Sampling fishes and decapods in shallow, estuarine, marsh habitats is challenging because of depth variation, soft substrates that make standing difficult, and the presence of submersed aquatic vegetation. Though often overlooked, a cast net is an efficient gear type for sampling nekton in this environment. Complaints about the cast net are that it is difficult to deploy successfully and the results are not repeatable. We present a method of standardization of cast-net deployment that reveals that most of the variation in area covered is among individual operators rather than within one individual. The 1.8-m cast net collected more species, more biomass, and faster-swimming nekton than the throw trap. There was no statistical difference in the total number of animals collected or the total number of species between the gear types. We conclude that the cast net is a useful gear type for sampling nekton communities in estuarine habitats especially when there are differences in the spatial and temporal occurrences and relative abundances of many different organisms in an area with complex and varying habitats.

Coastal landscapes in the northern Gulf of Mexico, specifically the Mississippi coast, have undergone rapid urbanization that may impact the suitability of salt-marsh ecosystems for maintaining and regulating estuarine faunal communities. We used a landscape ecology approach to quantify the composition and configuration of salt-marsh habitats and developed surfaces at multiple spatial scales surrounding three small, first-order salt-marsh tidal creeks arrayed along a gradient of urbanization in two river-dominated estuaries. From May 3 to June 4, 2010, nekton and macroinfauna were collected weekly at all six sites. Due to the greater abundance of grass shrimp Palaemonetes spp., brown shrimp Farfantepenaeus aztecus, blue crab Callinectes sapidus, Gulf Menhaden Brevoortia patronus, and Spot Leiostomus xanthurus, tidal creeks in intact natural (IN) salt-marsh landscapes supported a nekton assemblage that was significantly different from those in partially urbanized (PU) or completely urbanized (CU) salt-marsh landscapes. However, PU landscapes still supported an abundant nekton assemblage. In addition, the results illustrated a linkage between life history traits and landscape characteristics. Resident and transient nekton species that have specific habitat requirements are more likely to be impacted in urbanized landscapes than more mobile species that are able to exploit multiple habitats. Patterns were less clear for macroinfaunal assemblages, although they were comparatively less abundant in CU salt-marsh landscapes than in either IN or PU landscapes. The low abundance or absence of several macroinfaunal taxa in CU landscapes may be viewed as an additional indicator of poor habitat quality for nekton. The observed patterns also suggested that benthic sediments in the CU salt-marsh landscapes were altered in comparison with IN or PU landscapes. The amount of developed shoreline and various metrics related to salt marsh fragmentation were important drivers of observed patterns in nekton and macroinfaunal assemblages.

Observation of animal movements on small spatial scales provides a means to understand how large-scale species distributions are established from individual behavioral decisions. Small-scale vertical movements of 14 Summer Flounder Paralichthys dentatus residing in Chesapeake Bay were observed by using depth data collected with archival tags. A generalized linear mixed model was employed to examine the relationship between these vertical movements and environmental covariates such as tidal state, time of day, lunar phase, and temperature. Vertical movements increased with warming water temperatures, and this pattern was most apparent at night and during rising and falling tides. Fish generally exhibited greater vertical movements at night, but the difference between vertical movements in the day and those at night decreased as fish increased in size. Results from this study fill a void in understanding the small-scale movements of Summer Flounder and could be incorporated into individual-based models to investigate how species distributions develop in response to environmental conditions.

Seals (Phocidae) are known predators of Atlantic Salmon Salmo salar from their entry into the estuary as smolts until their return to freshwater as adults. We developed a written protocol for identifying seal-induced injuries on adult Atlantic Salmon returning to Maine rivers. The protocol, which includes photos and category definitions, has been used since 2006 by Maine Department of Marine Resources biologists when handling adult Atlantic Salmon at the Veazie Dam fishway on the Penobscot River and at other adult capture facilities in Maine. The written protocol has ensured that reporting is consistent among years and rivers; photos of wounds serve as quality assurance for the protocol. For adults returning to the Penobscot River in 2006 and 2007, seal-induced injuries were more likely to be found on two-sea-winter fish; to appear as gashes or arched wounds; to be open rather than healed; and to occur on the center third of the body below the lateral line. Larger two-sea-winter fish (>67 cm FL) returning to the Penobscot River early in the run (May-early July) were more likely to have a seal-induced injury. Injury rates increased from 1978 to 2010; this increase was correlated with seal aerial counts for the Gulf of Maine and Penobscot Bay. From 2006 to 2010, the annual seal-induced injury rate for Atlantic Salmon in six Maine rivers (including the Penobscot River) ranged from 0.00 to 0.30 across rivers. Rates of injury on Atlantic Salmon for all years combined did not differ among the six rivers, but low power likely affected our ability to detect any differences.

Hatchery supplementation programs have been implemented for several populations of American Shad Alosa sapidissima, which are declining across the species' native range due to disrupted access to spawning grounds, habitat degradation, and overfishing. The genetic impacts of stocking Pamunkey River-origin larvae into the James River American Shad population since 1994 were investigated, and the effects were considered within a regional context by including American Shad populations from other Chesapeake Bay tributaries that also received interbasin stockings from various rivers over the same period. Levels of genetic diversity for microsatellite markers were high in all populations except the Susquehanna River population, which showed a significant decline in diversity between the 1990s and 2007. Before supplementation of James River American Shad, the James and Pamunkey River populations exhibited subtle standardized differentiation among groups (F′_CT = 0.012), whereas differentiation was reduced after supplementation (F′_CT = 0.007), indicating that supplementation contributed to homogenization of population structure within the two rivers. Chesapeake Bay tributaries also displayed higher levels of differentiation in the 1990s (F′_CT = 0.063) than in contemporary, supplemented samples (F′_CT = 0.004). Bayesian analyses of population structure among 1990s Chesapeake Bay samples only identified the Susquehanna River as having a distinguishable population, and no population structure was detected among samples collected in the late 2000s. In light of the fact that Chesapeake Bay American Shad populations are not rebounding in response to supplementation, our observation of reduced genetic differentiation among populations is a likely signal of substitution by hatchery-origin fish rather than increasing natural recruitment. As such, spawning habitat improvement in conjunction with continued bay wide fishing regulation may be a more beneficial strategy for restoring viable American Shad populations than continued reliance on supplementation.

For the economically and ecologically important Red Snapper Lutjanus campechanus, depth distribution patterns across ontogeny are not well understood, particularly in the southeastern U.S. Atlantic Ocean (SEUSA). Using data derived from two fishery-independent surveys targeting hardbottom habitats, we examined patterns of age- and length-specific depth distributions of postjuvenile (age 1 ) Red Snapper in the SEUSA. We also compared age and length distributions between fishery-independent surveys and commercial hook-and-line catches to make inferences about gear-specific age and size selectivity, which could have implications for gear-specific interpretations of Red Snapper depth distribution patterns and for determining selectivity functions used in stock assessments. Older, larger Red Snapper were generally distributed throughout all depths, whereas the younger and smaller Red Snapper occurred disproportionately in relatively shallow waters. For Red Snapper equal to or larger than 50 cm FL, we found no evidence of a positive relationship between depth and age or length. Additionally, age and length distributions of Red Snapper ≥ 50 cm FL did not differ between fishery-independent surveys and the commercial hook-and-line fishery. These results provide no support for assertions of greater abundances of older and larger Red Snapper in deeper SEUSA waters. As observed in this study for Red Snapper in SEUSA waters, we suggest that patterns of increasing age and size with depth for multiple reef-associated fish species in SEUSA and Gulf of Mexico waters may be driven by younger and smaller fish occurring in shallower waters, and older and larger fish being distributed more equally across depths. Analyses to test this hypothesis for multiple species would be informative for their assessment and management and are recommended.

Stable isotope ratios of carbon and nitrogen (δ¹³C and δ¹⁵N) from muscle samples were used to examine the feeding ecology of a heavily exploited shark species, the Sandbar Shark Carcharhinus plumbeus. Two hundred and sixty two Sandbar Sharks were sampled in five South Carolina estuaries. There were no significant differences in average δ¹³C or δ¹⁵N signatures between estuaries, between sampling years, or between male and female Sandbar Sharks, suggesting that these variables do not affect diet. A potential ontogenetic diet shift between young-of-year and juvenile Sandbar Sharks in South Carolina, similar to a shift previously described in Virginia and Hawaii populations, is suggested by significant differences in average δ¹³C and average δ¹⁵N signatures between these age-classes. Results confirm that Sandbar Sharks in South Carolina are generalist predators and that juvenile Sandbar Sharks have a wider diet breadth than young-of-year sharks, a pattern common in elasmobranchs. Sandbar Shark diet in South Carolina is similar to that found in previous stomach content analysis studies. This study also demonstrates that nonlethal sampling methods can be applied to sharks to obtain diet and trophic information, including the detection of ontogenetic shifts in diet.

Common Snook Centropomus undecimalis were once abundant off the Texas coast, but these populations are now characterized by low abundance and erratic recruitment. Most research concerning Common Snook in North America has been conducted in Florida and very little is known about the specific biology and habitat needs of Common Snook in Texas. The primary objective of this study was to describe the habitat use patterns of juvenile Common Snook and their role in the fish assemblage in the lower portion of the Rio Grande, Texas. Secondarily, we documented the relationship between age and juvenile reproductive development. Fish were collected during January—March 2006 from the lower 51.5 km of the Rio Grande using a bottom trawl and boat-mounted electrofisher. Measurements of water quality and other habitat traits were recorded at each sampling site. We captured 225 Common Snook exclusively in freshwater habitats above river kilometer 12.9. The distribution of juvenile Common Snook was not random, but influenced primarily by turbidity and dissolved oxygen. Sex differentiation and gonadal development based on histological examination of gonads established that age-1 and age-2 Common Snook were juvenile, prepubertal males. There was no difference between the age groups in their overall distribution in the river. However, age-2 Common Snook were associated with deeper areas with faster currents, higher conductivity, and steeper banks. Overall, Common Snook in the lower Rio Grande show substantial differences in habitat use than their counterparts in other parts of the range of the species, but it is unclear whether this is due to differences in habitat availability, behavioral plasticity, or some combination thereof.

We evaluated how the use of bait as a fish attractant influenced the species and size composition of demersal fishes viewed with a stereo video lander at 160 sampling sites at Stonewall Bank, a deepwater rocky reef complex off the Oregon coast. We also studied the effectiveness of stereo video for generating estimates of fish length and distance from the cameras. Bait altered the species composition of fish encountered, increasing the mean counts of demersal fishes by 47%, with increases of 135–250% for Rosethorn Rockfish Sebastes helvomaculatus, Northern Ronquil Ronquilis jordani, and Spotted Ratfish Hydrolagus colliei. Increases in the mean counts of 35–150% for unidentified sculpins (Cottidae), Yelloweye Rockfish S. ruberrimus, and Quillback Rockfish S. maliger were nonsignificant. The calibrated stereo video lander provided acceptably precise estimates of fish length and camera-to-fish distance (range of three replicate measurements less than 3 cm for length and 20 cm for distance) for 34.3 % of the demersal fishes that were counted. The precision of length and distance estimates declined with increased distance; acceptable estimates of distance were typical when fish were within 200 cm and were infrequent when fish were beyond 500 cm. Bait reduced the mean distance at which acceptable estimates of length and distance were obtained from 264 cm to 200 cm, but had no effect on mean fish length for the three most frequently encountered demersal species. The combined effect of bait on demersal fish counts and mean distance more than doubled the efficiency of the stereo video lander for generating fish length and fish-camera distance estimates.

Red Snapper Lutjanus campechanus are the most economically important reef fish in the Gulf of Mexico and a heavily targeted fishery. When brought to the surface from deep water, this species often suffers pressure-related injuries collectively known as barotrauma. This trauma results in high discard mortality and has affected recovery of the fishery. In laboratory experiments using hyperbaric chambers, we assessed sublethal effects of barotrauma and subsequent survival rates of Red Snapper after capture events from pressures corresponding to 30 and 60 m deep. We then evaluated the use of rapid recompression and venting to increase survival and improve recovery after release in this controlled environment. Vented fish in simulated surface release and rapid-recompression treatments had 100% survival. Fish released at the surface that were not vented had 67% survival after decompression from 30 m but only 17% survival from 60 m, while nonvented rapidly recompressed fish had 100% survival from 30 m and 83% survival from 60 m. Fish that were vented upon release at the surface showed significantly better ability to achieve an upright orientation and evade a simulated predator. Results showed clear benefits of venting or recompression. Our data also show strong depth effects resulting in increased barotrauma injuries, more impaired reflexes, and greater mortality as depth increases. Overall, our data support venting or rapid recompression as effective tools for alleviating barotrauma symptoms, improving predator evasion, and increasing overall survival.

Stock assessments for the Gulf of Mexico (Gulf) Greater Amberjack Seriola dumerili continue to designate the stock as overfished and undergoing overfishing, despite increasing regulatory measures. Knowledge of sex-specific spatial distribution and fishing mortality may contribute to our understanding of the stock's overexploitation, especially since Greater Amberjacks may be subject to sex-specific mortality resulting from minimum size regulations. Currently, the sex ratio of the stock is assumed to be 1:1. An average and range of sex ratios were estimated for the Gulf stock based on sampling of fish landed in the recreational and commercial fisheries and based on released fish that were nonlethally sexed during a tagging study of sex-specific movement patterns and release mortality. The nonlethal method of sex determination was developed based on external features of the urogenital region; urogenital catheterization was used to validate the external sexing and to collect oocyte samples for determining maturity stages of females during the spawning season. Of the 238 fish (108 males and 130 females) for which sex was verified, only one smaller female was incorrectly sexed. Urogenital catheterization identified females that were spawning or that would likely spawn in the upcoming spawning season, but no differentiation could be made between immature and resting females. Analysis of published data sets suggested that the Gulf stock has an overall female-skewed sex ratio, with estimates ranging from 1:1.7 to 1:2.5 (male : female), while the nonlethal sexing data from the current study suggest that the overall sex ratio is slightly male skewed (1:0.8) in some regions. All studies report a female-skewed sex ratio of 1:2.3, on average, for 1,000-mm FL and larger fish in the Gulf. Sex ratios that deviate from the assumed 1:1 ratio should be incorporated into future assessments of the Gulf Greater Amberjack stock to investigate potential consequences for stock status and management.

Pop-up satellite archival tags (n = 31) were deployed on Yellowfin Tuna Thunnus albacares in the Gulf of Mexico for periods ranging from 14 to 95 d. Differences in diel vertical behavior were assessed by comparing time spent at temperature relative to the surface temperature (ΔT). Pooled samples revealed that 31% of darkness hours, 20% of twilight hours, and 12% of daylight hours were spent in the uniform-temperature surface layer (i.e., ΔT = 0). Total time spent above 100 m was less during daylight (90.0%) than during darkness (99.8%), suggesting greater exploration of deeper depths during daylight hours. Maximum depth visited ranged from 208 to 984 m, and minimum temperature visited ranged from 5.4°C to 11.8°C. Only a small proportion of total time was spent at temperatures colder than 8°C below the surface temperature. Horizontal excursions for the majority of individuals were less than 100 km from the point of release; however, three individuals moved distances of 411–1,124 km, suggesting that this species has the capability to move relatively long distances within the Gulf of Mexico. The ΔT values are provided in tabular format and serve as direct input variables for use in habitat standardization models.

Declines in dissolved oxygen (DO) concentrations in aquatic environments can lead to conditions of hypoxia (DO ≤ 2 mg/L), which can directly and indirectly affect aquatic organisms. Direct effects include changes in growth and mortality; indirect effects include changes in distribution, movement, and interactions with other species. For mobile species, such as the pelagic filter-feeding Gulf Menhaden Brevoortia patronus, indirect effects are more prevalent than direct effects. The northern Gulf of Mexico experiences one of the largest areas of seasonal hypoxia in the world; this area overlaps spatially and temporally with the Gulf Menhaden commercial purse-seine fishery, which is among the largest fisheries by weight in the United States. Harvest records from the Gulf Menhaden fishery in 2006–2009 and fine-scale spatial and temporal predictions from a physical—biogeochemical model were used with spatially varying regression models to examine the effects of bottom DO concentration, spatial location, depth, week, and year on four response variables: probability of fishing, total Gulf Menhaden catch, total fishery effort, and CPUE. We found nearshore shifts in the probability of fishing as DO concentration declined, and we detected a general westward shift in all response variables. We also found increases in CPUE as DO concentration declined in the Louisiana Bight, an area that experiences chronic, severe hypoxia. The overall effects of environmental conditions on fishing response variables appeared to be moderate. Nevertheless, movement of either Gulf Menhaden or the purse-seine fishery in response to environmental conditions could potentially affect the susceptibility of Gulf Menhaden to harvest and could therefore influence assessment of the stock and associated stock status indicators.

Circle hooks are required when targeting reef fishes in the U.S. federal waters of the Gulf of Mexico. However, limited data is available to evaluate circle hook performance (e.g., hooking location and catch rate) or selectivity in this fishery. Therefore, a fishing experiment was conducted to test the performance of a range of circle hook sizes (2/ 0 and 4/0 Mustad 39940BLN and 9/0, 12/0, and 15/0 Mustad 39960D) in the recreational reef fish fishery, as well as to estimate hook selectivity directly for Red Snapper Lutjanus campechanus, the most targeted reef fish in the northern Gulf of Mexico. Reef fish communities were surveyed with a micro remotely operated vehicle equipped with a laser scaler and then fished with one of five circle hook sizes. Hooking location typically was in the jaw for all hooks examined, with the mean percentage of jaw hooking being 94.1% for all reef fishes and 92.9% for Red Snapper. Fish size generally increased with hook size but at the cost of a reduced catch rate. The percentage of the catch constituted by Red Snapper decreased from 73% for 2/0 hooks to 60% for 9/0 hooks but then increased to 84% for 15/0 hooks. Dome-shaped (exponential logistic) selectivity functions resulted when fitting candidate models to hook-specific Red Snapper size at catch and remotely operated vehicle laser-scaled size distribution data. While Red Snapper median size at full selectivity increased with circle hook size, the difference in that parameter between the smallest and largest hooks was only 66 mm, or a difference of approximately one age-class. Results of this study suggest that mandating the use of large (e.g., ≥12/0) circle hooks would have relatively little effect on either Red Snapper catch rate or selectivity but would decrease the catch rate for other reef fishes, which would be problematic during closed Red Snapper seasons when fishermen attempt to target other species.

Bioeconomic models have been developed and applied to a range of fisheries around the world. However, an even greater number of fisheries are relatively data poor, and development of traditional bioeconomic models is not feasible. For small-scale fisheries, the cost of data collection and model development may exceed the additional value these models may generate. Fisheries biologists have grappled with similar issues and have developed a range of data-poor methods for estimating reference points related to fishing mortality based on life history characteristics and other indicators. In other cases, catch and effort data may be sufficient to estimate sustainable biomass levels. However, model-derived economic target reference points require robust biological models as well as appropriate economic information, both of which are often unavailable. In this paper, we extend the data-poor work to move from biological to economic target reference points for single-species fisheries. We show that the relationship between economic (maximum economic yield) and biological (maximum sustainable yield) reference points depends primarily on the cost : revenue ratio, and that, where unavailable, these can be inferred from fisheries characteristics. We show that good estimates of biomass- and effort-based economic target reference points can be achieved with limited data.

Implementation of circle hook regulations in the Gulf of Mexico will impact the length structure and age structure of the snapper-grouper fishery catch as well as demographic data for stock assessments; therefore, an understanding of circle hook selectivity patterns is critical. Indirect selectivity analysis of the vertical-line catch of Red Snapper Lutjanus campechanus and Vermilion Snapper Rhomboplites aurorubens showed that for both species, there were significant differences in mean FL among hook sizes, broad length frequency distributions, and wide selectivity curves. Although the results suggest that hook size regulations could be a useful management strategy for targeting desired size-classes of these snappers, the broadly overlapping length distributions indicate that undersized catch would not be eliminated. Selectivity curves generated from the different families of distributions produced equally good fit to the data and provided a basis for evaluating various selectivity curves when the size structure of the sampled population is unknown. If the size structure of the population is known, then the use of direct selectivity methods is recommended. Right-skewed distributions generally fit the data best, suggesting that hook regulations are likely to be more effective if the desired goal is to reduce the amount of undersized catch by eliminating small hook sizes. Conversely, elimination of large hooks appears to be less likely to reduce the catch of larger size-classes because mouth gape is likely the primary limiting factor and small hooks can catch large fish. Catch rates were significantly different among hook sizes; thus, regulations based on hook size could impact fishing effort and change the dynamics of how the snapper-grouper fishery is prosecuted. Tradeoffs between moderate improvements in size-class targeting, changes in effort, and various components of fishing mortality (i.e., catch and regulatory discards) will require further investigation through simulation modeling or field experimentation.

Conservation efforts under regulatory programs such as the U.S. Endangered Species Act and Magnuson-Stevens Fisheries Conservation and Management Act seek to restore species in decline to a level where the populations are no longer in jeopardy. Key to designing effective conservation plans for the more than 2,500 species currently managed by these two U.S. programs is the establishment of realistic restoration targets given changes in habitats and ecosystems. Accomplishing this is difficult, particularly for populations that have experienced significant habitat alterations. We developed and assessed an approach for establishing quantifiable goals for the recovery of a threatened species by (1) estimating historical population biomass prior to directed fishing, (2) identifying large-scale habitat modifications that limit available critical habitat, (3) assessing the relationship between historical baselines, habitat characteristics, and extant available habitat, and (4) using these relationships to inform recovery efforts in rivers where traditional stock assessment methods are not possible. In our case study of Gulf Sturgeon Acipenser oxyrinchus desotoi, we found that the current population levels in four of the seven river systems in the recovery plan are likely at or exceeding the mean carrying capacity, given the current levels of available habitat. In the remaining three rivers, extant Gulf Sturgeon populations are likely below their estimated carrying capacity levels. Our approach is of management importance because it establishes realistic recovery criteria through the assessment of changes in habitat from historic to present levels and is widely applicable across a species' range. An important application of this approach is to assess the potential benefits to fish species from management actions, such as dam removal or spawning habitat restoration, that are designed to restore habitat and promote species recovery.

The Pacific Cod Gadus macrocephalus in the eastern Bering Sea is the target of one of the most lucrative fisheries in Alaska; however, relatively little is known about the movement of Pacific Cod and how this interacts with intense fishing on local spawning aggregations of cod every spring (January–April). This study aimed to draw inferences on Pacific Cod movement using a single tag release group of fish and the fishery as a representative for movement by qualitatively examining both temporal and spatial patterns of tag recoveries. Based on the tag recoveries in this study and past genetic studies, there is evidence that Pacific Cod show both homing tendencies and site fidelity during the spring when large aggregations of cod form to spawn. This study also supports results from an earlier study on Pacific Cod movement in this region and presents new insights into cod movement patterns. The cod in this tag release group were widely distributed across the Bering Sea during the summer and fall months and returned to the vicinity of the release site in the spring, presumably to spawn. Understanding the movement of cod and their interactions with the fishery is essential to the successful management of the Pacific Cod stock.