Measurements of total scattering spectra from bocaccio (Sebastes paucispinis)

Marine sportfishing in southern California is a huge industry with annual revenues totaling many billions of dollars. However, the stocks of lingcod and six rockfish species have been declared overfished by the Pacific Fisheries Management Council. As part of a multifaceted fisheries management plan, marine conservation areas, covering many million square nautical miles, have been mandated. To monitor the recovery of the rockfish stocks in these areas, scientists are faced with the following challenges: 1) multiple species of rockfish exist in these areas; 2) the species reside near or on the bottom at depths of 80 to 300 m; and 3) they are low in numerical density. To meet these challenges, multifrequency echosounders, multibeam sonar, and cameras mounted on remotely operated vehicles are frequently used (Reynolds et al., 2001). The accuracy and precision of these echosounder results are largely dependent upon the accuracy of the species classification and target strength estimation (MacLennan and Simmonds, 1992).

A History of Benthic Research in the NMFS Northeast Fisheries Science Center

The Northeast Fisheries Science Center of NOAA's National Marine Fisheries Service has a long history of research on benthic invertebrates and habitats in support of the management of living marine resources. These studies began in the 1870's under Spencer F. Baird's guidance as part of an effort to characterize the Nation's fisheries and living marine resources and their ecological interactions. This century and a quarter of research has included many benthic invertebrate studies, including community characterizations, shellfish biology and culture, pathology, ecosystem energy budget modeling, habitat evaluations, assessments of human impacts, toxic chemical bioaccumulation in demersal food webs, habitat or endangered species management, benthic autecology, systematics (to define new species and species population boundaries), and other benthic studies. Here we review the scope of past and current studies as a background for strategic research planning and suggest areas for further research to support NOAA's goals of sustainable fisheries management, healthy coastal ecosystems, and protected species populations.

The Threatened Status of Steller Sea Lions, Eumetopias jubatus, under the Endangered Species Act: Effects on Alaska Groundfish Fisheries Management

In April 1990, the Steller sea lion, Eumetopias jubatus, was listed as threatened under the U.S. Endangered Species Act by emergency action. Competitive interactions with the billion-dollar Alaska commercial groundfish fisheries have been suggested as one of the possible contributing factors to the Steller sea lion population decline. Since the listing, fisheries managers have attempted to address the potential impacts of the groundfish fisheries on Steller sea lion recovery. In this paper, we review pertinent Federal legislation, biological information on the Steller sea lion decline, changes in the Alaska trawl fishery for walleye pollock, Theragra chalcogramma, since the late 1970's, andpossible interactions between fisheries and sea lions. Using three cases, we illustrate how the listing of Steller sea lions has affected Alaska groundfish fisheries through: I) actions taken at the time of listing designed to limit the potential for directhuman-related sea lion mortality, 2) actions addressing spatial and temporal separation of fisheries from sea lions, and 3) introduction of risk-adverse stock assessment methodologies and Steller sea lion conservation considerations directly in the annual quota-setting process. This discussion shows some of the ways that North Pacific groundfish resource managers have begun to explicitly consider the conservation ofmarine mammal and other nontarget species.

An Overview of Guam's Inshore Fisheries

Guam's nearshore reef fishery is a multi-gear, multispecies fishery that has undergone major changes through the years. Methods have evolved and become more modern. This, along with the changing economic status of Guam, has severely stressed the fishery. Top targeted species are being overexploited and "growth overharvesting" is occurring; the more serious form of "recruitment overharvesting," is happening to some of the key species. Major management concerns are discussed with respect to overfishing and habitat destruction. Management recommendations for this fishery include gear restrictions, size restrictions, and the establishment of marine conservation areas.

Bioacumulação de mercúrio total (HgT) em tecidos de atuns e afins coletados no Sudeste do Brasil

O mercúrio é um metal pesado que vem sendo reconhecido como um poluente potencialmente perigoso no ecossistema marinho devido à sua alta toxicidade e tendência a sofrer bioacumulação nos organismos e biomagnificação através das teias tróficas, podendo ser encontrado em elevadas concentrações em predadores de topo, como os atuns. O objetivo do presente estudo foi utilizar atuns e afins (Thunnus atlanticus, Thunnus albacares, Katsuwonus pelamis, Euthynnus alletteratus, Coryphaena hippurus e Sarda sarda) como indicadores da disponibilidade de mercúrio total (HgT) nas teias tróficas oceânicas do Rio de Janeiro. Os indivíduos foram coletados no período entre Fevereiro de 2009 a Janeiro de 2010, no desembarque pesqueiro da cidade de Cabo Frio, no Estado do Rio de Janeiro, no Sudeste do Brasil. A determinação das concentrações de mercúrio total foi baseada em Malm et al. (1989) e Bastos et al. (1998). As alíquotas de músculo e fígado foram digeridas através de uma mistura de ácidos e as concentrações de mercúrio total foram determinadas por espectrofotometria a vapor frio (FIMS-400, Perkin-Elmer). A precisão e exatidão dos métodos analíticos foram determinadas utilizando os materiais certificados, DORM-3 e DOLT-4, (NRC, Canadá). Os dados foram analisados estatisticamente através do programa STATISTICS 7.0 for Windows. As concentrações de mercúrio total (HgT) encontradas nos atuns e afins variaram significativamente entre as espécies para o músculo e fígado. As menores concentrações foram registradas em Coryphaena hippurus, (0,008 mg. Kg-1 no músculo e 0,003 mg. Kg-1 no fígado), enquanto as maiores concentrações foram reportadas no músculo de Thunnus atlanticus (1,300 mg. Kg-1) e no fígado de Sarda sarda (2,495 mg. Kg-1). Foram encontradas diferenças significativas entre as concentrações de mercúrio total musculares e hepáticas para Katsuwonus pelamis, Euthynnus alletteratus e Sarda sarda, com as concentrações mais elevadas encontradas no fígado. Além disso, o tamanho e o peso dos indivíduos foram fatores importantes, sendo positivamente correlacionados com as concentrações de mercúrio total em todas as espécies, com exceção das concentrações hepáticas encontradas em Katsuwonus pelamis e Euthynnus alleteratus. Ademais, nove indivíduos mostraram altas concentrações musculares, acima de 0,5 mg.Kg-1, limite máximo estabelecido pela Organização Mundial de Saúde (OMS) em peixes predadores para consumo humano. Estes resultados são preocupantes, uma vez que podem representar potencial risco à saúde. Considerando o mercúrio um micro poluente tóxico, as elevadas concentrações encontradas nesses peixes, podem causar efeitos neles e em seus consumidores. Portanto, é importante um contínuo monitoramento de peixes para auxiliar na sua conservação e permitir identificar quais espécies podem ser consumidas e com qual frequência.

Characterization of the U.S. Gulf of Mexico and South Atlantic penaeid and rock shrimp fisheries based on observer data

In July 2007, a mandatory Federal observer program was implemented to characterize the U.S. Gulf of Mexico penaeid shrimp (Farfantepenaeus aztecus, F. duorarum, and Litopenaeus setiferus) fishery. In June 2008, the program expanded to include the South Atlantic penaeid and rock shrimp, Sicyonia spp., fisheries. Data collected from 10,206 tows during 5,197 sea days of observations were analyzed by geographical area and target species. The majority of tows (~70%) sampled were off the coasts of Texas and Louisiana. Based on total hours towed, the highest concentrated effort occurred off South Texas and southwestern Florida. Gear information, such as net characteristics, bycatch reduction devices, and turtle excluder devices were fairly consistent among areas and target species. By species categories, finfish comprised the majority (≥57%) of the catch composition in the Gulf of Mexico and South Atlantic penaeid shrimp fisheries, while in the South Atlantic rock shrimp fishery the largest component (41%) was rock shrimp. Bycatch to shrimp ratios were lower than reported in previous studies for the Gulf of Mexico penaeid shrimp fishery. These decreased ratios may be attributed to several factors, notably decreased shrimp effort and higher shrimp catch per unit of effort (CPUE) in recent years. CPUE density surface plots for several species of interest illustrated spatial differences in distribution. Hot Spot Analyses for shrimp (penaeid and rock) and bycatch species identified areas with significant clustering of high or low CPUE values. Spatial and temporal distribution of protected species interactions were documented.

Benthic habitats of Buck Island Reef National Monument

NOAA’s Center for Coastal Monitoring and Assessment’s Biogeography Branch has mapped and characterized large portions of the coral reef ecosystems inside the U.S. coastal and territorial waters, including the U.S. Caribbean. The complementary protocols used in these efforts have enabled scientists and managers to quantitatively compare different marine ecosystems in tropical U.S. waters. The Biogeography Branch used these same general protocols to generate three seamless habitat maps of the Bank/Shelf (i.e., from 0 ≤50 meters) and the Bank/Shelf Escarpment (i.e., from 50 ≤1,000 meters and from 1,000 ≤ 1,830 meters) inside Buck Island Reef National Monument (BIRNM). While this mapping effort marks the fourth time that the shallow-water habitats of BIRNM have been mapped, it is the first time habitats deeper than 30 meters (m) have been characterized. Consequently, this habitat map provides information on the distribution of mesophotic and deep-water coral reef ecosystems and serves as a spatial baseline for monitoring change in the Monument. A benthic habitat map was developed for approximately 74.3 square kilometers or 98% of the BIRNM using a combination of semi-automated and manual classification methods. The remaining 2% was not mapped due to lack of imagery in the western part of the Monument at depths ranging from 1,000 to 1,400 meters. Habitats were interpreted from orthophotographs, LiDAR (Light Detection and Ranging) imagery and four different types of MBES (Multibeam Echosounder) imagery. Three minimum mapping units (MMUs) (100, 1,000 and 5,000 square meters) were used because of the wide range of depths present in the Monument. The majority of the area that was characterized was deeper than 30 m on the Bank/Shelf Escarpment. This escarpment area was dominated by uncolonized sand which transitioned to mud as depth increased. Bedrock was exposed in some areas of the escarpment, where steep slopes prevented sediment deposition. Mesophotic corals were seen in the underwater video, but were too sparsely distributed to be reliably mapped from the source imagery. Habitats on the Bank/Shelf were much more variable than those seen on the Bank/Shelf Escarpment. The majority of this shelf area was comprised of coral reef and hardbottom habitat dominated by various forms of turf, fleshy, coralline or filamentous algae. Even though algae was the dominant biological cover type, nearly a quarter (24.3%) of the Monument’s Bank/Shelf benthos hosted a cover of 10%-<50% live coral. In total, 198 unique combinations of habitat classes describing the geography, geology and biology of the sea-floor were identified from the three types of imagery listed above. No thematic accuracy assessment was conducted for areas deeper than about 50 meters, most of which was located in the Bank/Shelf Escarpment. The thematic accuracy of classes in waters shallower than approximately 50 meters ranged from 81.4% to 94.4%. These thematic accuracies are similar to those reported for other NOAA benthic habitat mapping efforts in St. John (>80%), the Main Eight Hawaiian Islands (>84.0%) and the Republic of Palau (>80.0%). These digital maps products can be used with confidence by scientists and resource managers for a multitude of different applications, including structuring monitoring programs, supporting management decisions, and establishing and managing marine conservation areas. The final deliverables for this project, including the benthic habitat maps, source imagery and in situ field data, are available to the public on a NOAA Biogeography Branch website (http://ccma.nos.noaa.gov/ecosystems/coralreef/stcroix.aspx) and through an interactive, web-based map application (http://ccma.nos.noaa.gov/explorer/biomapper/biomapper.html?id=BUIS). This report documents the process and methods used to create the shallow to deep-water benthic habitat maps for BIRNM. Chapter 1 provides a short introduction to BIRNM, including its history, marine life and ongoing research activities. Chapter 2 describes the benthic habitat classification scheme used to partition the different habitats into ecologically relevant groups. Chapter 3 explains the steps required to create a benthic habitat map using a combination of semi-automated and visual classification techniques. Chapter 4 details the steps used in the accuracy assessment and reports on the thematic accuracy of the final shallow-water map. Chapter 5 summarizes the type and abundance of each habitat class found inside BIRNM, how these habitats compare to past habitat maps and outlines how these new habitat maps may be used to inform future management activities.

Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat

Twenty-six stocks of Pacific salmon and trout (Oncorhynchus spp.), representing evolutionary significant units (ESU), are listed as threatened or endangered under the Endangered Species Act (ESA) and six more stocks are currently being evaluated for listing. The ecological and economic consequences of these listings are large; therefore considerable effort has been made to understand and respond to these declining populations. Until recently, Pacific harbor seals (Phoca vitulina richardsi) on the west coast increased an average of 5% to 7% per year as a result of the Marine Mammal Protection Act of 1972 (Brown and Kohlman2). Pacific salmon are seasonally important prey for harbor seals (Roffe and Mate, 1984; Olesiuk, 1993); therefore quantifying and understanding the interaction between these two protected species is important for Morphobiologically sound management strategies. Because some Pacific salmonid species in a given area may be threatened or endangered, while others are relatively abundant, it is important to distinguish the species of salmonid upon which the harbor seals are preying. This study takes the first step in understanding these interactions by using molecular genetic tools for species-level identification of salmonid skeletal remains recovered from Pacific harbor seal scats.

Aquatic resource conservation - The first Yangtze finless porpoise successfully born in captivity

Background. As the sole freshwater subspecies of finless porpoise (Neophocaena phocaenoides), the Yangtze finless porpoise (N. p. asiaeorientalis) lives only in the middle and lower reaches of the Yangtze River and its appended Poyang and Dongting Lakes. As a result of human activity on the river, including over and illegal fishing, pollution, transportation and dam construction, the population of Yangtze finless porpoises has been steadily and rapidly decreasing during the past several decades, which leads the animal to be endangered. Methods. For saving this unique animal from extinction, three corresponding measures, in situ conservation, ex situ conservation, and intensifying breeding research in captivity, were proposed and have been implemented since the 1980s. Results. After successfully rearing the animals in captivity for almost nine years, the first Yangtze finless porpoise was successfully born in captivity on July 5, 2005. The calf is male, with a body length of 69 cm. This is the first freshwater cetacean ever born in captivity. Conclusion. The successful birth of this calf confirms that it is possible to breed the Yangtze finless porpoise in captivity. Furthermore, this will greatly benefit the conservation efforts, and also greatly bolster our on-going efforts to study the reproductive biology of these animals. Recommendation. More studies and efforts are expected to establish a sustainable, captive colony of the Yangtze finless porpoise, which will not only greatly expand our knowledge about the reproduction biology of this animal, but also help to redeem the wild population through a careful yearly 'soft releasing' process.

Ontogenetic behavior and migration of Chinese sturgeon, Acipenser sinensis

The Chinese sturgeon, Acipenser sinensis, is an anadromous protected species that presently only spawns in the Yangtze River. Using laboratory experiments, we examined the behavioral preference of young Chinese sturgeon to physical habitat (water depth, illumination intensity, substrate color, and cover) and monitored their downstream migration. Hatchling free embryos were photopositive, preferred open habitat, and immediately upon hatching, swam far above the bottom using swim-up and drift. Downstream migration peaked on days 0-1, decreased about 50% or more during days 2-7, and ceased by day 8. Days 0-1 migrants were active both day and night, but days 2-7 migrants were most active during the day. After ceasing migration, days 8-11 embryos were photonegative, preferred dark substrate and sought cover. Free embryos developed into larvae and began feeding on day 12, when another shift in behavior occurred-larvae returned to photopositive behavior and preferred white substrate. The selective factor favoring migration of free embryos upon hatching and swimming far above the bottom may be avoidance of benthic predatory fishes. Free embryos, which must rely on yolk energy for activity and growth, only used 19 cumulative temperature degree-days for peak migration compared to 234 degree-days for growth to first feeding larvae, a 1 : 12 ratio of cumulative temperature units. This ratio suggests that sturgeon species with large migratory embryos, like Chinese sturgeon, which require a high level of energy to swim during migration, may migrate only a short time to conserve most yolk energy for growth.

The freeliving nematode genus Parodontophora Timm 1963 (Nematoda : Axonolaimidae) is not exclusively marine: Parodontophora limnophila sp nov from freshwater in China

Parodontophora limnophila sp. nov. is described from Poyang Lake, the largest freshwater lake of China. It is characterized by having an amphid with its posterior end close to the base of the stoma, relatively short cephalic setae, opisthocephalic setae arranged as two subdorsal groups of three longitudinally arranged setae and two single subventral setae, excretory pore at the level of the anterior part of the stoma and renette gland 34-47% of the oesophageal length. To date, the new species is the only Parodontophora species found in freshwater habitats.

RAPD profiling in detecting genetic variation in endemic Coelonema (Brassicaceae) of Qinghai-Tibet Plateau of China

Random amplified polymorphic DNA ( RAPD) markers were used to measure genetic diversity of Coelonema draboides ( Brassicaceae), a genus endemic to the Qilian Mountains of the Qinghai-Tibet Plateau. We sampled 90 individuals in 30 populations of Coelonema draboides from Datong and Huzhu counties of Qinghai Province in P. R. China. A total of 186 amplified bands were scored from the 14 RAPD primers, with a mean of 13.3 amplified bands per primer, and 87% ( 161 bands) polymorphic bands (PPB) was found. Analysis of molecular variance (AMOVA) shows that a large proportion of genetic variation (84.2%) resides among individuals within populations, while only 15.8% resides among populations. The species shows higher genetic diversity between individuals than other endemic and endangered plants. The RAPDs provide a useful tool for assessing genetic diversity of rare, endemic species and for resolving relationships among populations. The results show that the genetic diversity of this species is high, possibly allowing it to adapt more easily to environmental variations. The main factor responsible for the high level of differentiation within populations and the low level of diversity among populations is probably the outcrossing and long-lived nature of this species. Some long-distance dispersal, even among far separated populations, is also a crucial determinant for the pattern of genetic variation in the species. This distributive pattern of genetic variation of C. draboides populations provides important baseline data for conservation and collection strategies for the species. It is suggested that only populations in different habitats should be studied and protected, not all populations, so as to retain as much genetic diversity as possible.

The impact of conifer plantation forestry on the ecology of peatland lakes

Blanket bog lakes are a characteristic feature of blanket bog habitats and harbour many rare and threatened invertebrate species. Despite their potential conservation value, however, very little is known about their physico-chemical or biological characteristics in western Europe, and their reference conditions are still unknown in Ireland. Furthermore, they are under considerable threat in Ireland from a number of sources, particularly afforestation of their catchments by exotic conifers. Plantation forestry can potentially lead to the increased input of substances including hydrogen ions (H+), plants nutrients, dissolved organic carbon (DOC), heavy metals and sediment. The aims of this study were to investigate the effect of conifer plantation forestry on the hydrochemistry and ecology of blanket bog lakes in western Ireland. Lake hydrochemistry, littoral Chydoridae (Cladocera) and littoral macroinvertebrate communities were compared among replicate lakes selected from three distinct catchment land use categories: i) unplanted blanket bog only present in the catchment, ii) mature (closed-canopy) conifer plantation forests only present in the catchment and iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sandstone and granite. Lakes with afforested catchments across both geologies had elevated concentrations of phosphorus (P), nitrogen (N), total dissolved organic carbon (TDOC), aluminium (Al) and iron (Fe), with the highest concentrations of each parameter recorded from lakes with catchment clearfelling. Dissolved oxygen concentrations were also significantly reduced in the afforested lakes, particularly the clearfell lakes. This change in lake hydrochemistry was associated with profound changes in lake invertebrate communities. Within the chydorid communities, the dominance of Alonopsis elongata in the unplanted blanket bog lakes shifted to dominance by the smaller bodied Chydorus sphaericus, along with Alonella nana, Alonella excisa and Alonella exigua, in the plantation forestry-affected lakes, consistent with a shift in lake trophy. Similarly, there was marked changes in the macroinvertebrate communities, especially for the Coleoptera and Heteroptera assemblages which revealed increased taxon richness and abundance in the nutrient-enriched lakes. In terms of conservation status, despite having the greatest species-quality scores (SQS) and species richness, three of the four International Union for the Conservation of Nature (IUCN) red-listed species of Coleoptera and Odonata recorded during the study were absent from lakes subject to catchment clearfelling. The relative strengths of bottom-up (forestry-mediated nutrient enrichment) and top-down (fish) forces in structuring littoral macroinvertebrate communities was investigated in a separate study. Nutrient enrichment was shown to be the dominant force acting on communities, with fish having a lesser influence. These results confirmed that plantation forestry poses the single greatest threat to the conservation status of blanket bog lakes in western Ireland. The findings of this study have major implications for the management of afforested peatlands. Further research is required on blanket bog lakes to prevent any further plantation forestry-mediated habitat deterioration of this rare and protected habitat.

Institutional designs of customary fisheries management arrangements in Indonesia, Papua New Guinea, and Mexico

There are considerable efforts by governments, non-governmental organizations (NGOs), and academia to integrate marine conservation initiatives and customary practices, such as taboos that limit resource use. However, these efforts are often pursued without a fundamental understanding of customary institutions. This paper examines the operational rules in use and the presence of institutional design principles in long-enduring and dynamic customary fisheries management institutions in Papua New Guinea, Indonesia, and Mexico. Rather than a "blue print" for devising long-enduring institutions, this study relies on the design principles as a starting point to organize an inquiry into the institutional diversity found in customary governance regimes. Three important trends emerged from this comparative analysis: (1) despite it being notoriously difficult to define boundaries around marine resources, almost 3/4 of the cases in this study had clearly defined boundaries and membership; (2) all of the customary institutions were able to make and change rules, indicating a critical degree of flexibility and autonomy that may be necessary for adaptive management; (3) the customary institutions examined generally lacked key interactions with organizations operating at larger scales, suggesting that they may lack the institutional embeddedness required to confront some common pool resources (CPR) challenges from the broader socioeconomic, institutional and political settings in which they are embedded. Future research will be necessary to better understand how specific institutional designs are related to social and ecological outcomes in commons property institutions. © 2011 Elsevier Ltd.