Marine Fisheries Stock Assessment Improvement Plan: report of the National Marine Fisheries Service National Task Force for Improving Fish Stock Assessments

This report argues for greatly increased resources in terms of data collection facilities and staff to collect, process, and analyze the data, and to communicate the results, in order for NMFS to fulfill its mandate to conserve and manage marine resources. In fact, the authors of this report had great difficulty defining the "ideal" situation to which fisheries stock assessments and management should aspire. One of the primary objectives of fisheries management is to develop sustainable harvest policies that minimize the risks of overfishing both target species and associated species. This can be achieved in a wide spectrum of ways, ranging between the following two extremes. The first is to implement only simple management measures with correspondingly simple assessment demands, which will usually mean setting fishing mortality targets at relatively low levels in order to reduce the risk of unknowingly overfishing or driving ecosystems towards undesirable system states. The second is to expand existing data collection and analysis programs to provide an adequate knowledge base that can support higher fishing mortality targets while still ensuring low risk to target and associated species and ecosystems. However, defining "adequate" is difficult, especially when scientists have not even identified all marine species, and information on catches, abundances, and life histories of many target species, and most associated species, is sparse. Increasing calls from the public, stakeholders, and the scientific community to implement ecosystem-based stock assessment and management make it even more difficult to define "adequate," especially when "ecosystem-based management" is itself not well-defined. In attempting to describe the data collection and assessment needs for the latter, the authors took a pragmatic approach, rather than trying to estimate the resources required to develop a knowledge base about the fine-scale detailed distributions, abundances, and associations of all marine species. Thus, the specified resource requirements will not meet the expectations of some stakeholders. In addition, the Stock Assessment Improvement Plan is designed to be complementary to other related plans, and therefore does not duplicate the resource requirements detailed in those plans, except as otherwise noted.

Fish assemblages and benthic habitats of Buck Island Reef National Monument (St. Croix, U.S. Virgin Islands) and the surrounding seascape: A characterization of spatial and temporal patterns

Since 1999, NOAA’s Biogeography Branch of the Center for Coastal Monitoring and Assessment (CCMA-BB) has been working with federal and territorial partners to characterize, monitor, and assess the status of the marine environment around northeastern St. Croix, U.S. Virgin Islands. This effort is part of the broader NOAA Coral Reef Conservation Program’s (CRCP) National Coral Reef Ecosystem Monitoring Program (NCREMP). With support from CRCP’s NCREMP, CCMA conducts the “Caribbean Coral Reef Ecosystem Monitoring project” (CREM) with goals to: (1) spatially characterize and monitor the distribution, abundance, and size of marine fauna associated with shallow water coral reef seascapes (mosaics of coral reefs, seagrasses, sand and mangroves); (2) relate this information to in situ fine-scale habitat data and the spatial distribution and diversity of habitat types using benthic habitat maps; (3) use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; (4) establish the efficacy of those management decisions; and (5) develop data collection and data management protocols. The monitoring effort in northeastern St. Croix was conducted through partnerships with the National Park Service (NPS) and the Virgin Islands Department of Planning and Natural Resources (VI-DPNR). The geographical focal point of the research is Buck Island Reef National Monument (BIRNM), a protected area originally established in 1961 and greatly expanded in 2001; however, the work also encompassed a large portion of the recently created St. Croix East End Marine Park (EEMP). Project funding is primarily provided by NOAA CRCP, CCMA and NPS. In recent decades, scientific and non-scientific observations have indicated that the structure and function of the coral reef ecosystem around northeastern St. Croix have been adversely impacted by a wide range of environmental stressors. The major stressors have included the mass Diadema die off in the early 1980s, a series of hurricanes beginning with Hurricane Hugo in 1989, overfishing, mass mortality of Acropora corals due to disease and several coral bleaching events, with the most severe mass bleaching episode in 2005. The area is also an important recreational resource supporting boating, snorkeling, diving and other water based activities. With so many potential threats to the marine ecosystem and a dramatic change in management strategy in 2003 when the park’s Interim Regulations (Presidential Proclamation No. 7392) established BIRNM as one of the first fully protected marine areas in NPS system, it became critical to identify existing marine fauna and their spatial distributions and temporal dynamics. This provides ecologically meaningful data to assess ecosystem condition, support decision making in spatial planning (including the evaluation of efficacy of current management strategies) and determine future information needs. The ultimate goal of the work is to better understand the coral reef ecosystems and to provide information toward protecting and enhancing coral reef ecosystems for the benefit of the system itself and to sustain the many goods and services that it offers society. This Technical Memorandum contains analysis of the first six years of fish survey data (2001-2006) and associated characterization of the benthos (1999-2006). The primary objectives were to quantify changes in fish species and assemblage diversity, abundance, biomass and size structure and to provide spatially explicit information on the distribution of key species or groups of species and to compare community structure inside (protected) versus outside (fished) areas of BIRNM. (PDF contains 100 pages).

Spatial and temporal patterns of coral bleaching around Buck Island Reef National Monument, St. Croix, U.S. Virgin Islands

Since 2001, biannual fish and habitat monitoring has been conducted for the shallow (> 30 m), colonized pavement and gorgonian dominated Buck Island Reef National Monument (BIRNM) St. Croix, USVI and adjacent waters. during October, 2005, widespread coral bleaching was observed within the ∼50 square-kilometer study area that was preceded by 10 wks of higher than average water temperatures (28.9–30.1 °C). Random transects (100 square meters) were conducted on linear reefs, patch reefs, bedrock, pavement, and scattered coral/rock habitats during October 2005, and April and October 2006, and species specific bleaching patterns were documented. During October 2005 approximately 51% of live coral cover was bleached. Nineteen of 23 coral species within 16 genera and two hydrocoral species exhibited signs of bleaching. Coral cover for Montastraea annularis and species of the genus Agaricia were the most affected, while other species exhibited variability in their susceptibility to bleaching. Bleaching was evident at all depths (1.5–28 m), was negatively correlated with depth, and positively correlated with habitat complexity. Bleaching was less prevalent at all depths and habitat types upon subsequent monitoring during April (15%) and October (3%) 2006. Four species and one genus did not exhibit signs of bleaching throughout the study period (Dendrogyra cylindrus, Eusmilia fastigata, Mussa angulosa, Mycetophyllia aliciae, Scolymia spp.).

Spatial and temporal patterns of coral bleaching around Buck Island Reef National Monument, St. Croix, U.S. Virgin Islands [poster]

Limited information currently exists on the recovery periods of bleached corals as well as the spatial extent, causative factors, and the overall impact of bleaching on coral reef ecosystems. During October, 2005, widespread coral bleaching was observed within Buck Island Reef National Monument (BUIS) St. Croix, USVI. The bleaching event was preceded by 10 weeks of higher than average water temperatures (28.9-30.1°C). Random transects (100 square meters) over hard bottom habitats (N=94) revealed that approximately 51% of live coral cover was bleached. Nineteen of 23 coral species within 16 genera and two hydrocoral species exhibited signs of bleaching; species-specific bleaching patterns were variable throughout the study area. Coral cover for Montastraea annularisand species of the genus Agariciawere the most affected, while other species exhibited variability to bleaching. Although a weak but significant negative relationship (r2=0.10, P=0.0220) was observed, bleaching was evident at all depths (1.5-28 m). Bleaching was spatially autocorrelated (P=0.001) and hot-spot analysis identified a cluster of high bleaching stations northeast of Buck Island. Bleaching was significantly reduced within all depth zones and habitat types upon subsequent monitoring during April (15%) and October (3%) 2006.

Proceedings of the Nineteenth Annual Symposium on Sea Turtle Conservation and Biology, 2-6 March 1999 South Padre Island, Texas, U.S.A.

The 19th Annual Symposium on Sea Turtle Biology and Conservation was the largest to date. The beautiful venue was the South Padre Island Convention Centre on South Padre Island, Texas from March 2-6, 1999. Key features of the 19th were invited talks on the theme The Promise, the Pain, and the Progress of 50 years of Sea Turtle Research and Conservation, a mini-symposium on the Kemp's ridley and an increased emphasis on high quality poster sessions. Hosts for the meeting included Texas A&M University, the Texas Sea Grant College Program, The Gladys Porter Zoo and Sea Turtle, Inc. Co-sponsors included the National Marine Fisheries Service-Southeast Fisheries Science Center, the National Marine Fisheries Service-Protected Resources Branch, Padre Island National Seashore and the U.S. Fish and Wildlife Service. With the assistance of Jack Frazier, we were fortunate to obtain a $30,000 grant from the David and Lucile Packard Foundation. This grant provided travel support to 49 individuals from 24 nations who presented a total of 50 presentations. (PDF contains 309 pages)

Herpetofaunal Inventories of the National Parks of South Florida and the Caribbean: Volume II. Virgin Islands National Park

Amphibian declines and extinctions have been documented around the world, often in protected natural areas. Concern for this alarming trend has focused attention on the need to document all species of amphibians that occur within U.S. National Parks and to search for any signs that amphibians may be declining. This study, an inventory of amphibian species in Virgin Islands National Park, was conducted from 2001 to 2003. The goals of the project were to create a georeferenced inventory of amphibian species, use new analytical techniques to estimate proportion of sites occupied by each species, look for any signs of amphibian decline (missing species, disease, die-offs, etc.), and to establish a protocol that could be used for future monitoring efforts. Several sampling methods were used to accomplish these goals. Visual encounter surveys and anuran vocalization surveys were conducted in all habitats throughout the park to estimate the proportion of sites or proportion of area occupied (PAO) by amphibian species in each habitat. Line transect methods were used to estimate density of some amphibian species and double observer analysis was used to refine counts based on detection probabilities. Opportunistic collections were used to augment the visual encounter methods for rare species. Data were collected during four sampling periods and every major trail system throughout the park was surveyed. All of the amphibian species believed to occur on St. John were detected during these surveys. One species not previously reported, the Cuban treefrog (Osteopilus septentrionalis), was also added to the species list. That species and two others (Eleutherodactylus coqui and Eleutherodactylus lentus) bring the total number of introduced amphibians on St. John to three. We detected most of the reptile species thought to occur on St. John, but our methods were less suitable for reptiles compared to amphibians. No amphibian species appear to be in decline at this time. We found no evidence of disease or of malformations. Our surveys provide a snapshot picture of the status of the amphibian species, so continued monitoring would be necessary to determine long-term trends, but several potential threats to amphibians were identified. Invasive species, especially the Cuban treefrog, have the potential to decrease populations of native amphibians. Introduced mammalian predators are also a potential threat, especially to the reptiles of St. John, and mammalian grazers might have indirect effects on amphibians and reptiles through habitat modification. Finally, loss of habitat to development outside the park boundary could harm some important populations of amphibians and reptiles on the island.

Herpetofaunal Inventories of the National Parks of South Florida and the Caribbean: Volume III. Big Cypress National Preserve

Amphibian declines and extinctions have been documented around the world, often in protected natural areas. Concern for this trend has prompted the U.S. Geological Survey and the National Park Service to document all species of amphibians that occur within U.S. National Parks and to search for any signs that amphibians may be declining. This study, an inventory of amphibian species in Big Cypress National Preserve, was conducted from 2002 to 2003. The goals of the project were to create a georeferenced inventory of amphibian species, use new analytical techniques to estimate proportion of sites occupied by each species, look for any signs of amphibian decline (missing species, disease, die-offs, and so forth.), and to establish a protocol that could be used for future monitoring efforts. Several sampling methods were used to accomplish these goals. Visual encounter surveys and anuran vocalization surveys were conducted in all habitats throughout the park to estimate the proportion of sites or proportion of area occupied (PAO) by each amphibian species in each habitat. Opportunistic collections, as well as limited drift fence data, were used to augment the visual encounter methods for highly aquatic or cryptic species. A total of 545 visits to 104 sites were conducted for standard sampling alone, and 2,358 individual amphibians and 374 reptiles were encountered. Data analysis was conducted in program PRESENCE to provide PAO estimates for each of the anuran species. All of the amphibian species historically found in Big Cypress National Preserve were detected during this project. At least one individual of each of the four salamander species was captured during sampling. Each of the anuran species in the preserve was adequately sampled using standard herpetological sampling methods, and PAO estimates were produced for each species of anuran by habitat. This information serves as an indicator of habitat associations of the species and relative abundance of sites occupied, but it will also be useful as a comparative baseline for future monitoring efforts. In addition to sampling for amphibians, all encounters with reptiles were documented. The sampling methods used for detecting amphibians are also appropriate for many reptile species. These reptile locations are included in this report, but the number of reptile observations was not sufficient to estimate PAO for reptile species. We encountered 35 of the 46 species of reptiles believed to be present in Big Cypress National Preserve during this study, and evidence exists of the presence of four other reptile species in the Preserve. This study found no evidence of amphibian decline in Big Cypress National Preserve. Although no evidence of decline was observed, several threats to amphibians were identified. Introduced species, especially the Cuban treefrog (Osteopilus septentrionalis), are predators and competitors with several native frog species. The recreational use of off-road vehicles has the potential to affect some amphibian populations, and a study on those potential impacts is currently underway. Also, interference by humans with the natural hydrologic cycle of south Florida has the potential to alter the amphibian community. Continued monitoring of the amphibian species in Big Cypress National Preserve is recommended. The methods used in this study were adequate to produce reliable estimates of the proportion of sites occupied by most anuran species, and are a cost-effective means of determining the status of their populations.

Ecological condition of coastal ocean waters of the U.S. continental shelf off South Florida: 2007

A study was initiated with field work in May 2007 to assess the status of ecological condition and stressor impacts throughout the U.S. continental shelf off South Florida, focusing on soft-bottom habitats, and to provide this information as a baseline for evaluating future changes due to natural or human-induced disturbances. The boundaries of the study region extended from Anclote Key on the western coast of Florida to West Palm Beach on the eastern coast of Florida, inclusive of the Florida Keys National Marine Sanctuary (FKNMS), and from navigable depths along the shoreline seaward to the shelf break (~100m). The study incorporated standard methods and indicators applied in previous national coastal monitoring programs — U.S. Environmental Protection Agency’s (EPA) Environmental Monitoring and Assessment Program (EMAP) and National Coastal Assessment (NCA) — including multiple measures of water quality, sediment quality, and biological condition. Synoptic sampling of the various indicators provided an integrative weight-of-evidence approach to assessing condition at each station and a basis for examining potential associations between presence of stressors and biological responses. A probabilistic sampling design, which included 50 stations distributed randomly throughout the region, was used to provide a basis for estimating the spatial extent of condition relative to the various measured indicators and corresponding assessment endpoints (where available). The study was conducted through a large cooperative effort by National Oceanic and Atmospheric Administration (NOAA)/National Centers for Coastal Ocean Science (NCCOS), EPA, U.S. Geological Survey (USGS), NOAA/Oceanic and Atmospheric Research (OAR)/Atlantic Oceanographic and Meteorological Laboratory in Miami, FKNMS, and the Florida Fish and Wildlife Conservation Commission (FWC). The majority of the South Florida shelf had high levels of dissolved oxygen (DO) in near-bottom water (> 5 mg L-1) indicative of “good” water quality.. DO levels in bottom waters exceeded this upper threshold at 98.8% throughout the coastal-ocean survey area. Only 1.2% of the region had moderate DO levels (2-5 mg/L) and no part of the survey area had DO <2.0 mg/L. In addition, offshore waters throughout the region had relatively low levels of total suspended solids (TSS), nutrients, and chlorophyll a indicative of oligotrophic conditions. Results suggested good sediment quality as well. Sediments throughout the region, which ranged from sands to intermediate muddy sands, had low levels of total organic carbon (TOC) below bioeffect guidelines for benthic organisms. Chemical contaminants in sediments were also mostly at low, background levels. For example, none of the stations had chemicals in excess of corresponding Effects-Range Median (ERM) probable bioeffect values or more than one chemical in excess of lower-threshold Effects-Range Low (ERL) values. Cadmium was the only chemical that occurred at moderate concentrations between corresponding ERL and ERM values. Sixty fish samples from 28 stations were collected and analyzed for chemical contaminants. Eleven of these samples (39% of sites) had moderate levels of contaminants, between lower and upper non-cancer human-health thresholds, and ten (36% of sites) had high levels of contaminants above the upper threshold.

Proceedings of the Twenty-second Annual Symposium on Sea Turtle Biology and Conservation, 4-7 April, 2002, Miami, Florida

The 22nd Annual Symposium on Sea Turtle Biology and Conservation was held April 4-7, 2002 in Miami, Florida and hosted by the U.S. Fish and Wildlife Service. The 22nd symposium was the most globally diverse ever with 839 individuals from 73 countries attending the symposium and associated regional meetings. One third of the attendees were from outside the United States. This diverse attendance was made possible in large part because of substantial donations from The Packard Foundation, National Fish and Wildlife Foundation, National Marine Fisheries Service, U.S. Fish and Wildlife Service, Convention on Migratory Species, Oceanic Research Foundation, and International Sea Turtle Society which supported travel grants for 170 international travelers. (PDF contains 336 pages)

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 surveillance strategy for invasive species of concern in deepwater habitats of the Northwestern Hawaiian Islands

This report describes a surveillance strategy to detect deepwater invasive species in the Northwestern Hawaiian Islands. A need for this strategy was identified in the Papahānaumokuākea Marine National Monument Management Plan and the Monument’s Draft Natural Resources Science Plan. This strategy focuses on detecting two species of concern, the octocoral Carijoa riisei and the red alga Hypnea musciformis. Most research on invasive species in the Hawaiian archipelago has focused on shallow water habitats within the limits of conventional SCUBA (0-30 m). Deeper habitats such as mesophotic reefs are much more difficult to access and consequently little is known about the distribution of deepwater invasive species or their impacts. Recent deepwater (>30 m) sightings of H. musciformis and C. riisei, in and near NWHI, respectively, have prompted a call for further research and surveillance of invasive species in deepwater habitats. This report compiles the most up to date information about these two species of concern in deepwater habitats. A literature search and conversations with subject matter experts was used to identify their current distribution, preferred habitat types, optimal detection methods and ways to efficiently sample the vast extent of NWHI. The proposed sampling strategy prioritizes survey effort where C. riisei and H. musciformis are most likely to be found. At coarse spatial scales (tens to hundreds of kilometers), opportunistic observations and distance from the Main Hawaiian Islands, a principal propagule source, are used to identify high-risk islands and banks. At fine spatial scales (meters to tens of kilometers) a habitat suitability model was developed to identify high-risk habitats. The habitat suitability model focused on habitat preferences of C. riisei, since the species is well studied and adequate data exists to map habitats. There was insufficient information to identify suitable habitat for H. muscifomis. Habitat preferences for the algae are poorly understood and there is a lack of data at relevant spatial scales to map those preferences which are known. The principal habitats identified by the habitat suitability model were ledges and the edges of rugose coral reefs, where the shade loving octocoral would likely be found. Habitat suitability maps were developed for seven atolls and banks to aid in survey site selection. The protocol relied on technical divers to conduct visual surveys of benthic habitats. It was developed to increase the efficiency of surveys, maximize the probability of detection, identify important information relevant to future surveys and standardize results. The strategy, model and protocol were tested during a field mission in 2009 at several atolls and islands in NWHI. The field mission did not detect any invasive species among deepwater habitats and much was learned to improve future surveys. Data gaps and improvements are discussed.