A Bayesian method for identification of stock mixtures from molecular marker data

Molecular markers have been demonstrated to be useful for the estimation of stock mixture proportions where the origin of individuals is determined from baseline samples. Bayesian statistical methods are widely recognized as providing a preferable strategy for such analyses. In general, Bayesian estimation is based on standard latent class models using data augmentation through Markov chain Monte Carlo techniques. In this study, we introduce a novel approach based on recent developments in the estimation of genetic population structure. Our strategy combines analytical integration with stochastic optimization to identify stock mixtures. An important enhancement over previous methods is the possibility of appropriately handling data where only partial baseline sample information is available. We address the potential use of nonmolecular, auxiliary biological information in our Bayesian model.

Age composition and distribution of red drum (Sciaenops ocellatus) in offshore waters of the north central Gulf of Mexico: an evaluation of a stock under a federal harvest moratorium

Because of a lack of fishery-dependent data, assessment of the recovery of fish stocks that undergo the most aggressive form of management, namely harvest moratoriums, remains a challenge. Large schools of red drum (Sciaenops ocellatus) were common along the northern Gulf of Mexico until the late 1980s when increased fishing effort quickly depleted the stock. After 24 years of harvest moratorium on red drum in federal waters, the stock is in need of reassessment; however, fisherydependent data are not available in federal waters and fishery-independent data are limited. We document the distribution, age composition, growth, and condition of red drum in coastal waters of the north central Gulf of Mexico, using data collected from a nearshore, randomized, bottom longline survey. Age composition of the fishery-independent catch indicates low mortality of fish age 6 and above and confirms the effectiveness of the federal fishing moratorium. Bottom longline surveys may be a cost-effective method for developing fishery-independent indices for red drum provided additional effort can be added to nearshore waters (<20 m depth). As with most stocks under harvest bans, effective monitoring of the recovery of red drum will require the development of fishery-independent indices. With limited economic incentive to evaluate non-exploited stocks, the most cost-effective approach to developing such monitoring is expansion of existing fishery independent surveys. We examine this possibility for red drum in the Gulf of Mexico and recommend the bottom longline survey conducted by the National Marine Fisheries Service expand effort in nearshore areas to allow for the development of long-term abundance indices for red drum.

A prior for steepness in stock-recruitment relationships, based on an evolutionary persistence principle

Priors are existing information or beliefs that are needed in Bayesian analysis. Informative priors are important in obtaining the Bayesian posterior distributions for estimated parameters in stock assessment. In the case of the steepness parameter (h), the need for an informative prior is particularly important because it determines the stock-recruitment relationships in the model. However, specifications of the priors for the h parameter are often subjective. We used a simple population model to derive h priors based on life history considerations. The model was based on the evolutionary principle that persistence of any species, given its life history (i.e., natural mortality rate) and its exposure to recruitment variability, requires a minimum recruitment compensation that enables the species to rebound consistently from low critical abundances (Nc). Using the model, we derived the prior probability distributions of the h parameter for fish species that have a range of natural mortality, recruitment variabilities, and Nt values.

A catch-free stock assessment model with application to goliath grouper (Epinephelus itajara) off southern Florida

Many modern stock assessment methods provide the machinery for determining the status of a stock in relation to certain reference points and for estimating how quickly a stock can be rebuilt. However, these methods typically require catch data, which are not always available. We introduce a model-based framework for estimating reference points, stock status, and recovery times in situations where catch data and other measures of absolute abundance are unavailable. The specif ic estimator developed is essentially an age-structured production model recast in terms relative to pre-exploitation levels. A Bayesian estimation scheme is adopted to allow the incorporation of pertinent auxiliary information such as might be obtained from meta-analyses of similar stocks or anecdotal observations. The approach is applied to the population of goliath grouper (Epinephelus itajara) off southern Florida, for which there are three indices of relative abundance but no reliable catch data. The results confirm anecdotal accounts of a marked decline in abundance during the 1980s followed by a substantial increase after the harvest of goliath grouper was banned in 1990. The ban appears to have reduced fishing pressure to between 10% and 50% of the levels observed during the 1980s. Nevertheless, the predicted fishing mortality rate under the ban appears to remain substantial, perhaps owing to illegal harvest and depth-related release mortality. As a result, the base model predicts that there is less than a 40% chance that the spawning biomass will recover to a level that would produce a 50% spawning potential ratio.

Stock evaluation and development of a breeding program for common carp (Cyprinus carpio) in Karnataka, India: progress of a research project

Common carp (Cyprinus carpio) is the single most important species for aquaculture in the state of Karnataka, India, where it is generally grown in polyculture with Indian major carps. Precocious maturation and unwanted reproduction in the species have been identified as constraints to increase production in aquaculture and culture-based fisheries in Karnataka state. Stocks of C. carpio obtained from Hungary (Amur and P3), Indonesia (Rajdanu) and Vietnam (SV) are being assessed alongside two local stocks (L-BRP and L-FRS) in a series of culture performance trials with the objective of setting up a base population for selective breeding. The paper presents progress of research being undertaken at the Fisheries Research Station, University of Agricultural Sciences, Bangalore, India.

Culture of tropical sea cucumbers for stock restoration and enhancement

Severe overfishing of sea cucumbers has occurred in most countries of the tropical Indo-Pacific. The release of juveniles is being examined at the ICLARM Coastal Aquaculture Centre in the Solomon islands as a means of restoring and enhancing tropical sea cucumber stocks. Sandfish (Holothuria scabra) are the tropical species that show the best potential for stock enhancement. Sandfish are of high value, widely distributed and relatively easy to culture in simple systemss at a low cost. This paper summarizes information about the culture of H. scabra and compares it to that of the temperate species Stichopus japonicus.

A simple spreadsheet model to incorporate seasonal growth into length-based stock assessment methods

The paper describes a method by which seasonal growth can be incorporated into length-converted catch curves and cohort analyses using a spreadsheet. The method is based on calculating the length of fish using seasonal growth parameters on a daily basis. A LOOKUP function is then used to find the age corresponding to the length.

Collection of fish lengths for stock assessment in developing countries

A review of the data (handling) requirements for length-based stock assessment is presented, with emphasis on the relationship between the expected outputs and the key features of the samples required, and on biases and other sources of inaccuracy.

Life history characteristics for silvergray rockfish (Sebastes brevispinis) in British Columbia waters and the implications for stock assessment and management

We summarize the life history characteristics of silvergray rockfish (Sebastes brevispinis) based on commercial fishery data and biological samples from British Columbia waters. Silvergray rockfish occupy bottom depths of 100−300 m near the edge of the continental shelf. Within that range, they appear to make a seasonal movement from 100−200 m in late summer to 180−280 m in late winter. Maximum observed age in the data set was 81 and 82 years for females and males, respectively. Maximum length and round weight was 73 cm and 5032 g for females and 70 cm and 3430 g for males. The peak period of mating lasted from December to February and parturition was concentrated from May to July. Both sexes are 50% mature by 9 or 10 years and 90% are mature by age 16 for females and age 13 years for males. Fecundity was estimated from one sample of 132 females and ranged from 181,000 to 1,917,000 oocytes and there was no evidence of batch spawning. Infection by the copepod parasite Sarcotaces arcticus appears to be associated with lower fecundity. Sexual maturation appears to precede recruitment to the trawl fishery; thus spawning stock biomass per recruit analysis (SSB/R) indicates that a F50% harvest target would correspond to an F of 0.072, 20% greater than M (0.06). Fishery samples may bias estimates of age at maturity but a published meta-data analysis, in conjunction with fecundity data, independently supports an early age of maturity in relation to recruitment. Although delayed recruitment to the fishery may provide more resilience to exploitation, managers may wish to forego maximizing economic yield from this species. Silvergray rockfish are a relatively minor but unavoidable part of the multiple species trawl catch. Incorrectly “testing” the resilience of one species may cause it to be the weakest member of the specie

Sex-change rules, stock dynamics, and the performance of spawning-per-recruit measures in protogynous stocks

Predicting and under-standing the dynamics of a population requires knowledge of vital rates such as survival, growth, and reproduction. However, these variables are influenced by individual behavior, and when managing exploited populations, it is now generally realized that knowledge of a species’ behavior and life history strategies is required. However, predicting and understanding a response to novel conditions—such as increased fishing-induced mortality, changes in environmental conditions, or specific management strategies—also require knowing the endogenous or exogenous cues that induce phenotypic changes and knowing whether these behaviors and life history patterns are plastic. Although a wide variety of patterns of sex change have been observed in the wild, it is not known how the specific sex-change rule and cues that induce sex change affect stock dynamics. Using an individual based model, we examined the effect of the sex-change rule on the predicted stock dynamics, the effect of mating group size, and the performance of traditional spawning-per-recruit (SPR) measures in a protogynous stock. We considered four different patterns of sex change in which the probability of sex change is determined by 1) the absolute size of the individual, 2) the relative length of individuals at the mating site, 3) the frequency of smaller individuals at the mating site, and 4) expected reproductive success. All four pat-terns of sex change have distinct stock dynamics. Although each sex-change rule leads to the prediction that the stock will be sensitive to the size-selective fishing pattern and may crash if too many reproductive size classes are fished, the performance of traditional spawning-per-recruit measures, the fishing pattern that leads to the greatest yield, and the effect of mating group size all differ distinctly for the four sex-change rules. These results indicate that the management of individual species requires knowledge of whether sex change occurs, as well as an understanding of the endogenous or exogenous cues that induce sex change.

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.

A Brief Interpretation of Summer Flounder, Paralichthys dentatus, Movements and Stock Structure with New Tagging Data on Juveniles

Summer flounder, Paralichthys dentatus, are managed as a single stock along the Atlantic coast from the U.S.– Canada border to the southern border of North Carolina. Justification of the single-stock approach is based on lack of genetic evidence for multiple stocks and the difficulty presented by managing the species from Cape Hatteras to the U.S.–Canada border. In this review, we present an interpretation of various morphometric, meristic, biochemical, and tagging studies, published and unpublished, that indicate the presence of two, or possibly three, distinct stocks in the management area. In addition, we have included new data from a tagging study that was conducted on juveniles from Virginia that aids in defining the stock(s) north of Cape Hatteras. Summer flounder, overfished for the past two decades, is recovering, and reconsideration of proposed stock structure could have direct implications for management policy decisions.

A Review of Stock Identification of Haddock, Melanogrammus aeglefinus, in the Northwest Atlantic Ocean

Haddock, Melanogrammus aeglefinus, is a principal commercial species distributed throughout the northwest Atlantic Ocean, with major aggregations occurring on Georges Bank and on the Scotian Shelf. This review examines all available information on stock structure of haddock to evaluate the suitability of current stock units and to investigate areas that require further research. Combined information from tag-recapture, demographic, recruitment, meristic, parasitic, and genetic studies provide evidence for the identification of haddock stocks, with major population divisions occurring between New England, Nova Scotia, and Newfoundland waters. Within each of these major divisions a number of discrete stocks appear to exist, although uncertainty remains in the amount of separation found within each region. Research utilizing more recent stock identification techniques should refine and improve our understanding of haddock stock structure in the northwest Atlantic.

A report on the strategic stock assessment survey of the Colton Beck catchment 1994 with particular reference to salmonids

This is the report on the strategic stock assessment survey of the Colton Beck catchment in 1994 with particular reference to salmonids in Colton Beck, River Ea, River Gilpin and Rusland Pool. This report forms one part of the third year of a triennial survey programme for the South West Cumbria and South Cumbria catchments. It was produced by the National Rivers Authority in 1994. Colton Beck had excellent densities of sea trout (Salmo trutta) and a small population of salmon (Salmo salar) in its lowest reaches. The total productivity was very good throughout the catchment. Stocking of sea trout fry in 1993 has enhanced the population with survivors through to parr probably adding to the scoring of double class A at two sites in the survey in 1994. Stocking was not undertaken in 1994, but the population appears to be maintaining itself at a very high level.