The following questions were addressed in this study: (1) If a suite of 12–15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single-nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12-locus Fisheries and Oceans Canada (DFO) microsatellite suite range include adding either 4 microsatellites or 25 SNPs to the existing suite to achieve an overall population-specific accuracy of 86% across 60 populations. For the 13-locus Genetic Analysis of Pacific Salmon (GAPS) microsatellites, either 2 microsatellites or 20–25 SNPs can be added to the existing suite to achieve approximately 86% population-specific accuracy in estimated stock composition. The enhanced DFO (16 loci) and GAPS (15 loci) microsatellite baselines were projected to require 179 and 166 SNPs, respectively, for equivalent precision of the population-specific estimates. The level of regional accuracy of individual assignment available from the enhanced DFO and GAPS suites of microsatellites was projected to require 90 and 82 SNPs, respectively. The level of individual assignment to specific populations available from the enhanced DFO and GAPS suites of microsatellites was projected to require 137 and 121 SNPs, respectively.

Assessment of early life history characteristics requires effective sampling methods for larval fishes. Different gears are suitable for different habitats and frequently select different sizes or life history stages. In this study, two passive sampling methods were compared for use in collecting larval freshwater and estuarine fishes in two tropical streams. Drift nets and light traps were identified a priori as the most appropriate gears for sampling in these systems based on stream characteristics (including accessibility, size, and morphology). Catches were compared between sampling methods. Additionally, catches under different environmental conditions (flow, tide stage, and moon phase), during different sampling periods (time of day and week of summer), and at different depths were compared using mixed-effects analysis of variance. A total of 2,156 fish were captured in 954 h of sampling. The significant (α < 0.05) explanatory variables for total larval catch were stream, sampling method, week of summer, time of day, and moon phase. Eleven families were represented in the samples, with the families Gobiidae (n = 948), Eleotridae (n = 391), and Syngnathidae (n = 276) comprising 94.9% of the identifiable larvae collected. The variables that explained both the Gobiidae and Syngnathidae catches were gear, week of summer, and time of day. The Syngnathidae catch was highest in drift nets, but the Gobiidae catch was highest in light traps. Nighttime light trap sampling appeared to be the best overall technique for larval collection in these systems. However, a combination of light traps and drift nets would reduce the biases associated with size and species selectivity found for individual gears, and this approach would be preferable for sampling small tropical streams.

Subadult and small adult (375–475 mm total length) striped bass Morone saxatilis are abundant and represent an important component of the recovered U.S. Atlantic coast stocks. However, little is known about these large aggregations of striped bass during their annual foraging migrations to New England. A quantitative understanding of trends in the diets of subadult and small adult migrants is critical to research and management. Because of the complexity of the Massachusetts coast, we were able to compare diets at multiple spatial, temporal, and taxonomic scales and evaluate which of these provided the greatest insights into the foraging patterns of this size of fish. Specifically, during spring through autumn, we quantified the diets of 797 migratory striped bass collected from 13 Massachusetts estuaries distributed among three geographic regions in two biogeographic provinces. Our data provided three useful results. First, subadult and young adult striped bass ate a season-specific mixture of fish and invertebrates. For example, more juvenile Atlantic herring Clupea harengus were eaten in spring than in summer or autumn, more juvenile Atlantic menhaden Brevoortia tyrannus were eaten in autumn than in spring or summer, amphipods were eaten primarily in the southern biogeographic province, and shrimp Crangon sp. were eaten in all locations and seasons. Second, examining diets by season was essential because of the temporal variability in striped bass prey. Grouping prey by fish and invertebrates revealed the potential for predictable differences in growth across geographic locations and seasons, based on the output from simple bioenergetics simulations. Third, of the three spatial scales examined, region provided the most quantitative and interpretable ecological trends. Our results demonstrate the utility of comparing multiple scales to evaluate the best way to depict diet trends in a migrating predator that seasonally uses different geographic locations.

We used a caging system designed to minimize the adverse effects of caging fish in marine waters to evaluate the discard mortality of seven species of rockfish Sebastes with barotrauma. Altogether, 288 rockfish were captured, scored for barotrauma, evaluated behaviorally at the surface, and caged individually on the seafloor for 48 h to determine survival. With the exception of three blue rockfish S. mystinus, the condition of surviving fish after cage confinement from 41 to 71 h was excellent. At capture depths up to 54 m, survival was 100% for yelloweye rockfish S. ruberrimus (n = 25) and copper rockfish S. caurinus (n = 10) and 78% for blue rockfish (n = 36). At capture depths up to 64 m, survival was 100% for canary rockfish S. pinniger (n = 41) and quillback rockfish S. maliger (n = 28) and 90% for black rockfish S. melanops (n = 144). Black rockfish survival was negatively associated with capture depth (m) and the surface-bottom temperature differential (°C). Blue rockfish survival was negatively associated with capture depth. Barotrauma signs and surface behavior scores were not good indicators of survival potential across species but were useful within species. In black and blue rockfish, severe barotrauma was negatively associated with survival, while higher scores on reflex behaviors at the surface were positively associated with survival. The high survival rates and excellent condition of some species in this study suggest that requiring hook-and-line fishers to use recompression devices to help discarded rockfish return to depth may increase survival for some species.

The spatiotemporal variability in strontium (Sr), barium (Ba), magnesium (Mg), and manganese (Mn) elemental signatures of water and fish otoliths was assessed from July to October 2008 across river habitats of Albemarle Sound, North Carolina. We examined whether relationships in these signatures exist and the potential of otoliths to serve as innate chemical tags. Hatchery-reared age-0 striped bass Morone saxatilis were placed in cages at four different locations to test development of habitat-specific otolith signatures. Dissolved elemental water and otolith signatures exhibited spatial variability but did not vary temporally. Chemical water signatures classified habitats with 76–81% accuracy, and otolith signatures of caged fish displayed 59–63% total classification accuracy depending on the classification method used. The elements Sr, Ba, and Mn were the main habitat discriminators, as their concentrations in otoliths were significantly correlated with concentrations in the water. Otolith Mg was not related to water chemistry and did not vary among habitats. Natural physiochemical gradients, geochemical processes, and possibly anthropogenic inputs influenced the trace elemental signatures of Albemarle Sound habitats. The unique chemical signals of the sound's river habitats validate the use of otolith signatures for determining striped bass habitat utilization in this system. Use of otolith elemental signatures as natural tags provides a quantitative method to determine the proportion of juvenile striped bass recruiting to the adult spawning stock from specific habitats, thus aiding resource managers in identifying habitats that should receive priority in restoration and conservation decisions.

Spotfin croakers Roncador stearnsii, a prized recreational catch, were collected throughout the Southern California Bight, primarily as bycatch from a long-term, scientific gill-net collection effort. The maximum otolith-based age in the present study was 24 years—14 years greater than in a previous scale-based aging study. Multiple models were used to estimate mean length at age, including models that utilize larvae as well as juveniles and adults, and the model selection results suggest sexual dimorphism in growth patterns. The juvenile and adult catch per unit effort reflected a clear pattern of habitat selectivity, with fish strongly preferring soft-bottom habitats. Catches in rocky-reef areas were limited but tended to increase with water temperature. The data also suggest that spotfin croakers segregate themselves sexually during the spawning season, when recreational fishing from jetties will target males and fish caught in bays and estuaries are more likely to be spawning females. These results provide further evidence for the importance of protection and restoration efforts for estuaries and bays along this well-developed coastline. The growth of larvae captured in plankton tows in July and September 2004 was substantially faster than that of larvae sampled in May, which coincided with warmer sea surface temperatures, highlighting a potentially important relationship relating temperature (and therefore geography) and settlement success.

Variation at 17 microsatellite loci was analyzed for about 50,000 coho salmon Oncorhynchus kisutch sampled from 274 locations ranging from Russia to California (but largely from British Columbia), and the variation was applied to estimate stock composition in mixed-stock fishery samples. High resolution of mixed-stock samples was possible; accurate estimates of stock composition were available for coho salmon originating from 39 regions (Russia, 1 region; Yukon River, 1; southeast Alaska, 1; British Columbia, 28; Washington, 5; Columbia River, 1; Oregon, 1; California, 1). The power of a locus in providing accurate estimates of stock composition of simulated single-population mixtures was related to the number of alleles observed at the locus. Approximately 800 alleles were observed across the 17 microsatellites. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained; estimates from 37 of 39 regions had accuracy greater than 90%. Estimated stock compositions of five mixed-fishery samples collected in British Columbia and the San Juan Islands (Washington) reflected the presence and timing of migration of the local populations. Microsatellites provided accurate estimates of stock composition from many locations in the British Columbia distribution of coho salmon.

Current methods to restore Louisiana's estuaries include the reintroduction of Mississippi River water through freshwater diversions to wetlands that are hydrologically isolated from the main channel. The reduced salinities associated with freshwater input are likely affecting estuarine nekton, but these effects are poorly described. Ecopath with Ecosim was used to simulate the effects of salinity changes caused by the Caernarvon freshwater diversion on species biomass distributions of estuarine nekton. A base model was first created in Ecopath from 5 years of monitoring data collected prior to the opening of the diversion (1986–1990). The effects of freshwater discharge on food web dynamics and community composition were simulated using a novel application of Ecosim that allows the input of salinity as a forcing function coupled with user-specified salinity tolerance ranges for each biomass pool. The salinity function in Ecosim not only reveals the direct effects of salinity (i.e., increases in species biomass at their optimum salinity and decreases outside the optimal range) but also the indirect effects resulting from trophic interactions. Through multivariate analyses we determined that the simulated species biomass distributions in the estuary change significantly with distance from the diversion. However, the simulations do not show a significant difference estuarywide between the modeled distributions (with pooling of the data from different distances) before and after the opening of the diversion. This indicates a redistribution of species in the estuary rather than the replacement of species within the estuarine nekton community. The salinity function is a useful addition to the Ecopath with Ecosim software for estuarine ecologists and fisheries managers.

We explored patterns of small pelagic fish assemblages and biomass of gelatinous Zooplankton (jellyfish) in surface waters across four oceanographic subbasins of greater Puget Sound. Our study is the first to collect data documenting biomass of small pelagic fishes and jellyfish throughout Puget Sound; sampling was conducted opportunistically as part of a juvenile salmon survey of daytime monthly surface trawls at 52 sites during May–August 2003. Biomass composition differed spatially and temporally, but spatial differences were more distinct. Fish dominated in the two northern basins of Puget Sound, whereas jellyfish dominated in the two southern basins. Absolute and relative abundance of jellyfish, hatchery Chinook salmon Oncorhynchus tshawytscha, and chum salmon O. keta decreased with increasing latitude, whereas the absolute and relative abundance of most fish species and the average fish species richness increased with latitude. The abiotic factors with the strongest relationship to biomass composition were latitude, water clarity, and sampling date. Further study is needed to understand the spatial and temporal heterogeneity in the taxonomic composition we observed in Puget Sound surface waters, especially as they relate to natural and anthropogenic influences.

We present the first comprehensive description of the age, growth, and reproductive life history traits of scamps Mycteroperca phenax from the northern Gulf of Mexico. Scamps were collected from commercial and recreational vessels along the northern Gulf of Mexico in 1972–2002. Scamp age was determined using thin transverse sections of sagittal otoliths; growth increments were difficult to interpret, and age was estimated for only 85% of the 5,383 otolith sections we examined. Scamps sampled from the commercial and recreational fisheries ranged from 109 to 890 mm fork length (FL) and from 1 to 31 years of age. We fitted annual ages and observed FLs to two different von Bertalanffy growth models (standard and size-modified models). The size-modified model considered the effect of the size limit but resulted in growth parameters similar to those of the standard model (asymptotic length L_∞ = 772 mm FL; growth rate k = 0.09 mm/year). Histology confirmed that scamps are protogynous hermaphrodites; gonadosomatic index data indicated a prolonged spawning season (January—June, peaking in April). Females reached maturity at a median FL of 332 mm and a median age of 2 years. Scamp sizes sampled from the fisheries were similar for males (221–870 mm FL) and females (109–878 mm FL), but the larger size-classes and older age-classes were mostly composed of males. The scamp population in the northern Gulf of Mexico has never been assessed, and our data provide highly valuable model inputs.

Passive integrated transponder (PIT) technology is rarely utilized in estuaries due to (1) saline water's attenuation of an antenna's electromagnetic field, (2) rapidly changing water properties and levels, and (3) the challenges of installing and maintaining antennas in silty, brackish conditions. We present methods for the construction and installation of antennas that can detect 12-mm full-duplex PIT tags in salinities up to 33‰. We evaluated their reading performance under variable water salinities, temperatures, and depths in the upper estuaries of three streams. We found that water depth, salinity, and temperature were all negatively correlated with antenna current, but that the relative importance of these variables varied depending upon aspects of the antenna deployment. Since our antennas held amperage levels adequate for maintenance of a complete electromagnetic field throughout all test conditions, we suggest that successful detection was more dependent upon the antenna system's coverage of the water column and the swimming path of fish through the antenna system than individual antenna performance. In addition to fish, this technology could be applied to studies of mammals, crustaceans, and particles transported through estuarine channels.

Estuaries are among the most productive of all ecosystems and provide critical nursery habitat for many young-of-the-year (age-0) marine fish. Along the South Carolina coast, former rice field impoundments in some estuarine areas are now managed to provide habitat for waterfowl. Marine fish that enter these structures during water level manipulation become trapped and suffer high mortality rates. Because these fish cannot emigrate back to coastal waters to complete their life cycles, these impoundments appear to act as sinks for marine-transient species. Our goal was to identify which of a set of management options would maximize export of age-0 spot Leiostomus xanthurus from the Combahee River, South Carolina, to the coastal population. We used a structured decision-making approach to evaluate four decision alternatives: to maintain status quo, to close all impoundments while age-0 spot are most abundant in the river, to change the water level manipulation strategy to improve fish passage from impoundments, or to breach all impoundments. We also wanted to evaluate how impoundments and natural mortality influence the export of age-0 spot. The optimal management decision was to change the water level manipulation strategy to increase fish passage from the impoundments. Spot export was most sensitive to juvenile settlement in the estuary and natural mortality. The results of this model can be used adaptively for impoundment management along the Combahee River and can be modified for other estuarine areas or other fish species.

Despite the expenditure of millions of dollars on restoration efforts for depleted North American stocks of alosine fishes, rangewide abundance levels for multiple species have declined to historic lows. Stocking practices aimed at rebuilding spawning runs are deemed successful when numerical abundance levels are shown to increase in response. However, these practices may only yield short-term gains in abundance at the ultimate expense of population genetic integrity and do not ensure the long-term persistence and evolutionary potential of a species. Although molecular methods are now widely employed in fisheries management and provide a suite of powerful management tools, these approaches have not been well integrated into alosine management strategies. We review the net effects of stocking practices on population genetic integrity and species' long-term persistence as it is currently understood and highlight what is known in this regard for alosines in North America, with particular focus on American shad Alosa sapidissima. We find that stocking practices carry a substantial risk to the persistence of genetically distinct alosine spawning populations and suggest that future restoration efforts proceed by providing access to historical spawning grounds, either through dam removal or through providing effective fish passage, followed by natural recolonization of reclaimed habitat. We also identify important areas of research relevant to future alosine restoration that require exploration and identify recent developments that may alter future restoration decisions in an adaptive management framework.

After centuries of disturbance, environmental professionals now recognize the need to restore coastal watersheds for native fish and protect the larger ecosystems on which fish and other aquatic biota depend. Anadromous fish species are an important component of coastal ecosystems that are often adversely affected by human activities. Restoring native anadromous fish species is a common focus of both fish and coastal watershed restoration. Yet restoration efforts have met with uneven success, often due to lack of knowledge about habitat availability and use. Using habitat surveys and radio tracking of adult anadromous alewives Alosa pseudoharengus during their spring spawning migration, we illustrate a method for quantifying habitat using multiple approaches and for relating mobile fish distribution to habitat. In the Ipswich River, Massachusetts, measuring habitat units and physical conditions at transects (width, depth, and velocity) provided an ecological basis for the interpretation of landscape patterns of fish distribution. Mapping habitat units allowed us to efficiently census habitat relevant to alewives for the entire 20.6 river kilometers of interest. Our transect data reinforced the results of the habitat unit survey and provided useful, high-resolution ecological data for restoration efforts. Tagged alewives spent little time in riffle-run habitats and substantial time in pools, although the locations of pool occupancy varied. The insights we provide here can be used to (1) identify preferred habitats into which anadromous fish can be reintroduced in order to maximize fish survival and reproduction and (2) pinpoint habitat types in urgent need of protection or restoration.

Zooplankton composition and abundances were quantified in the lower Roanoke River and Albemarle Sound, North Carolina. The spatial and temporal overlap between larval alosines, including American shad Alosa sapidissima, river herring (alewife A. pseudoharengus and blueback herring A. aestivalis), hickory shad A. mediocris, and Zooplankton were examined to determine whether larval alosines in this system are food limited. Samples were collected weekly at 19 stations from March through June 2008–2009 in three habitats: River, Delta, and Sound. Spatial differences in Zooplankton were observed, with the abundance in the Sound (16,546 ± 14,678 [number/m³ ± SD]) being significantly higher than those in the River (4,934 ± 3,806) and Delta areas (4,647 ± 2,846). Zooplankton composition was dominated by Daphniidae, Bosminidae, calanoid and cyclopoid copepods, copepod nauplii, and rotifers. The spatial patterns in alosine abundance were the opposite of those for Zooplankton, being highest in the River (21.0 ± 127.6) and lower in the Delta (7.5 ± 35.5) and Sound (4.6 ± 24.8). Mouth gape models for each alosine species showed that copepod nauplii and rotifers are the most suitable-sized prey for the first feeding after yolk sac absorption. There was a high degree of spatial and temporal overlap between larval alosines and size-appropriate prey items, suggesting that the larval alosines are not food limited in Albemarle Sound.

We estimated the variation in the instantaneous rates of growth and mortality between cohorts of larval alewife Alosa pseudoharengus and blueback herring A. aestivalis in the Tar-Pamlico River, Pamlico Sound, North Carolina. The age of larvae captured by push net was estimated by counting the daily rings on sagittal otoliths. Weight-at-age and abundance-at-age data were used to generate instantaneous daily growth (G) and mortality rates (M) for 7-d cohorts. The instantaneous daily growth rate was relatively constant between cohorts, ranging from 0.103 to 0.277 for alewives and from 0.105 to 0.200 for blueback herring. The instantaneous daily mortality rate was more variable between cohorts, ranging from 0.064 to 0.270 for alewives and from 0.100 to 0.251 for blueback herring. All but one blueback herring cohort had an M/G value exceeding 1.0, indicating that these cohorts were losing biomass during the early larval stage. For alewives, M/G values were more variable, with 50% of the cohorts having values less than 1.0. The effect of habitat was consistent between species, with M/G values being higher and closer to 1.0 at sites in tributary creeks and backwater areas of Tar River. The overall M/G values were 0.57 for alewives and 1.60 for blueback herring from both backwater and main-channel sites, indicating that the environmental conditions in the Tar—Pamlico River are more favorable for alewives.

Widespread declines in American shad Alosa sapidissima along the Atlantic coast have been attributed to overfishing, a decrease in water quality, and loss of habitat. Recent surveys along the Roanoke River and Albemarle Sound, North Carolina, suggest that stocks are continuing to decline despite extensive management and stock enhancement efforts. Laboratory experiments were conducted to evaluate the effect of prey density on the growth and survival of American shad and to determine whether larvae can survive and grow in a riverine environment with a limited forage base. Larvae were reared from 11 to 20 d posthatch in one of five treatments: (1) no food; (2) low food (1 prey/L), which simulated the prey densities in the Roanoke River; (3) medium food (50 prey/L), which simulated the prey densities typical of coastal watersheds; (4) high food (500 prey/L); and (5) Artemia spp. (500/L). Larval survival was 35 ± 7% (mean ± SE) and was not significantly different among treatments. Treatments with starved fish had the lowest survival (22 ± 12%), while the highest survival was observed in treatments with high densities of wild Zooplankton (46 ± 18%) and Artemia (40 ± 16%). Length-specific growth rates were 0.017 mm/d for the starved treatments and 0.024, 0.029, 0.034, and 0.039 mm/d for the low-prey, medium-prey, high-prey, and Artemia treatments, respectively. Larval growth as a function of length was not significantly different between the Artemia and high-prey treatments; however, growth in these treatments was significantly higher than in those with lower prey densities. Weight-specific growth rates (G_w) were significantly higher for the Artemia treatment (G_w = 0.129) than for all the other treatments (G_w = 0.081). Analysis of stomach contents indicated that American shad were selectively feeding on the smallest Zooplankton (80–250 µm) and that larvae exhibited a strong preference for copepod nauplii and rotifers. These results suggest that spatial and temporal overlap between larvae and Zooplankton is important for larval growth and survival.

Anadromous blueback herring Alosa aestivalis are declining throughout much of their range, and fishery closures in some systems have failed to produce population recovery. A potential contributing factor is increased predation pressure from sympatric striped bass Morone saxatilis. We integrated data on the predator-prey interaction between striped bass and blueback herring during vernal migrations into the Connecticut River with data on the in-river striped bass fishery to assess the potential for mitigation of blueback herring mortality via increased striped bass harvest. Striped bass abundance, size structure, diets, and angler catches were assessed within a river segment during spring 2005–2008. We estimate that striped bass consumed 400,000 blueback herring (90% confidence interval = 200,000–800,000) annually in our study area during the spring migration season. The predator-prey interaction between striped bass and blueback herring was predator size dependent. Blueback herring were most commonly found in the stomachs of striped bass between 650 and 999 mm total length. Intermediate size-classes (650–799 mm) made the greatest contribution to population-level consumption. Highly abundant small striped bass (400–549 mm) consumed herring infrequently, yet still made substantial contributions to population-level consumption. Anglers caught 17,000 striped bass in our study area during March–June 2008; only 11% of these fish could be harvested under the current 28-in (710-mm) minimum length limit. Allowing anglers to harvest up to 15,000 sublegal striped bass from a “bonus harvest” slot limit would reduce annual predatory losses of blueback herring by up to 10%. Alternatively, a smaller bonus harvest of legal-sized striped bass could achieve reductions in consumption of up to 7%. The recreational fishery in our study area, however, may not be intense enough to realize such harvest levels.

Despite more than 250 years of development, the passage of American shad Alosa sapidissima at dams and other barriers frequently remains problematic. Few improvements in design based on knowledge of the swimming, schooling, and migratory behaviors of American shad have been incorporated into passage structures. Large-scale technical fishways designed for the passage of adult salmonids on the Columbia River have been presumed to have good performance for American shad but have never been rigorously evaluated for this species. Similar but smaller fishway designs on the East Coast frequently have poor performance. Provision of effective downstream passage for both juvenile and postspawning adult American shad has been given little consideration in most passage projects. Ways to attract and guide American shad to both fishway entrances and downstream bypasses remain marginally understood. The historical development of passage structures for American shad has resulted in assumptions and paradigms about American shad behavior and passage that are frequently unsubstantiated by supporting data or appropriate experimentation. We propose that many of these assumptions and paradigms are either unfounded or invalid and that significant improvements to American shad upstream and downstream passage can be made via a sequential program of behavioral experimentation, application of experimental results to the physical and hydraulic design of new structures, and controlled tests of large-scale prototype structures in the laboratory and field.

American shad Alosa sapidissima are in decline in their native range, and modeling possible management scenarios could help guide their restoration. We developed a density-dependent, deterministic, stage-based matrix model to predict the population-level results of transporting American shad to suitable spawning habitat upstream of dams on the Roanoke River, North Carolina and Virginia. We used data on sonic-tagged adult American shad and oxytetracycline-marked American shad fry both above and below dams on the Roanoke River with information from other systems to estimate a starting population size and vital rates. We modeled the adult female population over 30 years under plausible scenarios of adult transport, effective fecundity (egg production), and survival of adults (i.e., to return to spawn the next year) and juveniles (from spawned egg to age 1). We also evaluated the potential effects of increased survival for adults and juveniles. The adult female population size in the Roanoke River was estimated to be 5,224. With no transport, the model predicted a slow population increase over the next 30 years. Predicted population increases were highest when survival was improved during the first year of life. Transport was predicted to benefit the population only if high rates of effective fecundity and juvenile survival could be achieved. Currently, transported adults and young are less likely to successfully out-migrate than individuals below the dams, and the estimated adult population size is much smaller than either of two assumed values of carrying capacity for the lower river; therefore, transport is not predicted to help restore the stock under present conditions. Research on survival rates, density-dependent processes, and the impacts of structures to increase out-migration success would improve evaluation of the potential benefits of access to additional spawning habitat for American shad.

The Penobscot River basin, covering approximately 22,265 km², is the largest river wholly within Maine and the second largest river system in New England. The Penobscot River Restoration Project (PRRP) is a multimilliondollar endeavor that aims to restore native sea-run fish through the removal of two main-stem dams and improved fish passage at a third dam on the Penobscot River. We used geographical information systems, accounts of historic ranges, and barrier survey data to estimate species-specific distributions and habitat accessibility for 11 diadromous species before and after the proposed restoration. We predict a range of outcomes in terms of expected distribution and accessibility that are largely based on habitat use and life history differences. For 4 out of 11 species (Atlantic sturgeon Acipenser oxyrinchus, shortnose sturgeon A. brevirostrum, Atlantic tomcod Microgadus tomcod, and striped bass Morone saxatillis), the PRRP is anticipated to provide access to 100% of their historic freshwater habitat. However, for alewives Alosa pseudoharengus, approximately 69% of the historic spawning and rearing habitat will remain inaccessible due to the presence of other passage barriers. Our results demonstrate that the PRRP is an important step toward ecosystem recovery in the Penobscot River basin but that other restoration activities will be needed to realize the full potential of the PRRP, particularly for alosines. Further, our results provide the first spatial analysis of diadromous fish distribution and access following the PRRP and serve as the baseline for developing a guiding image for expected diadromous fish population responses following the dam removals.

American shad Alosa sapidissima in Atlantic coastal rivers of the New England states are affected by anthropogenic sources of mortality, such as discards of immature fish (bycatch) in various fisheries, directed fishing on prespawning adults, and the passage failure or mortality of mature fish at migratory barriers. We evaluated the relative importance of these factors, independently and in combination, by modeling the predicted lifetime spawning stock biomass of an age-1 female recruit (SSBR) with an assumed constant rate of natural mortality. Discard losses had the greatest impact on the SSBR, followed by directed fishing and upstream passage mortality, upstream passage failure (the fish survived but did not pass the barrier or spawn), and downstream losses of postspawning adults. Fishery managers strive to keep mortality rates below those that reduce SSBR to less than 30% of that of a stock with no anthropogenic mortality. In our modeling, SSBR dropped below that benchmark when bycatch rates exceeded 0.21, directed fishing or upstream passage mortality exceeded 0.45, and upriver passage failure without mortality exceeded 0.70. Since the downriver passage mortality of adults occurred after spawning, SSBR did not decline below the benchmark even at 100% downriver loss. The impacts of upstream passage mortality always exceeded those from comparable downstream passage mortality. Fishing and discard losses seriously reduced any gain in SSBR from reduced fish passage mortality or failure. The results in this paper suggest that among the anthropogenic factors evaluated, American shad in New England are most sensitive to discard losses of immature shad in ocean fisheries and that fish passage improvements at dams are most effective when they are developed in combination with reductions in fishery-related losses.

Directed commercial fisheries for American shad Alosa sapidissima in the primary Virginia tributaries of the Chesapeake Bay have been under moratorium since 1994. Monitoring of adult American shad within these rivers has been ongoing since 1998 through a cooperative program involving commercial fishers. The monitoring program is designed to mimic traditional commercial fishing practices so that stock status can be inferred by comparing contemporary catch-per-unit-effort levels with those derived from historic logbooks. In this paper, we present analyses of the available monitoring and historic catch rate data along with updated stock status information for American shad in the James, York, and Rappahannock rivers. Two analytical methods were used to derive annual indices of relative abundance; both methods yielded very similar patterns for each river system. Comparisons of contemporary and historic indices of relative abundance suggest that American shad in the James and York rivers continue to persist at low levels of abundance. Measures of stock abundance in the Rappahannock River have been higher than the logbook reference value for much of the monitoring period. However, current moratoria and restoration strategies, which include hatchery releases of fry, the removal of obstructions blocking spawning and nursery habitat, and reductions in bycatch from other fisheries, should continue into the foreseeable future.

American shad Alosa sapidissima once supported large commercial fisheries along the Atlantic coast, but by the early 1980s many of these fisheries had declined precipitously. In contrast to most Atlantic coastal rivers, the abundance of American shad in the Santee-Cooper River basin of South Carolina has grown substantially; still, much of their upstream spawning habitat in this watershed has been restricted or adversely affected by impoundments. In an effort to rebuild populations in upstream river reaches of the Santee-Cooper basin, state and federal agencies developed an approach relying on hatchery augmentation, the relocation of prespawning adults, and the construction of permanent fish passage structures. Genetic monitoring was adopted to ensure that the genetic integrity of the population remains intact during the rebuilding process. Our study provided an initial assessment of genetic diversity for the genetic monitoring program. There were three components to the study: an assessment of within-basin genetic stock structure, a comparison of genetic diversity (the number of alleles and observed heterozygosity) between hatchery and wild stocks, and an evaluation of molecular tags for monitoring hatchery returns. The estimation of genetic diversity and the assessment of molecular tags were based on 10 microsatellite loci. We found no apparent stock structure in the Santee-Cooper basin and no difference in genetic diversity between broodstock and their wild counterparts. Eight microsatellite markers provided enough resolution to successfully (>95% assignment success) match returning American shad with their respective hatchery parents. Our results highlight the utility and importance of integrating genetic information in supportive breeding programs in an effort to evaluate the programs' effectiveness (both in terms of increasing the census size and in terms of maintaining the long-term viability of a population).

It has been hypothesized that climate change is an underlying factor in determining fish abundances in the Hudson River estuary (HRE). To study the effects of hydrology and climate on the HRE fish community, we applied multivariate statistical methods to data on 20 species—life history stages collected from 1974 to 2005. We confirm that the HRE fish community has changed over this period. These changes are correlated with local hydrology (freshwater flow and water temperature) and regional climate (the Atlantic Multidecadal Oscillation [AMO] and North Atlantic Oscillation). We found that the abundances of striped bass Morone saxatilis larval stages are positively correlated with high freshwater flows and those of juvenile American shad Alosa sapidissima negatively correlated with the AMO or warmer sea surface temperatures. Our findings suggest that climate-related variability affects HRE juvenile shad abundances and that management strategies for this declining species should include the implications of climate change.

The freshwater behaviors of juvenile alewives Alosa pseudoharengus and the variables affecting their survival to recruitment are relatively unknown, even though recruitment to marine populations is critical to sustaining and restoring populations. Fish were collected in fall 2009 from a large watershed (the Hudson River, New York; N = 10) and a small watershed (the Peconic River, New York; N = 14), otolith chemistry was used to associate the fish to groups, and growth rates were compared both within and between rivers. Otolith Sr:Ca and Ba:Ca were measured along growth transects, and significant changes in these values were determined. In many instances, changes in these values are associated with changes in daily otolith growth increments. More variation was observed in the Ba: Ca ratios and daily growth rates of Hudson River alewives, possibly because they had more available nursery habitats. While there was variation in otolith chemistry and daily growth within Peconic River fish, fewer otolith chemistry patterns were observed in this group. Comparison of cumulative daily growth rates between the two groups showed that Hudson River alewives were smaller at younger ages but that their growth rate increased and their size at age eventually surpassed that of the Peconic River alewives. The results presented here provide the foundation for future work investigating the abiotic and biotic variables influencing juvenile alewife growth, behavior, and survival in different-size watersheds.

We used δ¹⁸O signatures in otoliths as a natural tag for hatch year to evaluate the scale-based age determination method used for adult American shad Alosa sapidissima in the York River, Virginia. Juveniles of the 2002 year-class exhibited high δ¹⁸O values in otolith cores that identified adult members of the cohort as they returned to spawn. Recruitment of the 2002 cohort was monitored for three consecutive years, identifying age-4, age-5, and age-6 individuals of the York River stock. The scale-based age determination method was not suitable for aging age-4, age-5, or age-6 American shad in the York River. On average, 50% of the individuals from the 2002 year-class were aged incorrectly using the scale-based method. These results suggest that the standard age determination method used for American shad is not applicable to the York River stock. Scientists and managers should use caution when applying scale-based age estimates to stock assessments for American shad in the York River and throughout their range, as the applicability of the scale-based method likely varies for each stock. This study highlights a promising new direction for otolith geochemistry to provide cohort-specific markers, and it identifies several factors that should be considered when applying the technique in the future.

Over the past two decades, declines in the populations of river herring (alewife Alosa pseudoharengus and blueback herring Alosa aestivalis) have been documented across both species' ranges. Information concerning the natal origins of spawning adult fish could aid in their restoration but has been unattainable. We investigated the efficacy of otolith microchemistry for identifying the natal environment of alewife and blueback herring in Connecticut. In both 2008 and 2009, water and juvenile and adult fish were sampled from 10 sites across the state. The relationships between water and otolith Sr: Ca ratios differed for alewives and blueback herring, necessitating the development of separate classification models for assigning individuals to capture locations. Reclassification of age-0 alewives to their site of origin was variable (50–100%) but demonstrated that age-0 fish could be accurately reclassified to their natal environment at some sites. Discriminant function reclassification rates to site of capture for adult alewives varied greatly (10–85%); the similarity of water chemical signatures among many sites likely contributed to the relatively low rates of assignment to the majority of collection locations. Adult blueback herring reclassification rates were low (15–33%) for three of four collection sites, probably due to overlapping elemental signatures. Blueback herring collected at the fourth site had a distinct signature and a reclassification rate (81 %) comparable to that of the highest alewife rate. Changes in Sr: Ca and Ba: Ca ratios across sectioned otoliths suggested a higher degree of movement across salinity boundaries during the first year of life than previously documented for anadromous alewives and blueback herring. Otolith microchemistry may be a useful tool with which to investigate alewife and blueback herring natal homing and life history, but its utility appears to be confined to particular sites with unique signatures or to broader regional assignments of natal origin.

The need to protect imperiled salmon stocks along the Pacific coast of North America has led to an increasing use of mark-selective fisheries (MSFs) as a management strategy to reduce harvest mortality of wild salmon while allowing harvest of abundant hatchery salmon. However, MSFs remain untested in ocean fisheries for Chinook salmon Oncorhynchus tshawytscha off the coasts of California and Oregon, where hatchery fish have been estimated to compose the majority of Chinook salmon but where harvests have been restricted to protect several imperiled stocks. We developed a quantitative framework based on conventional cohort models to examine how aggregate ocean harvest and in-river escapement of Sacramento River fall-run Chinook salmon, the numerically dominant stock in the region, would have differed under MSF scenarios compared with the historic, traditional fishery. At historic contact rates (fishing effort) for 1988–2007, we estimated that annual in-river escapement of natural-origin fish would have increased by 119% on average under MSF scenarios, while reductions in harvest would have been inversely proportional to the fraction of hatchery-origin fish. During the more recent period of constrained fishing (2001–2007), we estimated MSF outcomes for a range of plausible contact rates (40–60% of age-4 fish) and hatchery fractions (40–80% of Chinook salmon). The combination of these factors determined the magnitude of estimated harvest reductions or gains under MSFs, with total MSF harvest (2001–2007) ranging from 46% lower to 48% higher than historic harvest. Increases in total escapement of natural-origin fish (2001–2007) under MSFs ranged from 24% to 48% depending on the contact rate. Comparisons between the traditional fishery and simulated MSF outcomes were robust to a wide range of cohort parameter values, suggesting that our aggregate results provide useful insights into potential MSF outcomes and the effects of key uncertainties.

The black sea bass Centropristis striata is a commercially important perciform fish with a general distribution along the U.S. Atlantic coast from Cape Cod, Massachusetts, to Cape Canaveral, Florida, and in the Gulf of Mexico from Mobile Bay, Alabama, to Tampa Bay, Florida. Currently, black sea bass are managed as three separate stocks: one in the Gulf of Mexico and two along the U.S. Atlantic coast. Fish from the Gulf of Mexico represent a separate sub-species, C. striata melana. The Atlantic subspecies, C. striata striata, is divided into two management units (separated at Cape Hatteras, North Carolina) based on the hypothesis that this subspecies comprises two distinct populations exhibiting life history and morphometric differences. To further investigate this differentiation, we employed mitochondrial sequence data to test whether genetic differences are observed among the three managements units. The DNA sequence analysis revealed a significant amount of genetic variability partitioned among samples from the three management areas. Similar results were observed when the analyses were confined to the two Atlantic coast management units. These results support the designation of two distinct management units for black sea bass along the U.S. Atlantic coast.

Trawl studies from 1998 to 2009 indicated that juvenile Pacific salmon Oncorhynchus spp. and Pacific herring Clupea pallasii represented 98 % of the fish in the surface waters of the Strait of Georgia during the day in the spring and early summer. Standardized catches of all juvenile Pacific salmon in the trawl surveys were lowest in 2007. Catches of young-of-the-year Pacific herring were also extremely low in 2007. Three years later, the 2007 year-class had the lowest recruitment to the fishery in recorded history. In 2007, juvenile coho salmon O. kisutch and Chinook salmon O. tshawytscha were small and had the lowest condition of the fish in all surveys as well as a high percentage of empty stomachs. The early marine survival of coho salmon in 2007 and the total survival in 2008 were exceptionally poor. Trawl catches of juvenile chum salmon O. keta in 2007 were the lowest of all surveys. Adult chum salmon from these juveniles that returned in 2010 had extremely poor survival. Juvenile sockeye salmon O. nerka that entered the Strait of Georgia in the spring of 2007 and returned to the Fraser River as adults in 2009 also had such exceptionally poor marine survival that a judicial inquiry was conducted to determine the causes. The synchronous poor growth, survival, or both of all of the major species in the surface waters of the Strait of Georgia in the spring of 2007 indicated that there was a common cause which we propose as poor food production. The causes of the high mortality likely represented a unique extreme in the variability of the factors that normally affect the survival of juvenile Pacific salmon and Pacific herring in the early marine period in the Strait of Georgia.

Record low returns of sockeye salmon Oncorhynchus nerka to the Fraser River in 2009 were followed by record high returns to the river in 2010, providing an unprecedented opportunity to examine links between oceanic factors and the survival of Pacific salmon stocks. The low returns in 2009 indicated poor early marine survival of juvenile sockeye salmon in 2007. The poor survival was likely due to low food levels arising from unfavorable wind and runoff conditions in the Strait of Georgia and the Queen Charlotte Sound-Hecate Strait region in the spring of 2007. Conversely, the high returns in 2010 were associated with a large smolt output from the Fraser River and good early marine survival in 2008. This enhanced survival was likely associated with adequate food levels arising from favorable oceanic conditions in the Strait of Georgia and the Queen Charlotte Sound-Hecate Strait region in the spring of 2008. We speculate that ocean factors during the subsequent marine years also affected brood year strength. Specifically, the back-to-back La Nina winters of 2007–2008 and 2008–2009 would have negatively influenced the survivability of the 2007 entry stocks, while the El Niño winter of 2009–2010 would have positively affected the survivability of the 2008 entry stocks. We conclude that poor early marine survival leads to low production. However, if large numbers of healthy fish survive the early marine entry, and if conditions during at least one of the two ocean winters in the Gulf of Alaska are favorable to stock survivability, then returns to the river can be high.

Mortality in the early marine period in a particular habitat is related to the severity of the factors causing mortality and the time that juvenile Pacific salmon Oncorhynchus spp. spend in the habitat. Juvenile sockeye salmon O. nerka produced in the Fraser River rear in the Strait of Georgia immediately upon leaving freshwater. We used catches from trawl and purse seine surveys to develop two estimates of their average residence time in the Strait of Georgia and present a third estimate which pertains to Chilko Lake smolts in particular. The average time between the entry of the last 1% of juvenile sockeye salmon into the Strait of Georgia and the departure of the last juveniles was 54 d. The average time between the point when the maximum number of juvenile sockeye salmon entered the Strait of Georgia and the point when the maximum abundance in the strait occurred was 43 d. Individuals from the Chilko Lake population were shown to spend a minimum of 31–43 d in the Strait of Georgia, indicating that an average residence time of about 43–54 d is plausible.

We monitored fish assemblages monthly at estuarine and tidal freshwater sites in the lower Columbia River and estuary from January 2002 through September 2007 in order to identify specific salmon stocks and migration stages that may benefit from habitat restoration initiatives. We report landscape-scale and seasonal variation in abundance, size, hatchery production (based on adipose fin clips), and genetic stock of origin of juvenile Chinook salmon Oncorhynchus tshawytscha. From fish implanted with coded wire tags (CWTs), we also determined the sites of release and inferred migration patterns. Chinook salmon were found in diverse life history stages and forms, including fry migrants, fingerlings, and (fewer) yearlings. Abundance increased in February and decreased in August, but salmon were present in all months each year. Spatial gradients in abundance and size were strong, with fewer but larger fish in brackish than in tidal freshwater zones. Overall, 30% of the Chinook salmon measured were fry (≤60 mm) that were likely naturally produced fish. These occurred at higher mean monthly proportions in tidal freshwater than in estuarine zones. In contrast, most larger fish were probably raised in hatcheries. Genetic stock assessment revealed that the majority of the Chinook salmon analyzed were from fall-run stock groups originating in the lower Columbia River, with 15% originating from other stock groups. Of these minority contributors, about 6% were identified as upper Columbia River summer-fall-run Chinook salmon while seven other stock groups accounted for the remainder, including 3% from transplants originating in southern Oregon's Rogue River. Recaptures of tagged fish revealed maximum migration times of 143 d for subyearlings and 52 d for yearlings, and both CWT and genetic data indicated that fall Chinook salmon from coastal rivers occasionally entered the estuary. These data demonstrated a widespread temporal and spatial distribution of subyearling Chinook salmon in shallow-water habitats of the lower Columbia River and estuary.

In 2003, the U.S. distinct population segment of small tooth sawfish Pristis pectinata was listed as endangered under the U.S. Endangered Species Act (ESA). At that time, little was known about its habitat use patterns and, although required as part of the ESA, critical habitat could not be officially designated. Subsequently, studies were conducted that identified some of the specific habitats and environmental conditions important for the species. Facilitating recruitment into the adult population by protecting the species' nurseries was identified in the recovery plan as the key conservation objective, which would be supported by the designation of critical habitat. The location of nurseries was determined by applying published criteria developed for identifying elasmobranch nursery areas to a decade of encounter data. These largely nontraditional data were composed primarily of encounters voluntarily reported by the public to members of the recovery team. The nursery habitats essential to the conservation of the species were identified as those adjacent to red mangroves Rhizophora mangle and euryhaline habitats with water depths ≤0.9 m. Ultimately, two broad areas in southwest Florida that contain these habitats were designated as critical habitat for juvenile smalltooth sawfish: the Charlotte Harbor Estuary unit (896 km²) and the Ten Thousand Islands/Everglades unit (2,505 km²).

Finfish abundance indices, produced from seasonal trawl survey data collected in Long Island Sound, were examined for changes in community composition related to the dynamics of water temperature from 1984 to 2008. In general, seasonal mean catch of species identified a priori as cold adapted significantly decreased while warm-adapted and subtropical species significantly increased over the time series. Bottom water temperature also significantly increased. As a group, annual abundance of cold-adapted species exhibited significant negative correlation with mean bottom water temperatures while warm-adapted species, but not subtropical species, exhibited significant positive correlation. Multivariate analyses identified a shift in community structure producing two primary year-groupings. Spring groupings were clearly delineated as 1984–1998 (cold period) and 1999–2008 (warm period). Autumn groupings were temporally discontinuous in the 1990s with group membership shifting between cold and warm periods, although the distal ends of the time series were clearly divided. These patterns aligned with deviations from the 1984 to 2008 mean bottom water temperature, indicating that this estuary is experiencing a relatively rapid shift consistent with a response to climate warming. The more distinct delineation of community structure in spring suggests that the lack of advantageous spring conditions was a more important factor in the decline of cold-adapted species than increasingly stressful conditions in autumn.

The ecosystem approach is being promoted as the foundation of solutions to the unsustainability of fisheries. However, because the ecosystem approach is broadly inclusive, the science for its implementation is often considered to be overly complex and difficult. When the science needed for an ecosystem approach to fisheries is perceived this way, science products cannot keep pace with fisheries critics, thus encouraging partisan political interference in fisheries management and proliferation of “faith-based solutions. In this paper we argue that one way to effectively counter politicization of fisheries decision-making is to ensure that new ecosystem-based approaches in fisheries are viewed only as an emergent property of innovation in science and policy. We organize our essay using three major themes to focus the discussion: empirical, jurisdictional, and societal challenges. We undertake at least partial answers to the following questions: (1) has conventional fisheries management really failed?; (2) can short-comings in conventional fisheries management be augmented with new tools, such as allocation of rights?; (3) is the Ecosystem Approach to Fisheries (EAF) equivalent to Ecosystem-Based Management?; and (4) is restoration of degraded ecosystems a necessary component of an EAF?

Marine protected areas (MPAs) are increasingly used as a tool in fisheries management. However, implementation of an MPA violates common assumptions for fishery stock assessments that provide estimates of abundance and fishing mortality for management. Thus, it is important to understand the effects of MPAs on estimates from stock assessments. We conducted a simulation study to determine the effects of MPAs on accuracy of surplus production model (SPM) stock assessments. We simulated the dynamics of a population that had part of its range in an MPA, and we assessed the population with spatially aggregated and spatially explicit SPMs under a range of conditions, including different MPA sizes (percentage of the total stock area), different rates of migration between MPA and non-MPA regions, and scenarios with high and low observation error in the indices of abundance. We also considered a scenario in which there was no available index of abundance within the MPA. We used the median of the absolute value of relative error and the median relative error from 200 replicates/scenario to test SPM accuracy. In most cases, spatially explicit SPMs performed better in both accuracy and bias than spatially aggregated SPMs. The accuracy of the assessments also increased as MPA size increased except under the scenario of no index of abundance within the MPA; for that scenario, accuracy increased as MPA size decreased. Monitoring of the stock within the MPA is essential for conducting accurate stock assessments in areas with MPAs.

This study identifies important trophic links for epipelagic marine fish predators in Southeast Alaska to improve understanding of marine ecosystem dynamics in response to climate change. Fish predators can be viewed as autonomous samplers whose diets should integrate the available prey taxa commensurate with environmental conditions. We examined fish predators from annual (1997–2011) surveys conducted in May to September by the Southeast Coastal Monitoring (SECM) project of Auke Bay Laboratories in the marine waters of Southeast Alaska. This project has emphasized long-term monitoring of strait and coastal marine habitats used by juvenile Pacific salmon Oncorhynchus spp. and associated epipelagic fishes to understand how environmental variation affects the sustainability of salmon resources. From 1,295 surface trawl hauls, trophic links were identified for 2,473 fish representing 19 predator species, principally adult and immature salmon, immature walleye pollock Theragra chalcogramma, and spiny dogfish Squalus acanthias. The most common fish prey consumed were fish larvae, juvenile salmon, Pacific herring Clupea pallasii, capelin Mallotus villosus, walleye pollock, lanternfishes (Myctophidae), and Pacific sand lance Ammodytes hexapterus, whereas the most common invertebrate prey consumed were euphausiids, decapod larvae, pteropods, and amphipods. This study describes the degree of piscivory, incidence of juvenile salmon prey, and frequency and weight composition of prey in the diets of epipelagic fish predators, but it did not clearly detect an effect of warm-versus-cold climate years on the diets of key planktivorous or piscivorous predators over the 15-year time series. Identifying the persistence of trophic links in epipelagic waters over time is important because climate-related changes in the upper water column have the potential to impact Southeast Alaska marine ecosystem dynamics and the productivity of important regional fisheries by altering key prey resources and trophic interactions.

The application of ecosystem-based approaches in fisheries management has been limited by a lack of empirical data for quantifying the ecological interactions among many common and valuable fishery species. The red drum Sciaenops ocellatus, a large, carnivorous member of estuarine communities, is experiencing population recovery throughout its range in the U.S. South Atlantic and Gulf of Mexico. Using a field-based approach, we determined seasonal and ontogenetic variation in the contribution of valuable fishery resource species to red drum diets, estimated red drum daily ration, and quantified per capita and population-level predation by juvenile and subadult red drum in a North Carolina estuarine system. Despite seasonal, interannual, and ontogenetic variation in diet composition, red drum fed mainly on macrocrustaceans and juvenile fishes, including several economically important resource species (e.g., blue crab Callinectes sapidus, penaeid shrimp, and Atlantic menhaden Brevoortia tyrannus). Both juvenile and subadult red drum demonstrated strong diel feeding patterns, with peak feeding occurring during the hours just after dark. Gastric evacuation rates during periods of declining gut fullness were estimated on seven sampling dates and produced mean daily ration estimates between 1.2% and 3.4% of predator mass depending on age-group. Combining field-observed red drum growth rates with published laboratory estimates of gross growth efficiency suggested that our estimates of daily ration were likely biased low. During the seasonal period of rapid growth, the aggregate consumption of blue crabs, penaeid shrimp, and Atlantic menhaden by juvenile and subadult red drum in North Carolina waters was estimated at 3.4 × 10⁶ to 5.1 × 10⁶ kg/year.

The reproductive parameters of 1,194 sandbar sharks Carcharhinus plumbeus (701 females, 493 males) were examined for stock assessment. Size and age at 50% maturity was 151.6 cm FL (12.1 years) for males and 154.9 cm (13.1 years) for females; however, the size and age at which 50% of females were in maternal condition was 162.0 cm FL (15.5 years). Males and females showed distinct seasonal reproduction patterns, with peak mating and parturition occurring from April through July. The majority of near-term pregnant and postpartum females were observed in the Florida Keys, which is an extension of the previously reported nursery grounds for sandbar sharks in the western North Atlantic Ocean. Female fecundity averaged 8.0 pups, and there was a significant increase in fecundity with length and age. The ovarian cycle is at least biennial, although there is evidence that some females have triennial cycles.

Critical habitats for fish and wildlife are often small patches in landscapes, e.g., aquatic vegetation beds, reefs, isolated ponds and wetlands, remnant old-growth forests, etc., yet the same animal populations that depend on these patches for reproduction or survival can be extensive, ranging over large regions, even continents or major ocean basins. Whereas the ecological production functions that support these populations can be measured only at fine geographic scales and over brief periods of time, the ecosystem services (benefits that ecosystems convey to humans by supporting food production, water and air purification, recreational, esthetic, and cultural amenities, etc.) are delivered over extensive scales of space and time. These scale mismatches are particularly important for quantifying the economic values of ecosystem services. Examples can be seen in fish, shellfish, game, and bird populations. Moreover, there can be wide-scale mismatches in management regimes, e.g., coastal fisheries management versus habitat management in the coastal zone. We present concepts and case studies linking the production functions (contributions to recruitment) of critical habitats to commercial and recreational fishery values by combining sitespecific research data with spatial analysis and population models. We present examples illustrating various spatial scales of analysis, with indicators of economic value, for recreational Chinook Oncorhynchus tshawytscha salmon fisheries in the U.S. Pacific Northwest (Washington and Oregon) and commercial blue crab Callinectes sapidus and penaeid shrimp fisheries in the Gulf of Mexico.

Age-0 red snapper Lutjanus campechanus from the 2005–2007 year-classes were sampled in six regions across the Gulf of Mexico (Gulf) to develop nursery signatures from otolith element : Ca ratios (Ba:Ca, Mg:Ca, Mn:Ca, Sr:Ca, and Li:Ca) and stable isotope delta values (δ¹³C and δ¹⁸O). Element : Ca ratios were analyzed with sector field inductively coupled plasma mass spectrometry on dissolved right sagittae; isotope ratio mass spectrometry was employed to analyze pulverized left otoliths for δ¹³C and δ¹⁸O. Otolith chemical signatures were significantly different among regions in each year. Year-class-specific quadratic discriminant function analysis (QDFA) distinguished nursery regions with an accuracy of 82% for 2005, 70% for 2006, and 72% for 2007. However, samples were not obtained from all six study regions in 2005 and 2006. A QDFA of all year-classes combined produced an overall classification accuracy of 70%, thus indicating that region-specific otolith chemical signatures from adjacent sampling years could be used as surrogates for regions where samples were not obtained in a given year.

Fecundity estimates used in a 2004 stock assessment to evaluate the overall health of the population of California sheephead Semicossyphus pulcher were based primarily on two studies. The first estimated the total fecundity of only nine individuals captured near Santa Catalina Island, California, and the second estimated batch fecundity of individuals taken from only one artificial reef. In order to develop a current and more comprehensive estimate of fecundity, we collected California sheephead from seven locations off southern California throughout the spawning season (July through September). To estimate both total fecundity and batch fecundity, we categorized and counted oocytes from ovarian subsamples of 28 and 24 (respectively) mature females (stage 3, spawning capable; determined by histological analysis). Total and batch fecundity increased with somatic mass, standard length, and ovary mass. We found total fecundity to increase with somatic mass to a power of 5.5, which is considerably greater than the value (2.95) reported previously. Our observations therefore highlight the importance of large females in the reproductive potential of the California sheephead stock. Regression analysis indicates that ovary mass is the most accurate biological indicator of fecundity for California sheephead and should be used for subsequent stock analyses.

Central to ecology and resource management is knowledge of the spatiotemporal scales at which demographic rates vary and the ecological consequences of demographic variation, such as that due to density dependence. We quantified the spatiotemporal variation in eastern oyster Crassostrea virginica recruitment, density, growth, and survival and assessed density dependence within a network of no-take reserves in Pamlico Sound, North Carolina. From 2006 to 2008, average oyster recruitment and total density increased 15- and fivefold, respectively. The unprecedentedly high oyster densities in certain reserves (up to 6,500/m² at the end of the study) modified demographic rates such that further density increases were regulated by density-dependent survival. Oyster demographic rates varied significantly among reserves at relatively small spatial scales (20 km). Certain reserves were the strong “recruiters,” others the fast “growers,” and yet others the high “survivors.” Cohort dynamics altered the demographic rank order such that the demographically “best” reserves varied intra- and interannually. From a management perspective, the prevalence of density-dependent survival suggests that the oysters in this system are habitat rather than recruitment limited, which may minimize the utility of stock enhancement programs. Addition of habitat (i.e., artificial reefs) should focus on reserves characterized by high recruitment but density-dependent growth and survival. This study (1) supports the efficacy of marine reserves in rapidly increasing the density and age—size structure of protected species, (2) highlights the need for spatially explicit demographic data to support multifaceted management objectives, and (3) when combined with evidence of reserve larval connectivity, provides support for applying metapopulation concepts to this reserve system.

For fish stocks managed using biological reference points based upon spawning biomass, it is critical to have accurate maturity schedules. We investigated size- and age-dependent patterns in maturity for southern flounder Paralichthys lethostigma, a flatfish supporting valuable coastal fisheries in North Carolina and throughout its range. We evaluated both macroscopic and histological methods over two consecutive reproductive seasons. Histological analyses revealed that maturity occurred at larger sizes and older ages than previously estimated. Length at 50% maturity (L₅₀) was estimated at 408 mm total length (TL), which was more than 60 mm larger than currently assumed, and was relatively stable between study years. We found that only 44% of age-1 southern flounder were mature compared with an estimated 74% in an earlier study. We suspect that most of the differences in maturity timing of southern flounder between our findings and previous studies stem from macroscopic assignment error. During this study, only 61% of fish staged macroscopically as developing were found to be mature based on histological analysis. Assuming incorrectly that all of these fish were mature would have resulted in an L₅₀ of 375 mm TL, which is closer to previous estimates. Analysis of spawning stock biomass per recruit demonstrated that biological reference points (e.g., F_SPR) could be affected considerably by shifting maturity schedules, and the effects could be magnified at larger sizes at entry and higher harvest rates. Given the life history strategy of southern flounder and the lack of a developed offshore fishery or sampling program, which combine to prevent access to fish on the spawning grounds, it is probably most judicious to routinely analyze reproductive tissue samples histologically to ensure accurate information on the timing of maturity.

To support the growing interest in marine fisheries research in areas such as biotelemetry, tagging, and tracking, we assessed the ability of various sedatives to facilitate this research in juvenile cobias Rachycentron canadum (∼300 g), namely, tricaine methanesulfonate (MS-222; 150 mg/L), carbon dioxide (CO₂; ∼750 mg/L), eugenol (60 mg/L), benzocaine (150 mg/L), and pulsed-DC electrosedation (100 V, 30 Hz, 25% duty cycle, 5-s exposure). Induction times (CO₂ [z] > benzocaine [y] > eugenol [y] > MS-222 [y] > electrosedation [x]), recovery of equilibrium (CO₂ [z] > eugenol [z] > MS-222 [y] > benzocaine [y] > electrosedation [x]), and responsiveness to tactile stimulus (eugenol [z] > MS-222 [y] > benzocaine [y] > CO₂ [xy] > electrosedation [x]) differed significantly among the sedative treatments (treatments with the same letters are not significantly different). Total handling time from initial sedative exposure to recovery differed among the sedatives as well (CO₂ [z] > eugenol [y] > benzocaine [x] > MS-222 [x] > electrosedation [w]), with cumulative means ± SEs of 5.9 ± 0.2 min for CO₂, 4.1 ± 0.2 for eugenol, 2.7 ± 0.2 min for benzocaine and MS-222, and 1.0 ± 0.2 min for electrosedation. Physiological responses differed significantly over time, with transient increases in plasma Cortisol, glucose, osmolality, and lactate that were resolved within 6 h. The overall magnitude of the physiological responses differed among sedatives, depending on the response variable; however, in each case, CO₂ elicited the greatest response. Although variations in induction and recovery times were observed, it is likely that these differences can be reasonably accommodated within the context of typical research by adjusting the sedative treatments or allowing for longer induction and recovery times as needed.

A standard dual-frequency identification sonar (DIDSON) was deployed in the Herring River, Harwich, Massachusetts, for 3 d in late April 2011 to capture video-like images of migrating adult river herring (alewife Alosa pseudoharengus and blueback herring Alosa aestivalis). Images recorded 24 h a day were used to manually count and assign species based on DIDSON images of fish size, shape, and behavior. From these counts, the run size was estimated to be 1,976–2,059 individuals during the study. At first, river herring often hesitated to swim through the sample area where the weirs and DIDSON were deployed; however, they eventually did pass, often multiple times. This unique hesitation behavior complicated counting efforts, though it was beneficial to discerning species using DIDSON images. In addition, extremely shallow water upstream of the study site, lack of tree cover, and a high threat of avian predation likely contributed to river herring milling activity at the study site. By providing many clear images of river herring, DIDSON proved to be an effective type of sonar with which to monitor and count river herring continuously in a small coastal stream.