ROV-based Deep Water Monitoring of the Northern Channel Islands Marine Protected Areas Annual Report - 2007

Research cruises were conducted in August-October 2007 to complete the third annual remotely operated vehicle (ROV)-based assessments of nearshore rocky bottom finfish at ten sites in the northern Channel Islands. Annual surveys at the Channel Islands have been conducted since 2004 at four sites and were expanded to ten sites in 2005 to monitor potential marine protected area (MPA)effects on baseline fish density. Six of the ten sites are in MPAs and four in nearby fished reference areas. In 2007 the amount of soft-only substrate on the 141 track lines surveyed was again estimated in real-time in order to target rocky bottom habitat. These real-time estimates of hard and mixed substrate for all ten sites averaged 57%, 1% more than the post-processed average of 56%. Surveys generated 69.9 km of usable video for use in finfish density calculations, with target rocky bottom habitat accounting for 56% (39.1 km) for all sites combined. The amount of rocky habitat sampled by site averaged 3.8 km and ranged from 3.3 km sampled at South Point, a State Marine Reserve (SMR) off Santa Rosa Island, to 4.7 km at Anacapa Island SMR. A sampling goal of 75 transects at all 10 sites was met using real-time habitat estimates combined with precautionary over-sampling by 10%. A total of seventy kilometers of sampling is projected to produce at least seventy-five 100 m2 transects per site. Thirteen of 26 finfish taxa observed were selected for quantitative evaluation over the time series based on a minimum criterion of abundance (0.05/100 m2). Ten of these 13 finfish appear to be more abundant at the state marine reserves relative to fished areas when densities were averaged across the 2005 to 2007 period. One of the species that appears to be more abundant in fished areas was señorita, a relatively small prey species that is not a commercial or recreational target. (PDF contains 83 pages.)

Variations in year-class strength and estimates of the catchability coefficient of yellowfin tuna, Thunnus albacares, in the Eastern Pacific Ocean

ENGLISH: Year-class composition of catch, virtual population size and yearclass strength were determined from serial samples of size composition of catches and catch records. Murphy's Solution to the catch equation, which is free from the effects caused by changes in fishing pressure, was used to estimate year-class strength, i.e. the total population of fish age 3/4 years. The resultant estimates indicated that the X55, X56, X57, X62 and X63 year classes were above average and the X58, X59, X60, X61 and X64 year classes were below average. The year-class designation refers to the year of actual entry or presumed year of entry into the commercial fishery (at approximately 1 year of age). The strongest and poorest year classes were the X57 and X61 classes, respectively. The ratio of the strongest to the weakest year class was 2.6. This amount of variation is small compared to that found for other species of fish. It was found that the relationship between stock size and yearclass strength is of no value in predicting year-class strength. As a by-product of the analysis, estimates of the catchability coefficients (qN) of the age groups in the fishery were obtained, These estimates were found to vary with age and time. Age-two fish apparently showed the greatest vulnerability to fishing gear, followed by ages three and one, respectively. The average estimate of the catchability coefficient in weight was calculated and found to compare favorably with Schaefer's estimate. The influence of sea-surface water temperature upon year-class strength was investigated to determine whether the latter can be predicted from a knowledge of sea-surface temperatures prevailing during and following spawning. No correlation was evident. SPANISH: La composición de la clase anual en la captura, el tamaño de la población virtual y la fuerza de clase anual, fueron determinados según una serie de muestras de la composición de tamaño de las capturas y de los registros de captura. La Solución de Murphy de la ecuación de captura, que está libre de los efectos causados por los cambios de la presión de pesca, fue usada para estimar la fuerza de la clase anual, i.e. la población total de peces de 3/4 años. Las estimaciones resultantes indican que las clases anuales X55, X56, X57, X62 y X63 fueron superiores al promedio y que las clases anuales X58, X59, X60, X61 y X64 fueron inferiores al promedio. La designación de la clase anual se refiere al año actual de entrada o al año supuesto de entrada en la pesca comercial (aproximadamente a la edad de 1 año). Las clases anuales más fuertes y más pobres fueron la X57 y X61 respectivamente. La razón de la clase anual más fuerte en relación a la más débil fue 2.6. Esta cantidad de variación es pequeña comparada con la encontrada para otras especies de peces. Se encontró que la relación entre en tamaño del stock y la fuerza de la clase anual no tiene valor en predecir la fuerza de la clase anual. Se obtuvieron estimaciones de los coeficientes de capturabilidad (qN) de los grupos de edad en la pesquería como un producto derivado del análisis. Se encontraron que estas estimaciones variaron con la edad y tiempo. Los peces de edad dos aparentemente presentaron la vulnerabilidad más grande en relación al arte pesquero, seguidos por las edades tres y una, respectivamente. La estimación promedio del coeficiente de capturabilidad en peso fue calculada y se encontró que podía compararse favorablemente con la estimación de Schaefer. La influencia de la temperatura del agua superficial del mar sobre la fuerza de la clase anual fue investigada para determinar si se podía predecir esta última según el conocimíento de las temperaturas superficiales del mar prevalecientes durante el desove y después de éste. No hubo correlación evidente. (PDF contains 44 pages.)

Fecundity estimates for Maryland Striped Bass

Contemporary striped bass population modeling efforts on coastal stocks point to a reduced population fecundity in Chesapeake Bay being partially responsible for declining reproduction (Anonymous 1985; Boreman and Goodyear 1984). Fecundity values used in these models were based on earlier work by jackson and tiller (1952), lewis and Bonner (1966), Hollis (1967) and Holland and Yelverton (1973). An important feature to the Boreman and Goodyear (1985) model (FSIM) is an accurate determination of the fecundity weight regression equation used to determine the rate of egg deposition over time. Egg deposition models in turn can be used to determine how reproductive potential is changing over time in response to various management actions, i.e. reducing fishing mortality rates. thus it is imperative to follow population stock structure in the Bay system and to develop a contemporary fecundity relationship for striped bass. This report deals with the gonadal material collected in 1986 and 1987 from a coordinated Maryland field program. Samples were obtained from drift gill net collections during the spawning season from four localities: Potomac Estuary, Upper Bay, Chesapeake and Delaware Canal, and the Choptank Estuary (Figure 1).

Comparison of habitat-based indices of abundance with fishery-independent biomass estimates from bottom trawl surveys

Rockfish species are notoriously difficult to sample with multispecies bottom trawl survey methods. Typically, biomass estimates have high coefficients of variation and can fluctuate outside the bounds of biological reality from year to year. This variation may be due in part to their patchy distribution related to very specific habitat preferences. We successfully modeled the distribution of five commercially important and abundant rockf ish species. A two-stage modeling method (modeling both presence-absence and abundance) and a collection of important habitat variables were used to predict bottom trawl survey catch per unit of effort. The resulting models explained between 22% and 66% of the variation in rockfish distribution. The models were largely driven by depth, local slope, bottom temperature, abundance of coral and sponge, and measures of water column productivity (i.e., phytoplankton and zooplankton). A year-effect in the models was back-transformed and used as an index of the time series of abundance. The abundance index trajectories of three of five species were similar to the existing estimates of their biomass. In the majority of cases the habitat-based indices exhibited less interannual variability and similar precision when compared with stratified survey-based biomass estimates. These indices may provide for stock assessment models a more stable alternative to current biomass estimates produced by the multispecies bottom trawl survey in the Gulf of Alaska.

Survey- and fishery-derived estimates of Pacific cod (Gadus macrocephalus) biomass: implications for strategies to reduce interactions between groundfish fisheries and Steller sea lions (Eumetopias jubatus)

Survey- and fishery-derived biomass estimates have indicated that the harvest indices for Pacific cod (Gadus macrocephalus) within a portion of Steller sea lion (Eumetopias jubatus) critical habitat in February and March 2001 were five to 16 times greater than the annual rate for the entire Bering Sea-Aleutian Islands stock. A bottom trawl survey yielded a cod biomass estimate of 49,032 metric tons (t) for the entire area surveyed, of which less than half (23,329 t) was located within the area used primarily by the commercial fishery, which caught 11,631 t of Pacific cod. Leslie depletion analyses of fishery data yielded biomass estimates of approximately 14,500 t (95% confidence intervals of approximately 9,000–25,000 t), which are within the 95% confidence interval on the fished area survey estimate (12,846–33,812 t). These data indicate that Leslie analyses may be useful in estimating local fish biomass and harvest indices for certain marine fisheries that are well constrained spatially and relatively short in duration (weeks). In addition, fishery effects on prey availability within the time and space scales relevant to foraging sea lions may be much greater than the effects indicated by annual harvest rates estimated from stock assessments averaged across the range of the target spec

Tracking Pacific bluefin tuna (Thunnus thynnus orientalis) in the northeastern Pacific with an automated algorithm that estimates latitude by matching sea-surface-temperature data from satellites with temperature data from tags on fish

Data recovered from 11 popup satellite archival tags and 3 surgically implanted archival tags were used to analyze the movement patterns of juvenile northern bluefin tuna (Thunnus thynnus orientalis) in the eastern Pacific. The light sensors on archival and pop-up satellite transmitting archival tags (PSATs) provide data on the time of sunrise and sunset, allowing the calculation of an approximate geographic position of the animal. Light-based estimates of longitude are relatively robust but latitude estimates are prone to large degrees of error, particularly near the times of the equinoxes and when the tag is at low latitudes. Estimating latitude remains a problem for researchers using light-based geolocation algorithms and it has been suggested that sea surface temperature data from satellites may be a useful tool for refining latitude estimates. Tag data from bluefin tuna were subjected to a newly developed algorithm, called “PSAT Tracker,” which automatically matches sea surface temperature data from the tags with sea surface temperatures recorded by satellites. The results of this algorithm compared favorably to the estimates of latitude calculated with the lightbased algorithms and allowed for estimation of fish positions during times of the year when the lightbased algorithms failed. Three near one-year tracks produced by PSAT tracker showed that the fish range from the California−Oregon border to southern Baja California, Mexico, and that the majority of time is spent off the coast of central Baja Mexico. A seasonal movement pattern was evident; the fish spend winter and spring off central Baja California, and summer through fall is spent moving northward to Oregon and returning to Baja California.

Application of an acoustic–trawl survey design to improve estimates of rockfish biomass

Biomass estimates of several species of Alaskan rockfishes exhibit large interannual variations. Because rockfishes are long lived and relatively slow growing, large, short-term shifts in population abundance are not likely. We attribute the variations in biomass estimates to the high variability in the spatial distribution of rockfishes that is not well accounted for by the survey design currently used. We evaluated the performance of an experimental survey design, the Trawl and Acoustic Presence/Absence Survey (TAPAS), to reduce the variability in estimated biomass for Pacific ocean perch (Sebastes alutus). Analysis of archived acoustic backscatter data produced an acoustic threshold for delineating potential areas of high (“patch”) and low (“background”) catch per unit of effort (CPUE) in real time. In 2009, we conducted a 12-day TAPAS near Yakutat, Alaska. We completed 59 trawls at 19 patch stations and 40 background stations. The design performed well logistically, and Pacific ocean perch (POP) accounted for 55% of the 31 metric tons (t) of the catch from this survey. The resulting estimates of rockfish biomass were slightly less precise than estimates from simple random sampling. This difference in precision was due to the weak relationship of CPUE to mean volume backscattering and the relatively low variability of POP CPUE encountered. When the data were re-analyzed with a higher acoustic threshold than the one used in the field study, performance was slightly better with this revised design than with the original field design. The TAPAS design could be made more effective by establishing a stronger link between acoustic backscatter and CPUE and by deriving an acoustic threshold that allows better identification of backscatter as that from the target species.

Effect of sampling interval on estimates of larval supply

Estimates of larval supply can provide information on year-class strength that is useful for fisheries management. However, larval supply is difficult to monitor because long-term, high-frequency sampling is needed. The purpose of this study was to subsample an 11-year record of daily larval supply of blue crab (Callinectes sapidus) to determine the effect of sampling interval on variability in estimates of supply. The coefficient of variation in estimates of supply varied by 0.39 among years at a 2-day sampling interval and 0.84 at a 7-day sampling interval. For 8 of the 11 years, there was a significant correlation between mean daily larval supply and lagged fishery catch per trip (coefficient of correlation [r]=0.88). When these 8 years were subsampled, a 2-day sampling interval yielded a significant correlation with fishery data only 64.5% of the time and a 3-day sampling interval never yielded a significant correlation. Therefore, high-frequency sampling (daily or every other day) may be needed to characterize interannual variability in larval supply.

Fish lost at sea: the effect of soak time on pelagic longline catches

Our analyses of observer records reveal that abundance estimates are strongly influenced by the timing of longline operations in relation to dawn and dusk and soak time— the amount of time that baited hooks are available in the water. Catch data will underestimate the total mortality of several species because hooked animals are “lost at sea.” They fall off, are removed, or escape from the hook before the longline is retrieved. For example, longline segments with soak times of 20 hours were retrieved with fewer skipjack tuna and seabirds than segments with soak times of 5 hours. The mortality of some seabird species is up to 45% higher than previously estimated. The effects of soak time and timing vary considerably between species. Soak time and exposure to dusk periods have strong positive effects on the catch rates of many species. In particular, the catch rates of most shark and billfish species increase with soak time. At the end of longline retrieval, for example, expected catch rates for broadbill swordfish are four times those at the beginning of retrieval. Survival of the animal while it is hooked on the longline appears to be an important factor determining whether it is eventually brought on board the vessel. Catch rates of species that survive being hooked (e.g. blue shark) increase with soak time. In contrast, skipjack tuna and seabirds are usually dead at the time of retrieval. Their catch rates decline with time, perhaps because scavengers can easily remove hooked animals that are dead. The results of our study have important implications for fishery management and assessments that rely on longline catch data. A reduction in soak time since longlining commenced in the 1950s has introduced a systematic bias in estimates of mortality levels and abundance. The abundance of species like seabirds has been over-estimated in recent years. Simple modifications to procedures for data collection, such as recording the number of hooks retrieved without baits, would greatly improve mortality estimates.

Annual estimates of the unobserved incidental kill of pantropical spotted dolphin (Stenella attenuata attenuata) calves in the tuna purse-seine fishery of the eastern tropical Pacific

We estimated the total number of pantropical spotted dolphin (Stenella attenuata) mothers killed without their calves (“calf deficit”) in all tuna purse-seine sets from 1973– 90 and 1996–2000 in the eastern tropical Pacific. Estimates were based on a tally of the mothers killed as reported by color pattern and gender, several color-pattern-based frequency tables, and a weaning model. Over the time series, there was a decrease in the calf deficit from approximately 2800 for the western-southern stock and 5000 in the northeastern stock to about 60 missing calves per year. The mean deficit per set decreased from approximately 1.5 missing calves per set in the mid-1970s to 0.01 per set in the late-1990s. Over the time series examined, from 75% to 95% of the lactating females killed were killed without a calf. Under the assumption that these orphaned calves did not survive without their mothers, this calf deficit represents an approximately 14% increase in the reported kill of calves, which is relatively constant across the years examined. Because the calf deficit as we have defined it is based on the kill of mothers, the total number of missing calves that we estimate is potentially an underestimate of the actual number killed. Further research on the mechanism by which separation of mother and calf occurs is required to obtain better estimates of the unobserved kill of dolphin calves in this fishery.

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.

Mortality rates estimates for Metapenaeus monoceros (Fabricius) of Maputo Bay

The species Metapenaeus monoceros in Maputo Bay recruits to the fishery almost all over the year, but the main recruitment occurs over a short period of time, each year, during April-May. Growth curves were constructed by following the progression of modes over a period of time. The von Bertalanffy growth parameters were estimated as L∞=31.9 mm and K(monthly)=0.25, for males, and L∞=48.3 mm and K(monthly)=0.14, for females (Brinca and Sousa, 1984). Using data on growth and length composition of the catches, the following methods were applied to estimate mortality rates of M. monoceros: estimation of natural mortality by using approximative methods; use of c.p.u.e. data; catch curves; cohort analysis; average age and length methods.

Standing stock density estimates (kg/hectare) for fish from 1969 through 70 UNDP/FAO and 1976 EAFFRO trawl surveys in the Kenya waters of Lake Victoria

A statistical comparison of standing stock density estimates (Kg/hectare) from 26 UNDP/FAO 1%9 thru 70 and 63 EAFFRO 1976 bottom trawl surveys revealed the following; 1) Statistically significant differences between mean density values at 4 of 7 depths {4-9 to 30-39 m}. 2) The 1969 thru 70 UNDP/FAO Values were higher at the 4 levels. 3) No statistically significant menn density value differences at 3 depths (40-49 to 60-69 m), but decreased values for the 1976 EAFFRO survey at 40-49 and 50-59 m depth. It was concluded from these comparisons that no capital investment should be made into a trawler industry for fish meal production in the Kenya waters of Lake Victoria until further bottom trawl surveys can be conducted to either substantiate or disapprove these differences over the six year time span.