Use of genetic data to assess the uncertainty in stock assessments due to the assumed stock structure: the case of albacore (Thunnus alalunga) from the Atlantic Ocean

Stock assessments can be problematic because of uncertainties associated with the data or because of simplified assumptions made when modeling biological processes (Rosenberg and Restrepo, 1995). For example, the common assumption in stock assessments that stocks are homogeneous and discrete (i.e., there is no migration between the stocks) is not necessarily true (Kell et al., 2004a, 2004b).

Variability in supply and cross-shelf transport of pink shrimp (Farfantepenaeus duorarum) postlarvae into western Florida Bay

The variability in the supply of pink shrimp (Farfantepenaeus duorarum) postlarvae and the transport mechanisms of planktonic stages were investigated with field data and simulations of transport. Postlarvae entering the nursery grounds of Florida Bay were collected for three consecutive years at channels that connect the Bay with the Gulf of Mexico, and in channels of the Middle Florida Keys that connect the southeastern margin of the Bay with the Atlantic Ocean. The influx of postlarvae in the Middle Florida Keys was low in magnitude and varied seasonally and among years. In contrast, the greater postlarval influx occurred at the northwestern border of the Bay, where there was a strong seasonal pattern with peaks in influx from July through September each year. Planktonic stages need to travel up to 150 km eastward between spawning grounds (northeast of Dry Tortugas) and nursery grounds (western Florida Bay) in about 30 days, the estimated time of planktonic development for this species. A Lagrangian trajectory model was developed to estimate the drift of planktonic stages across the SW Florida shelf. The model simulated the maximal distance traveled by planktonic stages under various assumptions of behavior. Simulation results indicated that larvae traveling with the instantaneous current and exhibiting a diel behavior travel up to 65 km and 75% of the larvae travel only 30 km. However, the eastward distance traveled increased substantially when a larval response to tides was added to the behavioral variable (distance increased to 200 km and 85% of larvae traveled 150 km). The question is, when during larval development, and where on the shallow SW Florida shelf, does the tidal response become incorporated into the behavior of pink shrimp.

Food conversion efficiency and the von Bertalanffy growth function. Part II and conclusion: Extension of the new model to the generalized von Bertalanffy growth function

The simple model relating food conversion efficiency (K sub(1)) to body weight derived from the theoretical concepts behind von Bertalanffy's growth model, is extended here in the context of Pauly's generalization of that model. The exponent, which was fixed to 1/3 in the simple model, is in the extended model equivalent to 1-d, with d being the weight exponent of the anabolism term in Pauly's growth model. This makes the model applicable to fish for which the assumptions of the original (special) version of von Bertalanffy's growth model are violated.

Estimating exploitable stock biomass for the Maine green sea urchin (Strongylocentrotus droebachiensis) fishery using a spatial statistics approach

The objective of this study was to investigate the spatial patterns in green sea urchin (Strongylocentrotus droebachiensis) density off the coast of Maine, using data from a fishery-independent survey program, to estimate the exploitable biomass of this species. The dependence of sea urchin variables on the environment, the lack of stationarity, and the presence of discontinuities in the study area made intrinsic geostatistics inappropriate for the study; therefore, we used triangulated irregular networks (TINs) to characterize the large-scale patterns in sea urchin density. The resulting density surfaces were modified to include only areas of the appropriate substrate type and depth zone, and were used to calculate total biomass. Exploitable biomass was estimated by using two different sea urchin density threshold values, which made different assumptions about the fishing industry. We observed considerable spatial variability on both small and large scales, including large-scale patterns in sea urchin density related to depth and fishing pressure. We conclude that the TIN method provides a reasonable spatial approach for generating biomass estimates for a fishery unsuited to geostatistics, but we suggest further studies into uncertainty estimation and the selection of threshold density values.

Maximum likelihood estimation of mortality and growth with individual variability from multiple length-frequency data

We consider estimation of mortality rates and growth parameters from length-frequency data of a fish stock and derive the underlying length distribution of the population and the catch when there is individual variability in the von Bertalanffy growth parameter L∞. The model is flexible enough to accommodate 1) any recruitment pattern as a function of both time and length, 2) length-specific selectivity, and 3) varying fishing effort over time. The maximum likelihood method gives consistent estimates, provided the underlying distribution for individual variation in growth is correctly specified. Simulation results indicate that our method is reasonably robust to violations in the assumptions. The method is applied to tiger prawn data (Penaeus semisulcatus) to obtain estimates of natural and fishing mortality.

Simulation of Tail Weight Distributions in Biological Year 1986–2006 Landings of Brown Shrimp, Farfantepenaeus aztecus, from the Northern Gulf of Mexico Fishery

Size distribution within re- ported landings is an important aspect of northern Gulf of Mexico penaeid shrimp stock assessments. It reflects shrimp population characteristics such as numerical abundance of various sizes, age structure, and vital rates (e.g. recruitment, growth, and mortality), as well as effects of fishing, fishing power, fishing practices, sampling, size-grading, etc. The usual measure of shrimp size in archived landings data is count (C) the number of shrimp tails (abdomen or edible portion) per pound (0.4536 kg). Shrimp are marketed and landings reported in pounds within tail count categories. Statistically, these count categories are count class intervals or bins with upper and lower limits expressed in C. Count categories vary in width, overlap, and frequency of occurrence within the landings. The upper and lower limits of most count class intervals can be transformed to lower and upper limits (respectively) of class intervals expressed in pounds per shrimp tail, w, the reciprocal of C (i.e. w = 1/C). Age based stock assessments have relied on various algorithms to estimate numbers of shrimp from pounds landed within count categories. These algorithms required un- derlying explicit or implicit assumptions about the distribution of C or w. However, no attempts were made to assess the actual distribution of C or w. Therefore, validity of the algorithms and assumptions could not be determined. When different algorithms were applied to landings within the same size categories, they produced different estimates of numbers of shrimp. This paper demonstrates a method of simulating the distribution of w in reported biological year landings of shrimp. We used, as examples, landings of brown shrimp, Farfantepenaeus aztecus, from the northern Gulf of Mexico fishery in biological years 1986–2006. Brown shrimp biological year, Ti, is defined as beginning on 1 May of the same calendar year as Ti and ending on 30 April of the next calendar year, where subscript i is the place marker for biological year. Biological year landings encompass most if not all of the brown shrimp life cycle and life span. Simulated distributions of w reflect all factors influencing sizes of brown shrimp in the landings within a given biological year. Our method does not require a priori assumptions about the parent distributions of w or C, and it takes into account the variability in width, overlap, and frequency of occurrence of count categories within the landings. Simulated biological year distributions of w can be transformed to equivalent distributions of C. Our method may be useful in future testing of previously applied algorithms and development of new estimators based on statistical estimation theory and the underlying distribution of w or C. We also examine some applications of biological year distributions of w, and additional variables derived from them.

Nineteenth-century Ship-based Catches of Gray Whales, Eschrichtius robustus, in the Eastern North Pacific

The 19th century commercial ship-based fishery for gray whales, Eschrichtius robustus, in the eastern North Pacific began in 1846 and continued until the mid 1870’s in southern areas and the 1880’s in the north. Henderson identified three periods in the southern part of the fishery: Initial, 1846–1854; Bonanza, 1855–1865; and Declining, 1866–1874. The largest catches were made by “lagoon whaling” in or immediately outside the whale population’s main wintering areas in Mexico—Magdalena Bay, Scammon’s Lagoon, and San Ignacio Lagoon. Large catches were also made by “coastal” or “alongshore” whaling where the whalers attacked animals as they migrated along the coast. Gray whales were also hunted to a limited extent on their feeding grounds in the Bering and Chukchi Seas in summer. Using all available sources, we identified 657 visits by whaling vessels to the Mexican whaling grounds during the gray whale breeding and calving seasons between 1846 and 1874. We then estimated the total number of such visits in which the whalers engaged in gray whaling. We also read logbooks from a sample of known visits to estimate catch per visit and the rate at which struck animals were lost. This resulted in an overall estimate of 5,269 gray whales (SE = 223.4) landed by the ship-based fleet (including both American and foreign vessels) in the Mexican whaling grounds from 1846 to 1874. Our “best” estimate of the number of gray whales removed from the eastern North Pacific (i.e. catch plus hunting loss) lies somewhere between 6,124 and 8,021, depending on assumptions about survival of struck-but-lost whales. Our estimates can be compared to those by Henderson (1984), who estimated that 5,542–5,507 gray whales were secured and processed by ship-based whalers between 1846 and 1874; Scammon (1874), who believed the total kill over the same period (of eastern gray whales by all whalers in all areas) did not exceed 10,800; and Best (1987), who estimated the total landed catch of gray whales (eastern and western) by American ship-based whalers at 2,665 or 3,013 (method-dependent) from 1850 to 1879. Our new estimates are not high enough to resolve apparent inconsistencies between the catch history and estimates of historical abundance based on genetic variability. We suggest several lines of further research that may help resolve these inconsistencies.

Survey Assessment of Semi-pelagic Gadoids: The Example of Walleye Pollock, Theragra chalcogramma, in the Eastern Bering Sea

Assessment of walleye pollock, Theragra chalcogramma, in the eastern Bering Sea is complicated because the species is semi-pelagic in habit. Annual bottom trawl surveys provide estimates of demersal abundance on the eastern Bering Sea shelf. Every third year (starting in 1979), an extended area of the shelf and slope is surveyed and an echo integration-midwater trawl survey provides estimates of pollock abundance in midwater. Overall age-specific population and biomass estimates are obtained by summing the demersal and midwater results, assuming that the bottom trawl samples only pollock inhabiting the lower 3 m of the water column. Total population estimates have ranged from 134 x 109 fish in 1979 to 27 x 109 fish in 1988. The very high abundance observed in 1979 reflects the appearance of the unusually large 1978 year class. Changes in age-specific abundance estimates have documented the passage of strong (1978, 1982, and 1984) and weak year classes through the fishery. In general, older fish are more demersally oriented and younger fish are more abundant in midwater, but this trend was not always evident in the patterns of abundance of 1- and 2-year-old fish. As the average age of the population has increased, so has the relative proportion of pollock estimated by the demersal surveys. Consequently, it is unlikely that either technique can be used independently to monitor changes in abundance and age composition. Midwater assessment depends on pelagic trawl samples for size and age composition estimates, so both surveys are subject to biases resulting from gear performance and interactions between fish and gear. In this review, we discuss survey methodology and evaluate assumptions regarding catchability and availability as they relate to demersal, midwater, and overall assessment.

Overview of Mark-recovery Studies on Adult and Juvenile Atlantic Menhaden, Brevoortia tyrannus, and Gulf Menhaden, B. patronus

Extensive mark-recapture studies using internal ferromagnetic tags have been conducted on Atlantic menhaden, Brevoortia tyrannus, and Gulf menhaden, B. patronus. From 1966 through 1969, 1,066,357 adult Atlantic menhaden were tagged; subsequently, from 1970 through 1987, 428,272 juveniles of this species were tagged. Similarly, from 1969 through 1971, 75,673 adult Gulf menhaden were tagged; concurrently from 1970 through 1985, 236,936 juveniles were tagged and released. This report provides an overview of the history of the tagging program, methodologies for both release and recovery activities, a summary of release areas and number of fish tagged within each area, and a review of assumptions necessary for the analysis of this type of mark-recovery data. The resulting data sets have proven to be highly useful for a variety of analyses ranging from determination of migratory patterns and population structure to estimating mortality rates. The relatively wide range of acceptance of tagging results by laymen, industry, and analysts alike have made these data extremely useful for management-oriented analyses.

The Status of Loggerhead, Caretta caretta; Kemp's Ridley, Lepidochelys kempi; and Green, Chelonia mydas, Sea Turtles in U.S. Waters: A Reconsideration

Assessing the status of widely distributed marine species can prove difficult because virtually every sampling technique has assumptions, limitations, and biases that affect the results of the study. These biases often are overlooked when the biological and nonbiological implications of the results are discussed. In a recent review, Thompson (1988) used mostly unpublished population census data derived from studies conducted by the National Marine Fisheries Service (NMFS) to draw conclusions about the status of Kemp's ridley, Lepidochelys kempi; Atlantic coast green turtles, Chelonia mydas; and the loggerhead sea turtle, Caretta caretta.

Quantifying intrapopulation variability in stable isotope data for Spotted Seatrout (Cynoscion nebulosus)

Stable isotope (SI) values of carbon (δ13C) and nitrogen (δ15N) are useful for determining the trophic connectivity between species within an ecosystem, but interpretation of these data involves important assumptions about sources of intrapopulation variability. We compared intrapopulation variability in δ13C and δ15N for an estuarine omnivore, Spotted Seatrout (Cynoscion nebulosus), to test assumptions and assess the utility of SI analysis for delineation of the connectivity of this species with other species in estuarine food webs. Both δ13C and δ15N values showed patterns of enrichment in fish caught from coastal to offshore sites and as a function of fish size. Results for δ13C were consistent in liver and muscle tissue, but liver δ15N showed a negative bias when compared with muscle that increased with absolute δ15N value. Natural variability in both isotopes was 5–10 times higher than that observed in laboratory populations, indicating that environmentally driven intrapopulation variability is detectable particularly after individual bias is removed through sample pooling. These results corroborate the utility of SI analysis for examination of the position of Spotted Seatrout in an estuarine food web. On the basis of these results, we conclude that interpretation of SI data in fishes should account for measurable and ecologically relevant intrapopulation variability for each species and system on a case by case basis.

Estimates of total seabird bycatch by Atlantic pelagic longline fisheries from 2003 to 2006

Results of recent seabird bycatch studies in the International Commission for the Conservation of Atlantic Tunas Convention Area were combined to estimate total seabird bycatch of pelagic longline fishing in the Atlantic Ocean, and bycatch per selected species. Available studies do not apply to the full spatial and temporal extent of the fishing effort, so assumptions were made to account for missing information. Over the 4 years from 2003 to 2006 the total seabird bycatch estimate was 48,500. Results indicate that about 57% of the pelagic longline seabird bycatch was albatrosses (Diomedea, Phoebastria, Thalassarche, Phoebetria spp.). This mortality is at a level to cause concern for the smaller and more vulnerable albatross populations in the region. Variation in annual seabird bycatch was caused by variation in total fishing effort, and movement of effort away from areas of higher seabird bycatch rates.

Estuarine use assessment: trial project in Casco Bay, Maine

The National Centers for Coastal Ocean Science (NCCOS) of the National Oceanic and Atmospheric Administration (NOAA) is interested in developing a project to determine the health of estuaries based on the stated or desired uses of society. An estuarine use assessment could complement the National Coastal Assessment, which tracks coastal and estuarine health through a series of environmental indicators. These indicators are used to assign a “score” to each coastal region, with some indicators reflecting the ability of the region to support desired uses such as fishing and swimming. An estuarine use assessment could also provide valuable information to resource managers and other decision-makers as they face decisions about the optimal and most sustainable mix of activities in an estuary. An initial step of an estuarine use assessment would be to define and quantify the desired societal uses of the estuary. Society includes residents living near the estuary or industries relying on the estuary, seasonal residents and tourists that use the estuary on a more limited basis, and the public at-large that may use or value the estuary indirectly. The desired uses may include discrete, visible uses such as swimming, recreational or commercial fishing, and navigation. They also may extend to broader, more intangible uses such as maintaining ecological functions or aesthetic appeal. National legislation such as the Estuary Restoration Act, which promotes and funds the restoration of estuaries in the U.S., reflects the public’s desire for estuaries to retain their ecological structures and functions. This report summarizes a project carried out in 2003 that attempted to quantify the desired human uses of a specific estuary in Maine and to determine current measures of success used by coastal managers in Maine to track the ability of the estuary to support desired uses. Casco Bay was chosen as the spatial embayment for which to delineate uses, and nutrient enrichment was selected as the parameter for confirming assumptions about current measures of outcomes related to uses. The report highlights some of the challenges to completing an estuarine use assessment and offers general recommendations for addressing these challenges.

Economic valuation of natural resources: a handbook for coastal resource policymakers

Professionals who are responsible for coastal environmental and natural resource planning and management have a need to become conversant with new concepts designed to provide quantitative measures of the environmental benefits of natural resources. These amenities range from beaches to wetlands to clean water and other assets that normally are not bought and sold in everyday markets. At all levels of government — from federal agencies to townships and counties — decisionmakers are being asked to account for the costs and benefits of proposed actions. To non-specialists, the tools of professional economists are often poorly understood and sometimes inappropriate for the problem at hand. This handbook is intended to bridge this gap. The most widely used organizing tool for dealing with natural and environmental resource choices is benefit-cost analysis — it offers a convenient way to carefully identify and array, quantitatively if possible, the major costs, benefits, and consequences of a proposed policy or regulation. The major strength of benefit-cost analysis is not necessarily the predicted outcome, which depends upon assumptions and techniques, but the process itself, which forces an approach to decision-making that is based largely on rigorous and quantitative reasoning. However, a major shortfall of benefit-cost analysis has been the difficulty of quantifying both benefits and costs of actions that impact environmental assets not normally, nor even regularly, bought and sold in markets. Failure to account for these assets, to omit them from the benefit-cost equation, could seriously bias decisionmaking, often to the detriment of the environment. Economists and other social scientists have put a great deal of effort into addressing this shortcoming by developing techniques to quantify these non-market benefits. The major focus of this handbook is on introducing and illustrating concepts of environmental valuation, among them Travel Cost models and Contingent Valuation. These concepts, combined with advances in natural sciences that allow us to better understand how changes in the natural environment influence human behavior, aim to address some of the more serious shortcomings in the application of economic analysis to natural resource and environmental management and policy analysis. Because the handbook is intended for non-economists, it addresses basic concepts of economic value such as willingness-to-pay and other tools often used in decision making such as costeffectiveness analysis, economic impact analysis, and sustainable development. A number of regionally oriented case studies are included to illustrate the practical application of these concepts and techniques.

Marine eutrophication review. Part 1: Quantifying the effects of nitrogen enrichment on phytoplankton in coastal ecosystems; Part 2: Bibliography with abstracts

Professionals who are responsible for coastal environmental and natural resource planning and management have a need to become conversant with new concepts designed to provide quantitative measures of the environmental benefits of natural resources. These amenities range from beaches to wetlands to clean water and other assets that normally are not bought and sold in everyday markets. At all levels of government — from federal agencies to townships and counties — decisionmakers are being asked to account for the costs and benefits of proposed actions. To non-specialists, the tools of professional economists are often poorly understood and sometimes inappropriate for the problem at hand. This handbook is intended to bridge this gap. The most widely used organizing tool for dealing with natural and environmental resource choices is benefit-cost analysis — it offers a convenient way to carefully identify and array, quantitatively if possible, the major costs, benefits, and consequences of a proposed policy or regulation. The major strength of benefit-cost analysis is not necessarily the predicted outcome, which depends upon assumptions and techniques, but the process itself, which forces an approach to decision-making that is based largely on rigorous and quantitative reasoning. However, a major shortfall of benefit-cost analysis has been the difficulty of quantifying both benefits and costs of actions that impact environmental assets not normally, nor even regularly, bought and sold in markets. Failure to account for these assets, to omit them from the benefit-cost equation, could seriously bias decisionmaking, often to the detriment of the environment. Economists and other social scientists have put a great deal of effort into addressing this shortcoming by developing techniques to quantify these non-market benefits. The major focus of this handbook is on introducing and illustrating concepts of environmental valuation, among them Travel Cost models and Contingent Valuation. These concepts, combined with advances in natural sciences that allow us to better understand how changes in the natural environment influence human behavior, aim to address some of the more serious shortcomings in the application of economic analysis to natural resource and environmental management and policy analysis. Because the handbook is intended for non-economists, it addresses basic concepts of economic value such as willingness-to-pay and other tools often used in decision making such as costeffectiveness analysis, economic impact analysis, and sustainable development. A number of regionally oriented case studies are included to illustrate the practical application of these concepts and techniques.