A revised diet matrix to improve the parameterization of a West Florida Shelf Ecopath model for understanding harmful algal bloom impacts

Harmful algal blooms (HABs) are a growing concern in the West Florida Shelf (WFS) region. An Ecopath with Ecosim (EwE) model of the WFS explicitly simulating HABs was previously developed to illuminate the potential impacts of blooms of the dinoflagellate Karenia brevis (colloquially referred to as “red tides”) on the WFS ecosystem. However, the diet matrix of the Ecopath component of this EwE model (referred to as “WFS-HAB Ecopath”) was based largely on sparse, cursory information and not on local survey data. Here, we revise the diet matrix of the WFS-HAB Ecopath model using predictions of a robust statistical model that incorporates local survey data and employs the Dirichlet distribution and maximum likelihood estimation. The relative impacts of both the revised diet matrix and red tide mortality scenarios on model structure are explored by comparing four alternative WFS-HAB Ecopath models: (i) the base model; (ii) a model employing the revised diet matrix; (iii) a model with elevated red tide mortality; and (iv) a model with both the revised diet matrix and elevated red tide mortality. Incorporating the revised diet matrix into the WFS-HAB Ecopath model had a relatively large impact on ecosystem structure (i.e., trophic organization, mortality rates, trophic interaction strengths, and omnivory). Elevated red tide mortality had virtually no impact on ecosystem structure aside from altering the contribution of fishing, natural, and red tide mortalities to the total mortality of functional groups; however, elevated red tide mortality might have meaningful implications in dynamic simulations, which should be explored in future studies. Collectively, results showed that incorporating the revised diet matrix into WFS-HAB Ecopath, which revealed a number of new predator-prey linkages, led to a more complex and interconnected food web. Specifically, prey items were generally consumed by a broader variety of predators, which contrasts with the base WFS-HAB Ecopath model where many prey, particularly juvenile fishes, were subjected to exceedingly high predation mortality rates from specific predators. The incorporation of the revised diet matrix into the WFS-HAB Ecopath model discussed herein is a fundamental step towards increasing the realism of trophic interactions in the model, which is particularly important as these trophic interactions define starting conditions for dynamic simulations.publishedVersio

Spatiotemporal Overlap Of Spiny Dogfish (Squalus Acanthias) And Commercial Fisheries In The Northeast Us Shelf Large Marine Ecosystem

Commercial fishermen have argued that localized concentrations of spiny dogfish (Squalus acanthias) in the northeast U.S. shelf large marine ecosystem (NES LME) have impeded their fishing operations when monitoring surveys estimated lower relative abundances. Fishery-dependent and -independent data were analyzed simultaneously to examine whether increased spatial overlap between spiny dogfish and commercial fisheries may explain high catches of this species on fishing grounds. Spatial overlap was quantified between spiny dogfish distribution and commercial fisheries from 1989 to 2009 during autumn and spring in the NES LME. Combined, the sink gillnet (SGN) and otter trawl (OT) fisheries accounted for the majority of spiny dogfish catch (autumn: 85%; spring: 92%), either retained (SGN) or discarded (OT). Centers of spiny dogfish abundance illustrated spatial differences in local density within the NES LME and revealed seasonal differences in spiny dogfish density. Recent increases in spatial overlap indicate that a growing portion of the spiny dogfish stock was available to each fishery over the time series. Availability, estimated as the percentage of spiny dogfish present on fishing grounds, also increased and was generally higher during autumn than spring. Abundance of mature (total length.80 cm) female spiny dogfish was significantly related to availability, but trends were variable between fisheries and seasons. Although recent increases in abundance indicate recovery, research regarding the mechanisms behind these changes may help explain why abundance in the NES LME appears highly variable

Identifying trade-offs and reference points in support of ecosystem approaches to managing Gulf of Mexico menhaden

Gulf menhaden (Brevoortia patronus) support the largest fishery by yield in the Gulf of Mexico (GoM) and are a key forage species for many marine predators. While menhaden stock assessments indicated that overfishing was not likely to have occurred in the past, concerns have been raised regarding the possible effects of menhaden fishing on their predators. In this study, we used a US Gulfwide Ecopath with Ecosim (EwE) model to explore the predicted effects of increased menhaden harvest on the GoM ecosystem and focused our analyses on Gulf menhaden predators. Key menhaden predators identified included king mackerel (Scomberomorus cavalla), Spanish mackerel (Scomberomorus maculatus), sea trout (Cynoscion spp.), red drum (Sciaenops ocellatus), and pelagic coastal piscivores [e.g., bluefish (Pomatomus saltatrix)]. As expected, these predators exhibited reduced biomass in response to increased Gulf menhaden harvest, with a predicted 11% decrease in predator biomass at simulated fishing levels near historical highs. Our results indicate strong relationships between the effects of menhaden fishing and the predator fishing mortality for king mackerel and intermediate relationships for Spanish mackerel, blacktip shark (Carcharhinus limbatus), red drum, large coastal sharks, and pelagic coastal piscivores. Biomass of predator groups such as demersal coastal invertebrate feeders [e.g., drums and croakers (Sciaenidae)] are more affected by menhaden harvest (through trophodynamics interactions and bycatch removal) compared to the isolated effect of their fishing mortality. For almost all the groups examined in the trade-off analysis, with the exception of sea trout, current biomass (2016) was higher than their target biomass representing 75% of their biomass at maximum sustainable yield. In comparison to the time series of fishing mortality rates estimated by the most recent Gulf menhaden stock assessment, the mean ecological reference point (ERP) of 0.862 was exceeded in all but 1 year from 1977 to 2007; however, neither the target nor threshold upper ERP value has been exceeded since 2008. The observed Gulf menhaden landings from 2003 to the present were generally within the range of the projected equilibrium landings (i.e., within confidence intervals) at both the ERP target and threshold values except for three recent years

Diel Variations in Survey Catch Rates and Survey Catchability of Spiny Dogfish and their Pelagic Prey in the Northeast US Continental Shelf Large Marine Ecosystem

This study examines the potential uncertainty in survey biomass estimates of Spiny Dogfish Squalus acanthias in the Northeast U.S. Continental Shelf Large Marine Ecosystem (NES LME). Diel catch-per-unit-effort (CPUE) estimates are examined from the Northeast Fisheries Science Center bottom trawl surveys conducted during autumn (1963-2009) and spring (1968-2009). Influential environmental variables on survey catchability are identified for Spiny Dogfish life history stages and five pelagic prey species: Butterfish Peprilus triacanthus, Atlantic Herring Clupea harengus, shortfin squid Illex spp., longfin squid Doryteuthis spp., and Atlantic Mackerel Scomber scombrus. Daytime survey catchability was significantly higher than nighttime catchability for most species during autumn and for mature male Spiny Dogfish, shortfin squid, and longfin squid during spring in the NES LME. For most stages and species examined, breakpoint analyses identified significant increases in CPUE in the morning, peak CPUE during the day, and significant declines in CPUE in the late afternoon. Seasonal probabilities of daytime catch were largely driven by solar zenith angle for most species, with stronger trends identified during autumn. Unadjusted CPUE estimates appear to overestimate absolute abundance, with adjustments resulting in reductions in absolute abundance ranging from 41% for Spiny Dogfish to 91% for shortfin and longfin squids. These findings have important implications for Spiny Dogfish regarding estimates of population consumption of key pelagic prey species and their ecological footprint within the NES LME

Modeling Discards in Stock Assessments: Red Grouper Epinephelus morio in the U.S. Gulf of Mexico

To be as accurate as possible, stock assessments should account for discard mortality in fisheries if it occurs. Three common approaches to modeling discards in assessments are to lump dead discards with landings, treat dead discards as their own fleet, or link them conversely with landings through use of a retention function. The first approach (lumping) implicitly assumes that the selectivity of landings applies also to discards. In many cases, that assumption is false, for example, if discards comprise smaller fish than do landings. The latter two approaches avoid the assumption by modeling discards explicitly with their own selectivity pattern. Here, we examine these approaches to modeling discards. Using a simulation study, we demonstrate that the two approaches to modeling discards explicitly can provide identical results under both static and time-varying conditions. Then, using a stock assessment case study of red grouper Epinephelus morio in the U.S. Gulf of Mexico, we demonstrate that in practice the approaches to modeling discards can provide different outcomes, with implications for the resultant management advice. We conclude by comparing and contrasting the different approaches, calling for more research to elucidate which approach is most suitable under various sources of error typically encountered in discard data

Modeling Discards in Stock Assessments: Red Grouper <i>Epinephelus morio</i> in the U.S. Gulf of Mexico

To be as accurate as possible, stock assessments should account for discard mortality in fisheries if it occurs. Three common approaches to modeling discards in assessments are to lump dead discards with landings, treat dead discards as their own fleet, or link them conversely with landings through use of a retention function. The first approach (lumping) implicitly assumes that the selectivity of landings applies also to discards. In many cases, that assumption is false, for example, if discards comprise smaller fish than do landings. The latter two approaches avoid the assumption by modeling discards explicitly with their own selectivity pattern. Here, we examine these approaches to modeling discards. Using a simulation study, we demonstrate that the two approaches to modeling discards explicitly can provide identical results under both static and time-varying conditions. Then, using a stock assessment case study of red grouper Epinephelus morio in the U.S. Gulf of Mexico, we demonstrate that in practice the approaches to modeling discards can provide different outcomes, with implications for the resultant management advice. We conclude by comparing and contrasting the different approaches, calling for more research to elucidate which approach is most suitable under various sources of error typically encountered in discard data

Assessing the suitability of mangrove habitats for juvenile Atlantic goliath grouper

While juvenile Atlantic goliath grouper, Epinephelus itajara (Lichtenstein, 1822), are known to depend on mangrove root structure, relationships with water properties (e.g., salinity) and depth remain unclear or understudied. Because availability of suitable mangrove habitat has been suggested as the primary bottleneck to the recovery of this threatened species in the US, we investigated habitat associations of juvenile Atlantic goliath grouper with respect to physical water properties within mangrove habitats. Our study was conducted in six coastal rivers and three canals within the Ten Thousand Islands region of southwest Florida. Results suggested that juvenile Atlantic goliath grouper differed in how they associated with specific mangrove habitats based on season and size. We found that smaller juveniles (3 mg L−1) within mangrove habitat. For small juveniles, extreme temperatures influenced habitat association; for large juveniles, extreme salinity influenced distribution. We also found evidence that juvenile Atlantic goliath grouper associated more with natural rivers over man-made canals. The present study has utility for delineating suitable mangrove habitats for protection and potentially in the design of sampling surveys that aim to estimate population abundance

Ecosystem modeling in the Gulf of Mexico: current status and future needs to address ecosystem-based fisheries management and restoration activities

Many ecosystem-based fisheries management (EBFM) measures and restoration projects have been implemented to address the stressors that have negatively affected the United States (U.S.) Gulf of Mexico (GOM). Ecosystem simulation models are useful tools for tackling EBFM and restoration questions. Here, we review the current status of ecosystem modeling efforts for the U.S. GOM and whole GOM large marine ecosystem and identify future needs to address EBFM and restoration in these regions. Existing ecosystem models of the GOM are diverse, ranging from simple conceptual and qualitative models to biogeochemical-based end-to-end models and coupled and hybrid model platforms. Many models have focused on understanding the structure and functioning of GOM ecosystems and the impacts of EBFM measures such as bycatch reduction strategies and marine protected areas. By contrast, a small number of ecosystem models have been used specifically to address the other EBFM issues of the GOM and to assess restoration efforts (e.g., marsh restoration). The demands for EBFM and state and gulf-wide restoration activities will both be increasing in the GOM. Therefore, there is a critical need to better employ and enhance existing ecosystem models of the GOM, and to develop new ecosystem models, to more comprehensively address the different EBFM and restoration needs in the region. We provide suggestions to facilitate this endeavor. The development of consistent libraries of ecosystem models and gap analyses such as ours will help fisheries scientists to effectively tackle specific resource management questions in the different marine regions of the world

Identifying trade-offs and reference points in support of ecosystem approaches to managing Gulf of Mexico menhaden

Gulf menhaden (Brevoortia patronus) support the largest fishery by yield in the Gulf of Mexico (GoM) and are a key forage species for many marine predators. While menhaden stock assessments indicated that overfishing was not likely to have occurred in the past, concerns have been raised regarding the possible effects of menhaden fishing on their predators. In this study, we used a US Gulfwide Ecopath with Ecosim (EwE) model to explore the predicted effects of increased menhaden harvest on the GoM ecosystem and focused our analyses on Gulf menhaden predators. Key menhaden predators identified included king mackerel (Scomberomorus cavalla), Spanish mackerel (Scomberomorus maculatus), sea trout (Cynoscion spp.), red drum (Sciaenops ocellatus), and pelagic coastal piscivores [e.g., bluefish (Pomatomus saltatrix)]. As expected, these predators exhibited reduced biomass in response to increased Gulf menhaden harvest, with a predicted 11% decrease in predator biomass at simulated fishing levels near historical highs. Our results indicate strong relationships between the effects of menhaden fishing and the predator fishing mortality for king mackerel and intermediate relationships for Spanish mackerel, blacktip shark (Carcharhinus limbatus), red drum, large coastal sharks, and pelagic coastal piscivores. Biomass of predator groups such as demersal coastal invertebrate feeders [e.g., drums and croakers (Sciaenidae)] are more affected by menhaden harvest (through trophodynamics interactions and bycatch removal) compared to the isolated effect of their fishing mortality. For almost all the groups examined in the trade-off analysis, with the exception of sea trout, current biomass (2016) was higher than their target biomass representing 75% of their biomass at maximum sustainable yield. In comparison to the time series of fishing mortality rates estimated by the most recent Gulf menhaden stock assessment, the mean ecological reference point (ERP) of 0.862 was exceeded in all but 1 year from 1977 to 2007; however, neither the target nor threshold upper ERP value has been exceeded since 2008. The observed Gulf menhaden landings from 2003 to the present were generally within the range of the projected equilibrium landings (i.e., within confidence intervals) at both the ERP target and threshold values except for three recent years

A revised diet matrix to improve the parameterization of a West Florida Shelf Ecopath model for understanding harmful algal bloom impacts

Harmful algal blooms (HABs) are a growing concern in the West Florida Shelf (WFS) region. An Ecopath with Ecosim (EwE) model of the WFS explicitly simulating HABs was previously developed to illuminate the potential impacts of blooms of the dinoflagellate Karenia brevis (colloquially referred to as “red tides”) on the WFS ecosystem. However, the diet matrix of the Ecopath component of this EwE model (referred to as “WFS-HAB Ecopath”) was based largely on sparse, cursory information and not on local survey data. Here, we revise the diet matrix of the WFS-HAB Ecopath model using predictions of a robust statistical model that incorporates local survey data and employs the Dirichlet distribution and maximum likelihood estimation. The relative impacts of both the revised diet matrix and red tide mortality scenarios on model structure are explored by comparing four alternative WFS-HAB Ecopath models: (i) the base model; (ii) a model employing the revised diet matrix; (iii) a model with elevated red tide mortality; and (iv) a model with both the revised diet matrix and elevated red tide mortality. Incorporating the revised diet matrix into the WFS-HAB Ecopath model had a relatively large impact on ecosystem structure (i.e., trophic organization, mortality rates, trophic interaction strengths, and omnivory). Elevated red tide mortality had virtually no impact on ecosystem structure aside from altering the contribution of fishing, natural, and red tide mortalities to the total mortality of functional groups; however, elevated red tide mortality might have meaningful implications in dynamic simulations, which should be explored in future studies. Collectively, results showed that incorporating the revised diet matrix into WFS-HAB Ecopath, which revealed a number of new predator-prey linkages, led to a more complex and interconnected food web. Specifically, prey items were generally consumed by a broader variety of predators, which contrasts with the base WFS-HAB Ecopath model where many prey, particularly juvenile fishes, were subjected to exceedingly high predation mortality rates from specific predators. The incorporation of the revised diet matrix into the WFS-HAB Ecopath model discussed herein is a fundamental step towards increasing the realism of trophic interactions in the model, which is particularly important as these trophic interactions define starting conditions for dynamic simulations