (common measurement types) weighted by the inverse variability. There was little difference between annual stock-specific round weight-straight fork length relationships, with an overall difference of 6% in weight. The predicted weight by month was estimated as an additional component in the exponent of the weight-length function. The analyses of monthly variations of fish condition by stock, maturity state and geographic area reflect annual cycles of spawning and feeding behavior. We update and improve upon the biometric relationships for bluefin currently used by the International Commission for the Conservation of Atlantic Tunas, by incorporating substantially larger datasets than ever previously compiled, providing complete documentation of sources and employing robust statistical fitting.WLRs and other conversion factors estimated in this study differ from the ones used in previous bluefin stock assessments., SI