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

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

Ontogenetic spatial distributions of red grouper (Epinephelus morio) and gag grouper (Mycteroperca microlepis) in the U.S. Gulf of Mexico

•We developed statistical models for red and gag grouper juveniles and adults.•Predictions concur with understanding of grouper distributions in the Gulf of Mexico.•Our approach identified potential spawning grounds for gag grouper.•Our study will help improve the maps fed into ecosystem models of the Gulf of Mexico. 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 60m. Both older juvenile and adult female gags were predicted to be encountered from Apalachicola, Florida, to the region northwest of Tampa, Florida, along the 20m 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 (>40m) 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

DataSheet_1_Identifying trade-offs and reference points in support of ecosystem approaches to managing Gulf of Mexico menhaden.docx

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.</p

Evidence for ecosystem changes within a temperate lagoon following a hurricane-induced barrier island breach

The Great South Bay (GSB) is a shallow temperate lagoon in New York, USA, that has experienced a long-term decline in ecosystem maturity, defined as possessing increased complexity, stability, and resilience, dating back to the nineteenth century that is attributed to the loss of filter-feeding and upper trophic-level diversity and biomass. The observed decline is hypothesized to result from reduced connectivity to the Atlantic Ocean following installation of permanent inlets along the barrier island that reduce the probability of “rapid state” change through breaching. In October 2012, Hurricane Sandy created a breach in Fire Island that increased connectivity between GSB and the ocean, resulting in higher bay-wide salinity. We hypothesized that increased connectivity would result in a state change reminiscent of a mature system, characterized by higher nekton and mobile invertebrate species richness and diversity, and occurrence of migratory biomass. Otter trawl surveys were conducted throughout GSB from 2013 through 2015 and compared to a pre-breach survey conducted in 2007. An increase in species richness, diversity, and biomass in the 3 years following the breach and a difference in the dominant species collected between sampling periods was observed. Transition in the nekton and mobile invertebrate assemblage was also observed, whereby the assemblages in 2007 and 2015 differed from 2013 and 2014, with the greatest differentiation between the 2007 and 2015 assemblages, highlighting the influence of the breach rather than seasonal and/or inter-annual variation in driving these assemblages. This temporal trajectory of assemblage change clearly aligned with observed changes in salinity; however, this conclusion should be interpreted with caution given the lack of pre-breach survey replication. Nonetheless, our findings suggest that even a modest breach can cause detectible change in the community assembly in GSB. The expanded community diversity observed in GSB is suggestive of initial recovery of ecosystem maturity and underscores the importance of breaching as fundamental in maintaining lagoon ecosystems

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