Marine fishes are heterogeneously distributed across their ranges according to population dynamics governed by complex spatiotemporal relationships between ontogenetic habitat usage, species interactions, environmental variability, and harvest patterns. However, few stock assessments incorporate spatial population structure in the determination of population status and sustainable catch limits. A small number of generalized stock assessment software platforms are utilized worldwide to assess a large number of marine fish populations. Although each platform relies on similar underlying population dynamics, the spatial capabilities and functionality often differ among them. We catalogue spatial dynamics and capabilities across stock assessment platforms to leverage collective experiences and identify future needs for next generation assessment software packages. Despite commonalities across platforms (e.g., most models allow for a single population with spatial heterogeneity, apportionment of recruitment, and age-varying connectivity), no single platform is flexible enough to address the full breadth of spatial dynamics observed for managed marine fish species. Our review clarifies spatial assessment design and modeling ‘good practices’, while emphasizing the need for more generalizable and modular next generation assessment platforms that can account for the spatiotemporal complexity of marine resources (such as natal homing and spawning migrations, ontogenetic movement patterns, metapopulation structure, and complex fleet dynamics). Generalized, spatially-integrated assessment platforms will be key decision-tools to account for spatiotemporal species and fishery interactions, particularly as managers attempt to address climate change and implement ecosystem-based fisheries management.

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.

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.

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.

Stock assessments are often used to provide management advice, such as a total allowable catch (TAC), to fishery managers. Many stocks are not assessed annually, and the TAC from the previous assessment is often maintained in years between assessments. We developed two interim management procedures (MPs) that update the estimate of current vulnerable biomass from a surveyed index of abundance to adjust the TAC from a previous assessment. These MPs differ in how they handle uncertainty in observed indices. Using closed-loop simulation, we evaluated the two interim MPs (with 10- and 5-year assessment intervals) against several "status quo" approaches: (1) an annual assessment, and (2) a stock assessment every 5 or 10 years with (a) fixed TACs or (b) projections between assessments. We evaluated performance across three life-history types and six operating model scenarios. The interim MPs performed similarly to annual assessments in terms of trends in biomass and yield, regardless of the assessment interval of the interim MPs. The interim MPs often produced more yield than the Fixed TAC MP with 10-year assessment intervals, for example, in depleted scenarios. The Fixed TAC MP performed more similarly to interim MPs when the assessment interval for the Fixed TAC MP was decreased to five years. The interim MPs can also perform well when circumstances arise that are not accounted for in the Projection MP. Our results show that interim MPs should be considered for infrequently assessed stocks or rebuilding stocks, and highlight potential cost savings of interim MPs over annual assessments.

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.

The ideal stock assessment would be able to estimate all of the key parameters related to population processes within a framework that assigns appropriate weight to the data, fits the data adequately, and captures all sources of uncertainty related to estimation, including model uncertainty, process uncertainty, and observation uncertainty. The aim of good practice guidelines is to avoid the pitfalls of earlier analysis methods, and consequently provide assessments that reflect objective scientific information on which management decisions can be based. This paper outlines a framework for the component of a stock assessment related to fitting population dynamics models to monitoring data to support decision making, which follows from what would be considered good (but not necessarily best) practice in the field. The paper identifies current good and best practices related to selecting a model structure, parameterizing growth, recruitment, natural mortality and the stock-recruitment relationship, as well as how to select among model configurations based on diagnostics and weight data and priors within assessments based on the existing literature, including past Center for the Advancement of Population Assessment Methodology (CAPAM) workshop reports and the results of simulation studies that explored the performances of different ways to configure stock assessments.

Many marine fish form spawning aggregations (FSAs) and exhibit meta-population stock structure, affecting reproductive resilience and the optimal spatial scale of management. Red drum use a known FSA site off Tampa Bay (TB FSA site) and another presumed FSA site off Charlotte Harbor (CH FSA site). We studied these sites for 3 years (2012-2014) to assess space use and annual abundance at the TB FSA site using: (i) genetically profiled fish, non-lethally sampled by purse seine (n=9087); (ii) aerial surveys (n=37); and (iii) acoustic telemetry (n=122 fish). Thousands of fish concentrated at the TB FSA site to spawn each year, dispersing afterward to an area of at least approximate to 150km along the coast and 90km offshore. Fish acoustically tagged at the TB FSA site showed strong annual spawning site fidelity (91% in 2013 and 85% in 2014) and the straying rate to the CH FSA site to the south was low (6-13%). Annual abundance at the TB FSA site varied, with the estimated abundance in 2013 being four times greater than that estimated for 2014. Similarly, aerial surveys in 2013 sighted 2.5 times as many aggregations as in 2014. However, fine-scale space use, which typically goes unassessed in abundance estimates (short-term surface behaviour and temporary migration), also differed between these years and needs to be integrated into future capture-mark-recapture models.

Maximum sustainable yield (MSY)-based reference points are often prescribed by national and international laws as the basis for catch limits (e.g., the Magnuson-Stevens Reauthorization Act in the United States). However, MSY is highly dependent on the assumed selectivity pattern and catch allocation of the fisheries. The addition of bycatch fleets or mortality from discarding further complicates MSY calculations, and no prescribed approach has been agreed upon for including complex fleet dynamics in dynamic pool models. Using the Gulf of Mexico Red Snapper Lutjanus campechanus fishery as an example, we demonstrate the various ways that MSY can be computed when multiple fleets and bycatch fisheries exist, and we illustrate the tradeoffs that occur between yield and spawning stock biomass (SSB). Presenting the full array of alternative MSY proxies, however, can lead to subjective decision making that may diminish the value of scientific advice by encouraging the maximization of yield at the expense of maintaining stocks within safe biological limits. We propose that the spawning potential ratio (SPR) associated with the global (theoretical maximum) MSY can be utilized as a reasonable proxy in most fishery applications. The yield streams required to achieve SPRMSY can then be calculated conditional on extant selectivity patterns and bycatch levels. Our approach utilizes the inherently sustainable SSB associated with the global MSY as a rebuilding target while limiting disruption to the fishery by accounting for current fleet dynamics and avoiding unsustainable proxies that may result when bycatch or discard rates are high.

Recent advances in methodology allow the history of the total mortality rate experienced by a population to be estimated from periodic (e.g., annual) observations on themean length of the population. This approach is generalized to allow data on several species that are caught together to be analyzed simultaneously based on the theory that changes in fishing effort are likely to affect several species; thus, the estimation of times when the mortality rate changes for one species borrows strength from data on other, concurrently caught species. Information theory can be used to select among models describing the degree of synchrony (if any) in mortality changes for a suite of species. This approach is illustrated using data on Puerto Rican handline fishery catches of three snapper species: Silk Snapper Lutjanus vivanus, Blackfin Snapper L. buccanella, and Vermilion Snapper Rhomboplites aurorubens. We identified the best model as the one that provided for simultaneous decreases in mortality rate around the year 1997 and for separate, species-specific magnitudes of change in total mortality. The simultaneous estimation of parameters for multiple species can provide for more credibility in the inferred mortality trends than is possible with independent estimation for each species.

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 theML 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 year when mortality changed) were smaller in the MLCR model than in the ML model, indicating that the MLCR model can better account for variable recruitment. Both methods were then applied to Mutton Snapper Lutjanus analis in Puerto Rico to illustrate their potential application to assess data-limited stocks. The ML model estimated an increase in Z, but the MLCR model also estimated a subsequent reduction in Z when the catch rate data were considered.

The first two forms of auction, trade and market data of Atlantic bluefin tuna for the period of 1995 to 2012, gathered within the scope of the ICCAT GBYP, were formally approved by the ICCAT SCRS in 2014. These data were further filtered excluding less reliable records according to the standards set by the SCRS BFT Species Group in 2015 and finally a unique dataset on 209,491 individual bluefin tuna weights was created, with all relevant information on fish product and fishing operation. The dataset was used to develop extensive series of graphics on weight frequencies, based on fish origin, year, fishing area and fishing gear. These selected market data have potentially great value because they might fill some important gaps in ICCAT data collections and therefore serve for improved stock assessment.

Few data exist to evaluate the performance or assess the potential impacts of hook regulations on catchability or selectivity of recreational fisheries in the northern Gulf of Mexico. The purpose of this study was to test the effects of hook type (circle vs. J hook) and hook size (1/0, 4/0, and 7/0) on catch composition, traumatic hooking, species-specific catches, and size-selectivity of red snapper, Lutjanus campechanus, and grey triggerfish, Balistes capriscus. Selectivity was estimated by conditioning size distributions from hook-specific catches against in situ size distributions observed with a remotely operated vehicle. Deep hooking (hook set in gills or beyond) was low in all hook treatments for red snapper (<10%) and grey triggerfish (<6%), but was generally higher with J hooks, especially for other fishes caught with the largest J hook (34%). Hook type did not significantly affect catches, but catches decreased significantly with increasing hook size in all groups except red snapper. Selectivity curves were dome-shaped for both focus species in all hook treatments and selection peaks were similar among treatments for red snapper. Peak selectivity was 78.1 mm larger for J hooks than circle hooks for grey triggerfish. Overall, study results indicate that the circle hook regulation may have reduced traumatic hooking mortality by up to 50%, and that catchability is similar between hook types for both red snapper and grey triggerfish when controlling for hook size. Strong dome-shaped selection estimated for nearly all selectivity curves suggest logistic size-selectivity assumptions in assessment models are likely inappropriate for recreational sectors targeting red snapper or grey triggerfish.

Forecasts of the future abundance of western Atlantic bluefin tuna (Thunnus thynnus) have, for nearly two decades, been based on two competing views of future recruitment potential: (1) a "low" recruitment scenario based on hockey-stick (two-line) curve where the expected level of recruitment is set equal to the geometric mean of the recruitment estimates for the years after a supposed regime-shift in 1975, and (2) a "high" recruitment scenario based on a Beverton-Holt curve fit to the time series of spawner-recruit pairs beginning in 1970. Several investigators inferred the relative plausibility of these two scenarios based on measures of their ability to fit estimates of spawning biomass and recruitment derived from stock assessment outputs. Typically, these comparisons have assumed the assessment estimates of spawning biomass are known without error. It is shown here that ignoring error in the spawning biomass estimates can predispose model-choice approaches to favor the regime-shift hypothesis over the Beverton-Holt curve with higher recruitment potential. When the variance of the observation error approaches that which is typically estimated for assessment outputs, the same model-choice approaches tend to favor the single Beverton-Holt curve. For this and other reasons, it is argued that standard model-choice approaches are insufficient to make the case for a regime shift in the recruitment dynamics of western Atlantic bluefin tuna. A more fruitful course of action may be to move away from the current high/low recruitment dichotomy and focus instead on adopting biological reference points and management procedures that are robust to these and other sources of uncertainty.

Stock assessments provide scientific advice in support of fisheries decision making. Ideally, assessments involve fitting population dynamics models to fishery and monitoring data to provide estimates of time trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as B-MSY and F-MSY, along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We review the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages are considered, five based on surplus production models, one based on a delay-difference model, and the remainder based on age-structured models. Most of the packages are freely available for use by analysts in the US and around the world, have been evaluated using simulations, and can form the basis for forecasts. The packages differ in their ease of use and the types of data inputs they can use. This paper highlights the benefits of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use. Crown Copyright (C) 2016 Published by Elsevier B.V. All rights reserved.

Understanding dynamics and stock structures of fish is particularly relevant to assessments and management of marine living resources. Using the nonparametric, nonlinear time series (NLTS) approach, we modeled dynamics of red snapper (Lutjanus campechanus) represented by time series of two fisheries-independent abundance indices and two fisheries-dependent abundance indices in the eastern and western portions of the U.S. Gulf of Mexico (Gulf). Further, we examined regional dynamics of red snapper in the two areas and explored the utility of NLTS models in generating short term forecasts. Overall, red snapper in the eastern Gulf and western Gulf displayed distinct patterns in terms of the Gulf-wide ecosystem indicators, which likely implies different underlying regional dynamics of the species. Moreover, dynamic features of red snapper differed between the two regions. Specifically, the system dimension (mean±SE), i.e., the number of potential processes affecting the underlying dynamics of the species, was higher in the western Gulf (5.5±1.32) than in the eastern Gulf (3.75±1.44). The NLTS models exhibited significant skill (i.e., a measure of the goodness of fit (ρ) between observations and predictions) in forecasting red snapper abundance indices. The forecast skill (one year ahead) was 0.48±0.01 for indices representing the eastern Gulf and 0.33±0.05 for indices representing the western Gulf. The average dimension and forecast skill was 3±1.43 and 0.37±0.01 for fisheries-dependent indices, and 6.25±1.32 and 0.45±0.05 for fisheries-independent indices. These findings have implications for the Gulf red snapper fisheries in that the NLTS approach shows potential for forecasting stock abundance indices, and provides new information regarding the appropriate spatial scale for management of the species. Moreover, the ecosystem considerations in this study can be further explored to forecast the dynamics of red snapper for better assessments and management of the species.

The discovery of 67 bluefin tuna larvae in waters off the northeast US continental shelf is certainly of considerable scientific interest, but the paper in PNAS by Richardson et al. (1) makes several broad assertions that go beyond what the data support. The authors extrapolate differences in larval catch rates to conclude that the majority of spawning occurs outside of the Gulf of Mexico. This contention equates 1 y of opportunistic samples with 32 y of a design-based survey, fails to apply standard larval data corrections (2, 3), and ignores the high variance that makes comparison of these catch rates unreliable. The situation resembles the 1985 … [↵][1]1To whom correspondence should be addressed. Email: john.f.walter{at}noaa.gov. [1]: #xref-corresp-1-1

In 2011, a large multivessel survey was conducted to provide nearly synoptic sampling of Red Snapper Lutjanus campechanus throughout their reproductive season in the U.S. Gulf of Mexico. A total of 2,487 Red Snapper were caught with a female : male ratio that was approximately 1:1. The ovaries of 1,002 females were histologically examined. Females ( n = 391) were found with spawning markers (postovulatory follicles and hydrated oocytes) throughout the study area, but primarily in outer shelf waters. Statistical models were developed to quantify and test the dependence of the proportion of females bearing spawning markers (spawning fraction) on female length and age, time of year, depth, gear type (vertical line or longline), or region (east or west of the Mississippi River). Most of the variance in spawning fraction was explained by the time of year; spawning fractions were generally low in spring, peaked in midsummer, and declined by fall. There was also strong statistical evidence of a positive relationship between spawning fraction and either age or length. The effects of region and gear type were not significant once time of year and size or age were accounted for. These results demonstrate the need to account for differences in the time of year and age structure of the population when the productivity of populations of Red Snapper are compared. For example, productivity has been hypothesized to be greater in the western Gulf than in the eastern Gulf, as evidenced by regional patterns of egg and larval abundance. Our results suggest that this regional difference is not due to any intrinsic difference in the biology of the fish, but simply a consequence of there being more large, old Red Snapper in the western Gulf. Recent stock assessments have indicated that Red Snapper are increasing in abundance and there is a need to continue monitoring to detect any possible compensation in reproduction. Received November 25, 2014; accepted April 2, 2015