Shifts in the estuarine demersal fish community after a fishery closure in Puget Sound, Washington

Puget Sound is one of the largest and most ecologically significant estuaries in the United States, but the status and trends of many of its biological components are not well known. We analyzed a 21-year time series of data from standardized bottom trawl sampling at a single study area to provide the first assessment of population trends of Puget Sound groundfishes after the closure of bottom trawl fisheries. The expected increase in abundance was observed for only 3 of 14 species after this closure, and catch rates of most (10) of the abundant species declined through time. Many of these changes were stepwise (abrupt) rather than gradual, and many stocks exhibited changes in catch rate during the 3-year period from 1997 through 2000. No detectable change was recorded for either temperature or surface salinity over the entire sampling period. The abrupt density reductions that were observed likely do not reflect changes in demographic rates but may instead represent distributional shifts within Puget Sound.

Food habits of Sowerby's beaked whales (Mesoplodon bidens) taken in the pelagic drift gillnet fishery of the western North Atlantic

We describe the food habits of the Sowerby’s beaked whale (Mesoplodon bidens) from observations of 10 individuals taken as bycatch in the pelagic drift gillnet fishery for Swordfish (Xiphias gladius) in the western North Atlantic and 1 stranded individual from Kennebunk, Maine. The stomachs of 8 bycaught whales were intact and contained prey. The diet of these 8 whales was dominated by meso- and benthopelagic fishes that composed 98.5% of the prey items found in their stomachs and cephalopods that accounted for only 1.5% of the number of prey. Otoliths and jaws representing at least 31 fish taxa from 15 families were present in the stomach contents. Fishes, primarily from the families Moridae (37.9% of prey), Myctophidae (22.9%), Macrouridae (11.2%), and Phycidae (7.2%), were present in all 8 stomachs. Most prey were from 5 fish taxa: Shortbeard Codling (Laemonema barbatulum) accounted for 35.3% of otoliths, Cocco’s Lanternfish (Lobianchia gemellarii) contributed 12.9%, Marlin-spike (Nezumia bairdii) composed 10.8%, lanternfishes (Lampanyctus spp.) accounted for 8.4%; and Longfin Hake (Phycis chesteri) contributed 6.7%. The mean number of otoliths per stomach was 1196 (range: 327–3452). Most of the fish prey found in the stomachs was quite small, ranging in length from 4.0 to 27.7 cm. We conclude that the Sowerby’s beaked whales that we examined in this study fed on large numbers of relatively small meso- and benthopelagic fishes that are abundant along the slope and shelf break of the western North Atlantic.

Population genetics of Cobia (Rachycentron canadum): implications for fishery management along the coast of the southeastern United States

Cobia (Rachycentron canadum) is a pelagic, migratory species with a transoceanic distribution in tropical and subtropical waters. Recreational fishing pressure on Cobia in the United States has increased substantially during the last decade, especially in areas of its annual inshore aggregations, making this species potentially susceptible to overfishing. Although Cobia along the Atlantic and Gulf coasts of the southeastern United States are currently managed as a single fishery, the genetic composition of Cobias in these areas is unclear. On the basis of a robust microsatellite data set from collections along the U.S. Atlantic coast (2008–09), offshore groups were genetically homogenous. However, the 2 sampled inshore aggregations (South Carolina and Virginia) were genetically distinct from each other, as well as from the offshore group. The recapture of stocked fish within their release estuary 2 years after release indicates that some degree of estuarine fidelity occurs within these inshore aggregations and supports the detection of their unique genetic structure at the population level. These results complement the observed high site fidelity of Cobias in South Carolina and support a recent study that confirms that Cobia spawn in the inshore aggregations. Our increased understanding of Cobia life history will be beneficial for determining the appropriate scale of fishery management for Cobia.

Co-occurrence of bycatch and target species in the groundfish demersal trawl fishery of the U.S. west coast; with special consideration of rebuilding stocks

Bycatch and resultant discard mortality are issues of global concern. The groundfish demersal trawl fishery on the west coast of the United States is a multispecies fishery with significant catch of target and nontarget species. These catches are of particular concern in regard to species that have previously been declared overfished and are currently rebuilding biomass back to target levels. To understand these interactions better, we used data from the West Coast Groundfish Observer Program in a series of cluster analyses to evaluate 3 questions: 1) Are there identifiable associations between species caught in the bottom trawl fishery; 2) Do species that are undergoing population rebuilding toward target biomass levels (“rebuilding species”) cluster with targeted species in a consistent way; 3) Are the relationships between rebuilding bycatch species and target species more resolved at particular spatial scales or are relationships spatially consistent across the whole data set? Two strong species clusters emerged—a deepwater slope cluster and a shelf cluster—neither of which included rebuilding species. The likelihood of encountering rebuilding rockfish species is relatively low. To evaluate whether weak clustering of rebuilding rockfish was attributable to their low rate of occurrence, we specified null models of species occurrence. Results indicated that the ability to predict occurrence of rebuilding rockfish when target species were caught was low. Cluster analyses performed at a variety of spatial scales indicated that the most reliable clustering of rebuilding species was at the spatial scale of individual fishing ports. This finding underscores the value of spatially resolved data for fishery management.

Estimating overall fish bycatch in U.S. commercial fisheries

Bycatch, or the unintended capture of fish, marine mammals, sea turtles, and seabirds by fishing gear, occurs to some degree in most fisheries. The recently released National Marine Fisheries Service’s (NMFS) U.S. National Bycatch Report provides information on bycatch in U.S. commercial fisheries by fishery and species. The report also provides national statistics in the form of national bycatch ratio and a national bycatch estimate. We describe the methods used to develop these statistics and compare them to similar studies. We conclude that the national bycatch ratio and national bycatch estimates developed by NMFS represent the best available information on bycatch in U.S. fisheries. However, given changes in bycatch management over time, as well as inter-annual variability in bycatch levels and a high percentage of fisheries for which data on bycatch are not currently available, we recommend that NMFS continue to support bycatch data collection and reporting efforts to improve the quality and quantity of bycatch data and estimates available to fisheries managers and scientists over time. This will enable NMFS to meet its requirements for bycatch reporting under the Magnuson-Stevens Act (MSA), as well as requirements for bycatch minimization under the MSA, Marine Mammal Protection Act, and Endangered Species Act.

Protocols for conducting dolphin capture-release health assessment studies

Marine mammals, such as dolphins, can serve as key indicator species in coastal areas by reflecting the effects of natural and anthropogenic stressors. As such they are often considered sentinels of environmental and ecosystem health (Bossart 2006; Wells et al. 2004; Fair and Becker 2000). The bottlenose dolphin is an apex predator and a key component of many estuarine environments in the southeastern United States (Woodward-Clyde Consultants 1994; SCDNR 2005). Health assessments of dolphins are especially critical in areas where populations are depleted, show signs of epidemic disease and/or high mortality and/or where habitat is being altered or impacted by human activities. Recent assessments of environmental conditions in the Indian River Lagoon, Florida (IRL) and the estuarine waters surrounding Charleston, South Carolina (CHS) highlight the need for studies of the health of local bottlenose dolphins. While the condition of southeastern estuaries was rated as fair in the National Coastal Condition Report (U.S. EPA 2001), it was noted that the IRL was characterized by poorer than expected benthic communities, significant sediment toxicity and increased nutrient concentrations. Similarly, portions of the CHS estuary have sediment concentrations of aliphatic aromatic hydrocarbons, select inorganic metals, and some persistent pesticides far in excess of reported bioeffect levels (Hyland et al. 1998). Long-term trends in water quality monitoring and recent scientific research suggest that waste load assimilation, non-point source runoff impacts, contaminated sediments, and toxic pollutants are key issues in the CHS estuary system. Several ‘hot spots’ with high levels of heavy metals and organic compounds have been identified (Van Dolah et al. 2004). High concentrations of anthropogenic trace metals, polychlorinated biphenyls (PCB’s) and pesticides have been found in the sediments of Charleston Harbor, as well as the Ashley and Cooper Rivers (Long et al. 1998). Two superfund sites are located within the CHS estuary and the key contaminants of concern associated with these sites are: polycyclic aromatic hydrocarbons (PAH), lead, chromium, copper, arsenic, zinc and dioxin. Concerns related to the overall health of IRL dolphins and dermatologic disease observed in many dolphins in the area (Bossart et al. 2003) initiated an investigation of potential factors which may have impacted dolphin health. From May-August 2001, 35 bottlenose dolphins died in the IRL during an unusual mortality event (MMC 2003). Many of these dolphins were diagnosed with a variety of skin lesions including proliferative ulcerative dermatitis due to protozoa and fungi, dolphin pox and a vesicular dermatopathy of unknown etiology (Bossart et al. 2003). Multiple species from fish to dolphins in the IRL system have exhibited skin lesions of various known and unknown etiologies (Kane et al. 2000; Bossart et al. 2003; Reif et al. 2006). On-going photo-identification (photo-ID) studies have documented skin diseases in IRL dolphins (Mazzoil et al. 2005). In addition, up to 70% of green sea turtles in the IRL exhibit fibropapillomas, with the highest rates of occurrence being seen in turtles from the southern IRL (Hirama 2001).

A pilot study to determine the movements of buoy line used in the crab pot fishery to assess bottlenose dolphin entanglement

A pilot study on the characteristics of crab pot buoy line movements to assess bottlenose dolphin entanglement was conducted from 19 September to 30 September 2005 in the Charleston Harbor, Charleston, South Carolina. The objectives of this study were to determine: 1) the movements of the buoy line in the water at various tidal stages, current strengths, lengths of line, and water depth, 2) if lead-core rope was a better alternative to nylon rope, 3) and if the manner of deployment of the gear affected the suspension of the line in the water and on the bottom. Diamond braided nylon (#10) rope of varying length (20 ft. – 80 ft.) were used during 31 trials and stiffened (polypropylene lead-core) rope was used in four trials. Observations of the buoy line movements were captured with an Atlantis underwater camera attached to a Digital DPC-1000 video recorder. Results from this study showed that: 1) the method used for deployment was important in keeping the buoy line from arcing or coiling, 2) little to no arcing occurred in water current velocities of >0.20 m/s, 3) rope lengths of ≥50 ft. deployed in <10 ft. of water produced waving in the water column and arcing on the bottom, 4) slack tide was a period of increased risk of entanglement for bottlenose dolphins, and 5) poly lead-core rope was not a good alternative to nylon rope unless in deep water with strong water current velocities. This pilot study produced questions that can be used for future studies on the characteristics of buoy line movements in the crab pot fishery as it relates to bottlenose dolphin entanglements.

Integration of fisheries acoustics surveys and bathymetric mapping to characterize midwater-seafloor habitats of US Virgin Islands and Puerto Rico (2008-2010)

NOAA’s Coral Reef Conservation program (CRCP) develops coral reef management priorities by bringing together various partners to better understand threats to coral reef ecosystems with the goal of conserving, protecting and restoring these resources. Place-based and ecosystem-based management approaches employed by CRCP require that spatially explicit information about benthic habitats and fish utilization are available to characterize coral reef ecosystems and set conservation priorities. To accomplish this, seafloor habitat mapping of coral reefs around the U.S. Virgin Islands (USVI) and Puerto Rico has been ongoing since 2004. In 2008, fishery acoustics surveys were added to NOAA survey missions in the USVI and Puerto Rico to assess fish distribution and abundance in relation to benthic habitats in high priority conservation areas. NOAA’s National Centers for Coastal Ocean Science (NCCOS) have developed fisheries acoustics survey capabilities onboard the NOAA ship Nancy Foster to complement the CRCP seafloor habitat mapping effort spearheaded by the Center for Coastal Monitoring and Assessment Biogeography Branch (CCMA-BB). The integration of these activities has evolved on the Nancy Foster over the three years summarized in this report. A strategy for improved operations and products has emerged over that time. Not only has the concurrent operation of multibeam and fisheries acoustics surveys been beneficial in terms of optimizing ship time and resources, this joint effort has advanced an integrated approach to characterizing bottom and mid-water habitats and the fishes associated with them. CCMA conducts multibeam surveys to systematically map and characterize coral reef ecosystems, resulting in products such as high resolution bathymetric maps, backscatter information, and benthic habitat classification maps. These products focus on benthic features and live bottom habitats associated with them. NCCOS Centers (the Center for Coastal Fisheries and Habitat Research and the Center for Coastal Environmental Health and Biomolecular Research) characterize coral reef ecosystems by using fisheries acoustics methods to capture biological information through the entire water column. Spatially-explicit information on marine resources derived from fisheries acoustics surveys, such as maps of fish density, supports marine spatial planning strategies and decision making by providing a biological metric for evaluating coral reef ecosystems and assessing impacts from pollution, fishing pressure, and climate change. Data from fisheries acoustics surveys address management needs by providing a measure of biomass in management areas, detecting spatial and temporal responses in distribution relative to natural and anthropogenic impacts, and identifying hotspots that support high fish abundance or fish aggregations. Fisheries acoustics surveys conducted alongside multibeam mapping efforts inherently couple water column data with information on benthic habitats and provide information on the heterogeneity of both benthic habitats and biota in the water column. Building on this information serves to inform resource managers regarding how fishes are organized around habitat structure and the scale at which these relationships are important. Where resource managers require place-based assessments regarding the location of critical habitats along with high abundances of fish, concurrent multibeam and fisheries acoustics surveys serve as an important tool for characterizing and prioritizing coral reef ecosystems. This report summarizes the evolution of fisheries acoustics surveys onboard the NOAA ship Nancy Foster from 2008 to 2010, in conjunction with multibeam data collection, aimed at characterizing benthic and mid-water habitats in high priority conservation areas around the USVI and Puerto Rico. It also serves as a resource for the continued development of consistent data products derived from acoustic surveys. By focusing on the activities of 2010, this report highlights the progress made to date and illustrates the potential application of fisheries data derived from acoustic surveys to the management of coral reef ecosystems.

Swimming crab Callinectes amnicola (Decapoda-Portunidae) capture analysis of a lagoon with high continental influence (Aby Lagoon, Cote d'Ivoire, West Africa)

The study describes the main causes of captures and productions decreasing of swimming crab Callinectes amnicola (Decapoda Portunidae) in Aby lagoon complex. For that, docks of two Sub Prefectures of Adiaké and Assini-Mafia respectively including the villages of Adiaké, Anga, Assomlan, Epleman, Aby and Man-Man, M'Bratty, Assini-Ngouankro and Assini-Mafia were studied from 2006 to 2009 and completed with previous results obtained from 1988 to 2005. Field investigators were identified by site/village and they recorded daily activities of fishermen (number of effective fishermen, number of gears and area of fishing, duration of fishing, types and quantity of bait) and landing of swimming crabs. During recent period of the study, total production decreased from 3742 tons in 2006 to 1500 tons in 2009. Matrix correlations and correlation analysis indicated that this downward trend was due to the increase of the number of fishermen, number of fishing gear, the decrease in female crabs capture and degradation of the environment related to gradual closure of the Assini-Mafia channel. Despite this decline, total production in Aby lagoon remained high compared to the productions of some lagoons of the country and the region. Given the importance of fishing swimming crabs in Aby lagoon, since it concerns many young people and it is a source of income, stringent measures for sustainable and responsible management must be taken and implemented as part of a co-management plan involving all stakeholders to sustainably manage the resource

Annual estimates of the unobserved incidental kill of pantropical spotted dolphin (Stenella attenuata attenuata) calves in the tuna purse-seine fishery of the eastern tropical Pacific

We estimated the total number of pantropical spotted dolphin (Stenella attenuata) mothers killed without their calves (“calf deficit”) in all tuna purse-seine sets from 1973– 90 and 1996–2000 in the eastern tropical Pacific. Estimates were based on a tally of the mothers killed as reported by color pattern and gender, several color-pattern-based frequency tables, and a weaning model. Over the time series, there was a decrease in the calf deficit from approximately 2800 for the western-southern stock and 5000 in the northeastern stock to about 60 missing calves per year. The mean deficit per set decreased from approximately 1.5 missing calves per set in the mid-1970s to 0.01 per set in the late-1990s. Over the time series examined, from 75% to 95% of the lactating females killed were killed without a calf. Under the assumption that these orphaned calves did not survive without their mothers, this calf deficit represents an approximately 14% increase in the reported kill of calves, which is relatively constant across the years examined. Because the calf deficit as we have defined it is based on the kill of mothers, the total number of missing calves that we estimate is potentially an underestimate of the actual number killed. Further research on the mechanism by which separation of mother and calf occurs is required to obtain better estimates of the unobserved kill of dolphin calves in this fishery.

Maori octopus (Octopus maorum) bycatch and southern rock lobster (Jasus edwardsii) mortality in the South Australian lobster fishery

Octopuses are commonly taken as bycatch in many trap fisheries for spiny lobsters (Decapoda: Palinuridae) and can cause significant levels of within-trap lobster mortality. This article describes spatiotemporal patterns for Maori octopus (Octopus maorum) catch rates and rock lobster (Jasus edwardsii) mortality rates and examines factors that are associated with within-trap lobster mortality in the South Australian rock lobster fishery (SARLF). Since 1983, between 38,000 and 119,000 octopuses per annum have been taken in SARLF traps. Catch rates have fluctuated between 2.2 and 6.2 octopus/100 trap-lifts each day. There is no evidence to suggest that catch rates have declined or that this level of bycatch is unsustainable. Over the last five years, approximately 240,000 lobsters per annum have been killed in traps, representing ~4% of the total catch. Field studies show that over 98% of within-trap lobster mortality is attributable to octopus predation. Lobster mortality rates are positively correlated with the catch rates of octopus. The highest octopus catch rates and lobster mortality rates are recorded during summer and in the more productive southern zone of the fishery. In the southern zone, within-trap lobster mortality rates have increased in recent years, apparently in response to the increase in the number of lobsters in traps and the resultant increase in the probability of octopus encountering traps containing one or more lobsters. Lobster mortality rates are also positively correlated with soak-times in the southern zone fishery and with lobster size. Minimizing trap soak-times is one method currently available for reducing lobster mortality rates. More significant reductions in the rates of within-trap lobster mortality may require a change in the design of lobster traps.

Fishery dynamics of the California market squid (Loligo opalescens), as measured by satellite remote sensing

Novel data on the spatial and temporal distribution of fishing effort and population abundance are presented for the market squid fishery (Loligo opalescens) in the Southern California Bight, 1992−2000. Fishing effort was measured by the detection of boat lights by the Defense Meteorological Satellite Program (DMSP) Operational Linescan System (OLS). Visual confirmation of fishing vessels by nocturnal aerial surveys indicated that lights detected by satellites are reliable indicators of fishing effort. Overall, fishing activity was concentrated off the following Channel Islands: Santa Rosa, Santa Cruz, Anacapa, and Santa Catalina. Fishing activity occurred at depths of 100 m or less. Landings, effort, and squid abundance (measured as landings per unit of effort, LPUE) markedly declined during the 1997−98 El Niño; landings and LPUE increased afterwards. Within a fishing season, the location of fishing activity shifted from the northern shores of Santa Rosa and Santa Cruz Islands in October, the typical starting date for squid fishing in the Bight, to the southern shores by March, the typical end of the squid season. Light detection by satellites offers a source of fine-scale spatial and temporal data on fishing effort for the market squid fishery off California, and these data can be integrated with environmental data and fishing logbook data in the development of a management plan.