The statistical properties of recreational catch rate data for some fish stocks off the northeast U.S. coast

Recreational fisheries in the waters off the northeast U.S. target a variety of pelagic and demersal fish species, and catch and effort data sampled from recreational fisheries are a critical component of the information used in resource evaluation and management. Standardized indices of stock abundance developed from recreational fishery catch rates are routinely used in stock assessments. The statistical properties of both simulated and empirical recreational fishery catch-rate data such as those collected by the National Marine Fisheries Service (NMFS) Marine Recreational Fishery Statistics Survey (MRFSS) are examined, and the potential effects of different assumptions about the error structure of the catch-rate frequency distributions in computing indices of stock abundance are evaluated. Recreational fishery catch distributions sampled by the MRFSS are highly contagious and overdispersed in relation to the normal distribution and are generally best characterized by the Poisson or negative binomial distributions. The modeling of both the simulated and empirical MRFSS catch rates indicates that one may draw erroneous conclusions about stock trends by assuming the wrong error distribution in procedures used to developed standardized indices of stock abundance. The results demonstrate the importance of considering not only the overall model fit and significance of classification effects, but also the possible effects of model misspecification, when determining the most appropriate model construction.

On statistical comparison of efficiencies of fishing gear

The distribution of fish caught by experimental gill nets has been found to be in the Poisson or Negative binomial form. Using this information, application of Chi-square test as suggested by Mood et al. (1974) has been illustrated, for comparing the efficiencies of gill nets. This test provides an alternative to Anova F-test especially in the context of significance of non-additivity for the two-way model. Based on the present work and the findings by Nair (1982) and Nair & Alagaraja (1982, 1984) an outline approach for statistical comparison of the efficiencies of fishing gear is presented.

Distribution, movements, and habitat use of small striped bass (Morone saxatilis) across multiple spatial scales

Distribution, movements, and habitat use of small (<46 cm, juveniles and individuals of unknown maturity) striped bass (Morone saxatilis) were investigated with multiple techniques and at multiple spatial scales (surveys and tag-recapture in the estuary and ocean, and telemetry in the estuary) over multiple years to determine the frequency and duration of use of non-natal estuaries. These unique comparisons suggest, at least in New Jersey, that smaller individuals (<20 cm) may disperse from natal estuaries and arrive in non-natal estuaries early in life and take up residence for several years. During this period of estuarine residence, individuals spend all seasons primarily in the low salinity portions of the estuary. At larger sizes, they then leave these non-natal estuaries to begin coastal migrations with those individuals from nurseries in natal estuaries. These composite observations of frequency and duration of habitat use indicate that non-natal estuaries may provide important habitat for a portion of the striped bass population.

Potentials for different models for freshwater aquaculture development in the Red River Delta (Vietnam) using GIS analysis

This study was an attempt to apply land-based GIS analysis for freshwater aquaculture planning in the Red River Delta of Vietnam. It was based on diverse data sources in order to help decision makers at the site and also to contribute to the modelling of selection processes for aquaculture development planning in the region.

Seasonal, horizontal, and vertical distribution of phytoplankton chlorophyll a in the Northeast U.S. Continental Shelf Ecosystem

The broad scale features in the horizontal, vertical, and seasonal distribution of phytoplankton chlorophyll a on the northeast U.S. continental shelf are described based on 57,088 measurements made during 78 oceanographic surveys from 1977 through 1988. Highest mean water column chlorophyll concentration (Chlw,) is usually observed in nearshore areas adjacent to the mouths of the estuaries in the Middle Atlantic Bight (MAB), over the shallow water on Georges Bank, and a small area sampled along the southeast edge of Nantucket Shoals. Lowest Chlw «0.125 ug l-1) is usually restricted to the most seaward stations sampled along the shelf-break and the central deep waters in the Gulf of Maine. There is at least a twofold seasonal variation in phytoplankton biomass in all areas, with highest phytoplankton concentrations (m3) and highest integrated standing stocks (m2) occurring during the winter-spring (WS) bloom, and the lowest during summer, when vertical density stratification is maximal. In most regions, a secondary phytoplankton biomass pulse is evident during convective destratification in fall, usually in October. Fall bloom in some areas of Georges Bank approaches the magnitude of the WS-bloom, but Georges Bank and Middle Atlantic Bight fall blooms are clearly subordinate to WS-blooms. Measurements of chlorophyll in two size-fractions of the phytoplankton, netplankton (>20 um) and nanoplankton «20 um), revealed that the smaller nanoplankton are responsible for most of the phytoplankton biomass on the northeast U.S. shelf. Netplankton tend to be more abundant in nearshore areas of the MAB and shallow water on Georges Bank, where chlorophyll a is usually high; nanoplankton dominate deeper water at the shelf-break and deep water in the Gulf of Maine, where Chlw is usually low. As a general rule, the percent of phytoplankton in the netplankton size-fraction increases with increasing depth below surface and decreases proceeding offshore. There are distinct seasonal and regional patterns in the vertical distribution of chlorophyll a and percent netplankton, as revealed in composite vertical profiles of chlorophyll a constructed for 11 layers of the water column. Subsurface chlorophyll a maxima are ubiquitous during summer in stratified water. Chlorophyll a in the subsurface maximum layer is generally 2-8 times the concentration in the overlying and underlying water and approaches 50 to 75% of the levels observed in surface water during WS-bloom. The distribution of the ratio of the subsurface maximum chlorophyll a to surface chlorophyll a (SSR) during summer parallels the shelfwide pattern for stability, indexed as the difference in density (sigma-t) between 40 m and surface (stability 40. The weakest stability and lowest SSR's are found in shallow tidally-mixed water on Georges Bank; the greatest stability and highest SSR's (8-12:1) are along the mid and outer MAB shelf, over the winter residual water known as the "cold band." On Georges Bank, the distribution of SSR and the stability40 are roughly congruent with the pattern for maximum surface tidal current velocity, with values above 50 cms-1 defining SSR's less than 2:1 and the well-mixed area. Physical factors (bathymetry, vertical mixing by strong tidal currents, and seasonal and regional differences in the intensity and duration of vertical stratification) appear to explain much of the variability in phytoplankton chlorophyll a throughout this ecosystem. (PDF file contains 126 pages.)

Catch rates and demographics of loggerhead sea turtles (Caretta caretta) captured from the Charleston, South Carolina, shipping channel during the period of mandatory use of turtle excluder devices (TEDs)

Trawling was conducted in the Charleston, South Carolina, shipping channel between May and August during 2004–07 to evaluate loggerhead sea turtle (Caretta caretta) catch rates and demographic distributions. Two hundred and twenty individual loggerheads were captured in 432 trawling events during eight sampling periods lasting 2–10 days each. Catch was analyzed by using a generalized linear model. Data were fitted to a negative binomial distribution with the log of standardized sampling effort (i.e., an hour of sampling with a net head rope length standardized to 30.5 m) for each event treated as an offset term. Among 21 variables, factors, and interactions, five terms were significant in the final model, which accounted for 45% of model deviance. Highly significant differences in catch were noted among sampling periods and sampling locations within the channel, with greatest catch furthest seaward consistent with historical observations. Loggerhead sea turtle catch rates in 2004–07 were greater than in 1991–92 when mandatory use of turtle excluder devices was beginning to be phased in. Concurrent with increased catch rates, loggerheads captured in 2004–07 were larger than in 1991–92. Eighty-five percent of loggerheads captured were ≤75.0 cm straight-line carapace length (nuchal notch to tip of carapace) and there was a 3.9:1 female-to-male bias, consistent with limited data for this location two decades earlier. Only juvenile loggerheads ≤75.0 cm possessed haplotypes other than CC-A01 or CC-A02 that dominate in the region. Six rare and one un-described haplotype were predominantly found in June 2004.

A general framework for integrating environmental time series into stock assessment models: model description, simulation testing, and example

We present a method to integrate environmental time series into stock assessment models and to test the significance of correlations between population processes and the environmental time series. Parameters that relate the environmental time series to population processes are included in the stock assessment model, and likelihood ratio tests are used to determine if the parameters improve the fit to the data significantly. Two approaches are considered to integrate the environmental relationship. In the environmental model, the population dynamics process (e.g. recruitment) is proportional to the environmental variable, whereas in the environmental model with process error it is proportional to the environmental variable, but the model allows an additional temporal variation (process error) constrained by a log-normal distribution. The methods are tested by using simulation analysis and compared to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. In the traditional method, the estimates of recruitment were provided by a model that allowed the recruitment only to have a temporal variation constrained by a log-normal distribution. We illustrate the methods by applying them to test the statistical significance of the correlation between sea-surface temperature (SST) and recruitment to the snapper (Pagrus auratus) stock in the Hauraki Gulf–Bay of Plenty, New Zealand. Simulation analyses indicated that the integrated approach with additional process error is superior to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. The results suggest that, for the snapper stock, recruitment is positively correlated with SST at the time of spawning.

Characterization of the benthos, marine debris and bottom fish at Gray’s Reef National Marine Sanctuary

Executive Summary: Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary. The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect. GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces. The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS. Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions). GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items. Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown. Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata. Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

Species and size relationships within schools of yellowfin and skipjack tuna as indicated by catches in the Eastern Tropical Pacific Ocean

ENGLISH: Yellowfin tuna, Neothunnus macropterus, and skipjack tuna, Katsuwonus pelamis, are fished intensively off the west coast of the Americas in an area from about the California-Mexico border in the north to the Peru-Chile border in the south. The historical development of this fishery, and its expansion by the long-range California fleets of bait and purse-seine vessels, are well documented by Godsil (1938), Scofield (1951) and Shimada and Sehaefer (1956). The quarterly distribution of the tuna catches within this area has been reported for some recent years by Alverson (1959). SPANISH: Los atunes aleta amarilla, Neothunnus macropterus, y barrilete, Katsuwonus pelamis, son pescados con intensidad frente a la costa occidental del continente americano, en un área comprendida más o menos entre la frontera California-México en el norte y el límite Perú-Chile en el sur. El desarrollo histórico de esta pesquería y la expansión que le han dado las flotas californianas de largo radio de acción, formadas por los barcos de carnada y rederos, están bien documentados por Godsil (1938), Scofield (1951) y Shimada y Schaefer (1956). La distribución trimestral de las pescas de atún dentro de esta área ha sido tratada por Alverson (1959) con referencia a años recientes.

Aquaculture genetics research and issues in INGA member countries/institutions

The information presented here is extracted from the presentations and discussions at the Sixth Steering Committee Meeting of the International Network on Genetics in Aquaculture (INGA) held in Hanoi, Vietnam on 8-10 May 2001. The main topics discussed were: review of genetics research progress and planned activities in member countries and Associate Member institutions; genetics improvement technologies; strategies and action plans for distribution of improved fish breeds to small-scale farmers; ecological risk assessment for genetically improved fish breeds; methods for monitoring the uptake of improved strains and impact assessment; and network activities and collaborations.

Evaluation of a Pound Net Leader Designed to Reduce Sea Turtle Bycatch

Offshore pound net leaders in the southern portion of Chesapeake Bay in Virginia waters were documented to incidentally take protected loggerhead, Caretta caretta, and Kemp’s ridley, Lepidochelys kempii, sea turtles. Because of these losses, NOAA’s National Marine Fisheries Service (NMFS) in 2004 closed the area to offshore pound net leaders annually from 6 May to 15 July and initiated a study of an experimental leader design that replaced the top two-thirds of the traditional mesh panel leader with vertical ropes (0.95 cm) spaced 61 cm apart. This experimental leader was tested on four pound net sites on the eastern shore of Chesapeake Bay in 2004 and 2005. During the 2 trial periods, 21 loggerhead and Kemp’s ridley sea turtles were found interacting with the control leader and 1 leatherback turtle, Dermochelys coriacea, was found interacting with the experimental leader. Results of a negative binomial regression analysis comparing the two leader designs found the experimental leader significantly reduced sea turtle interactions (p=0.03). Finfish were sampled from the pound nets in the study to assess finfish catch performance differences between the two leader designs. Although the conclusions from this element of the experiment are not robust, paired t-test and Wilcoxon signed rank test results determined no significant harvest weight difference between the two leaders. Kolmogorov-Smirnov tests did not reveal any substantive size selectivity differences between the two leaders.

An approach to estimating rockfish biomass based on larval production, with application to Sebastes jordani

An assessment of the total biomass of shortbelly rockfish (Sebastes jordani) off the central California coast is presented that is based on a spatially extensive but temporally restricted ichthyoplankton survey conducted during the 1991 spawning season. Contemporaneous samples of adults were obtained by trawl sampling in the study region. Daily larval production (7.56 × 1010 larvae/d) and the larval mortality rate (Z=0.11/d) during the cruise were estimated from a larval “catch curve,” wherein the logarithm of total age-specific larval abundance was regressed against larval age. For this analysis, larval age compositions at each of the 150 sample sites were determined by examination of otolith microstructure from subsampled larvae (n=2203), which were weighted by the polygonal Sette-Ahlstrom area surrounding each station. Female population weight-specific fecundity was estimated through a life table analysis that incorporated sex-specific differences in adult growth rate, female maturity, fecundity, and natural mortality (M). The resulting statistic (102.17 larvae/g) was insensitive to errors in estimating M and to the pattern of recruitment. Together, the two analyses indicated that a total biomass equal to 1366 metric tons (t)/d of age-1+ shortbelly rockfish (sexes combined) was needed to account for the observed level of spawning output during the cruise. Given the long-term seasonal distribution of spawning activity in the study area, as elucidated from a retrospective examination of California Cooperative Oceanic Fisheries Investigation (CalCOFI) ichthyoplankton samples from 1952 to 1984, the “daily” total biomass was expanded to an annual total of 67,392 t. An attempt to account for all sources of error in the derivation of this estimate was made by application of the delta-method, which yielded a coefficient of variation of 19%. The relatively high precision of this larval production method, and the rapidity with which an absolute biomass estimate can be obtained, establishes that, for some species of rockfish (Sebastes spp.), it is an attractive alternative to traditional age-structured stock assessments.

The three dimensional model with the affection of stratified density (Caspian Sea)

The hydro dynamical actions in big Lakes directly influence dynamic, physical and chemical affairs. The circulation's models and temperature have something to do with the movements of fluids, and analysis for circulation in Caspian sea is because of the lack of observation through which the circulations and out comings are determined. Through the studies, three dimensional simulations (Large- Scale) are planned and performed, according to Smolakiewicz and Margolin works. This is a non- hydrostatic and Boussinesq approximation is used in its formulation is used in its formulation on the basis of Lipps (1990) theorem and curve lines, the fluid is constant adiabatic and stratified, and the wind power is considered zero. The profile of speed according to previous depth and before ridge can be drawn on the basis of density available between northern and southern ridges. The circulation field is drawn from 3 cm/s to 13 cm/s on the plate z= 5 cm , the vertical changes of speed on the plate is 0.02 m/s. Vertical profile , horizontal speed in previous on, and after the ridges on are drawn on different spaces. It changes from 0.5 cm/s to 1 cm/s before ridges.

Beverton and Holt equations: spreadsheet functions and uncertainty

This contribution illustrates how modern spreadsheets aid the calculation and visualization of yield models and how the effects of uncertainties may be incorporated using Monte Carlo simulation. It is argued that analogous approaches can be implemented for other assessment models of simple to medium complexity justifying wider use of spreadsheets in fisheries analysis and training.