An Evaluation of the area stratification used for sampling tunas in the eastern Pacific Ocean and implications for estimating total annual catches

The Inter-American Tropical Tuna Commission (IATTC) staff has been sampling the size distributions of tunas in the eastern Pacific Ocean (EPO) since 1954, and the species composition of the catches since 2000. The IATTC staff use the data from the species composition samples, in conjunction with observer and/or logbook data, and unloading data from the canneries to estimate the total annual catches of yellowfin (Thunnus albacares), skipjack (Katsuwonus pelamis), and bigeye (Thunnus obesus) tunas. These sample data are collected based on a stratified sampling design. I propose an update of the stratification of the EPO into more homogenous areas in order to reduce the variance in the estimates of the total annual catches and incorporate the geographical shifts resulting from the expansion of the floating-object fishery during the 1990s. The sampling model used by the IATTC is a stratified two-stage (cluster) random sampling design with first stage units varying (unequal) in size. The strata are month, area, and set type. Wells, the first cluster stage, are selected to be sampled only if all of the fish were caught in the same month, same area, and same set type. Fish, the second cluster stage, are sampled for lengths, and independently, for species composition of the catch. The EPO is divided into 13 sampling areas, which were defined in 1968, based on the catch distributions of yellowfin and skipjack tunas. This area stratification does not reflect the multi-species, multi-set-type fishery of today. In order to define more homogenous areas, I used agglomerative cluster analysis to look for groupings of the size data and the catch and effort data for 2000–2006. I plotted the results from both datasets against the IATTC Sampling Areas, and then created new areas. I also used the results of the cluster analysis to update the substitution scheme for strata with catch, but no sample. I then calculated the total annual catch (and variance) by species by stratifying the data into new Proposed Sampling Areas and compared the results to those reported by the IATTC. Results showed that re-stratifying the areas produced smaller variances of the catch estimates for some species in some years, but the results were not significant.

A-SCALA: an age-structured statistical catch-at-length analysis for assessing tuna stocks in the eastern tropical Pacific Ocean

English: We describe an age-structured statistical catch-at-length analysis (A-SCALA) based on the MULTIFAN-CL model of Fournier et al. (1998). The analysis is applied independently to both the yellowfin and the bigeye tuna populations of the eastern Pacific Ocean (EPO). We model the populations from 1975 to 1999, based on quarterly time steps. Only a single stock for each species is assumed for each analysis, but multiple fisheries that are spatially separate are modeled to allow for spatial differences in catchability and selectivity. The analysis allows for error in the effort-fishing mortality relationship, temporal trends in catchability, temporal variation in recruitment, relationships between the environment and recruitment and between the environment and catchability, and differences in selectivity and catchability among fisheries. The model is fit to total catch data and proportional catch-at-length data conditioned on effort. The A-SCALA method is a statistical approach, and therefore recognizes that the data collected from the fishery do not perfectly represent the population. Also, there is uncertainty in our knowledge about the dynamics of the system and uncertainty about how the observed data relate to the real population. The use of likelihood functions allow us to model the uncertainty in the data collected from the population, and the inclusion of estimable process error allows us to model the uncertainties in the dynamics of the system. The statistical approach allows for the calculation of confidence intervals and the testing of hypotheses. We use a Bayesian version of the maximum likelihood framework that includes distributional constraints on temporal variation in recruitment, the effort-fishing mortality relationship, and catchability. Curvature penalties for selectivity parameters and penalties on extreme fishing mortality rates are also included in the objective function. The mode of the joint posterior distribution is used as an estimate of the model parameters. Confidence intervals are calculated using the normal approximation method. It should be noted that the estimation method includes constraints and priors and therefore the confidence intervals are different from traditionally calculated confidence intervals. Management reference points are calculated, and forward projections are carried out to provide advice for making management decisions for the yellowfin and bigeye populations. Spanish: Describimos un análisis estadístico de captura a talla estructurado por edad, A-SCALA (del inglés age-structured statistical catch-at-length analysis), basado en el modelo MULTIFAN- CL de Fournier et al. (1998). Se aplica el análisis independientemente a las poblaciones de atunes aleta amarilla y patudo del Océano Pacífico oriental (OPO). Modelamos las poblaciones de 1975 a 1999, en pasos trimestrales. Se supone solamente una sola población para cada especie para cada análisis, pero se modelan pesquerías múltiples espacialmente separadas para tomar en cuenta diferencias espaciales en la capturabilidad y selectividad. El análisis toma en cuenta error en la relación esfuerzo-mortalidad por pesca, tendencias temporales en la capturabilidad, variación temporal en el reclutamiento, relaciones entre el medio ambiente y el reclutamiento y entre el medio ambiente y la capturabilidad, y diferencias en selectividad y capturabilidad entre pesquerías. Se ajusta el modelo a datos de captura total y a datos de captura a talla proporcional condicionados sobre esfuerzo. El método A-SCALA es un enfoque estadístico, y reconoce por lo tanto que los datos obtenidos de la pesca no representan la población perfectamente. Además, hay incertidumbre en nuestros conocimientos de la dinámica del sistema e incertidumbre sobre la relación entre los datos observados y la población real. El uso de funciones de verosimilitud nos permite modelar la incertidumbre en los datos obtenidos de la población, y la inclusión de un error de proceso estimable nos permite modelar las incertidumbres en la dinámica del sistema. El enfoque estadístico permite calcular intervalos de confianza y comprobar hipótesis. Usamos una versión bayesiana del marco de verosimilitud máxima que incluye constreñimientos distribucionales sobre la variación temporal en el reclutamiento, la relación esfuerzo-mortalidad por pesca, y la capturabilidad. Se incluyen también en la función objetivo penalidades por curvatura para los parámetros de selectividad y penalidades por tasas extremas de mortalidad por pesca. Se usa la moda de la distribución posterior conjunta como estimación de los parámetros del modelo. Se calculan los intervalos de confianza usando el método de aproximación normal. Cabe destacar que el método de estimación incluye constreñimientos y distribuciones previas y por lo tanto los intervalos de confianza son diferentes de los intervalos de confianza calculados de forma tradicional. Se calculan puntos de referencia para el ordenamiento, y se realizan proyecciones a futuro para asesorar la toma de decisiones para el ordenamiento de las poblaciones de aleta amarilla y patudo.

Growth of Skipjack tuna (Katsuwonus pelamis) in the eastern Pacific Ocean as estimated from tagging data

English: Data obtained from tagging experiments initiated during 1953-1958 and 1969-1981 for skipjack tuna from the coastal eastern Pacific Ocean (EPO) are reanalyzed, using the Schnute generalized growth model. The objective is to provide information that can be used to generate a growth transition matrix for use in a length-structured population dynamics model. The analysis includes statistical approaches to include individual variability in growth as a function of length at release and time at liberty, measurement error, and transcription error. The tagging data are divided into northern and southern regions, and the results suggest that growth rates differ between the two regions. The Schnute model provides a significantly better fit to the data than the von Bertalanffy model, a sub-model of the Schnute model, for the northern region, but not for the southern region. Individual variation in growth is best described as a function of time at liberty and as a function of growth increment for the northern and southern regions, respectively. Measurement error is a significant part of the total variation, but the results suggest that there is no bias caused by the measurement error. Additional information, particularly for small and large fish, is needed to produce an adequate growth transition matrix that can be used in a length-structured population dynamics model for skipjack tuna in the EPO. Spanish: Los datos obtenidos de los experimentos de marcado iniciados durante los períodos de 1953- 1958 y de 1969-1981 para el atún barrilete en las costas del Océano Pacífico Oriental (OPO) fueron analizados nuevamente, utilizando el modelo de crecimiento generalizado de Schnute. El objetivo es brindar información que sea útil para producir una matriz sobre la tran-sición de crecimiento que pueda utilizarse en un modelo de dinámica poblacional estructurado por talla. El análisis usa enfoques estadísticos para poder incluir la variabilidad individual del crecimiento como función de la talla de liberación y tiempo en libertad, el error de medición, y el error de transcripción. Los datos de marcado son divididos en regiones norte y sur, y los resultados sugieren que las tasas de crecimiento en las dos regiones son diferentes. En la región norte, pero no en la región sur, el modelo de Schnute se ajusta significativamente mejor a los datos que el modelo von Bertalanffy, un sub-modelo del modelo de Schnute. La mejor descripción de la variación individual en el crecimiento es como una función del tiempo en libertad y como una función del incremento de crecimiento para las regiones norte y sur, respectivamente. El error de medición es una parte significativa de la variación total, pero los resultados sugieren que no existe un sesgo causado por el error de medición. Se necesita información adicional, particularmente para peces pequeños y grandes, para poder producir una matriz de transición de crecimiento adecuada que pueda utilizarse en el modelo de dinámica poblacional estructurado por tallas para el atún barrilete en el OPO.

A model of the pelagic ecossystem in the eastern tropical Pacific Ocean

English: Recent calls for a more holistic approach to fisheries management have motivated development of trophic mass-balance models of ecosystems that underlie fisheries production. We developed a model hypothesis of the pelagic ecosystem in the eastern tropical Pacific Ocean (ETP) to gain insight into the relationships among the various species in the system and to explore the ecological implications of alternative methods of harvesting tunas. We represented the biomasses of and fluxes between the principal elements in the ecosystem with Ecopath, and examined the ecosystem's dynamic, time-series behavior with Ecosim. We parameterized the model for 38 species or groups of species, and described the sources, justifications, assumptions, and revisions of our estimates of the various parameters, diet relations, fisheries landings, and fisheries discards in the model. We conducted sensitivity analyses with an intermediate version of the model, for both the Ecopath mass-balance and the dynamic trajectories predicted by Ecosim. The analysis showed that changes in the basic parameters for two components at middle trophic levels, Cephalopods and Auxis spp., exert the greatest influence on the system. When the Cephalopod Q/B and Auxis spp. P/B were altered from their initial values and the model was rebalanced, the trends of the biomass trajectories predicted by Ecosim were not sensitive, but the scaling was sensitive for several components. We described the review process the model was subjected to, which included reviews by the IATTC Purse-seine Bycatch Working Group and by a working group supported by the National Center for Ecological Analysis and Synthesis. We fitted the model to historical time series of catches per unit of effort and mortality rates for yellowfin and bigeye tunas in simulations that incorporated historical fishing effort and a climate driver to represent the effect of El Niño-Southern Oscillation-scale variation on the system. The model was designed to evaluate the possible ecological implications of fishing for tunas in various ways. We recognize that a model cannot possibly represent all the complexity of a pelagic ocean ecosystem, but we believe that the ETP model provides insight into the structure and function of the pelagic ETP. Spanish: Llamamientos recientes hacia un enfoque más holístico al ordenamiento de la pesca han motivado el desarrollo de modelos tróficos de balance de masas de los ecosistemas que sostienen la producción pesquera. Desarrollamos una hipótesis modelo del ecosistema pelágico en el Océano Pacífico oriental tropical (POT) con miras a mejorar los conocimientos de las relaciones entre las distintas especies en el sistema y explorar las implicaciones ecológicas de métodos alternativos de capturar atunes. Con Ecopath representamos las biomasas de los elementos principales en el ecosistema, y los flujos entre los mismos, y con Ecosim examinamos el comportamiento dinámico del ecosistema con el tiempo. Parametrizamos el modelo para 38 especies o grupos de especies (denominados “componentes” del modelo), y describimos las fuentes, justificaciones, supuestos, y revisiones de nuestras estimaciones de los distintos parámetros, relaciones basadas en dieta, capturas retenidas de las pesquerías, y descartes de las mismas en el modelo. Realizamos análisis de sensibilidad con una versión intermedia del modelo, para el balance de masas de Ecopath y las trayectorias dinámicas predichas por Ecosim también. El análisis demostró que cambios en los parámetros básicos para dos componentes en niveles tróficos medianos, Cefalópodos y Auxis spp., ejercieron la mayor influencia sobre el sistema. Cuando se alteraron el Q/B de los Cefalópodos y el P/B de los Auxis spp. de sus valores iniciales y se balanceó el modelo de nuevo, las tendencias de las trayectorias de la biomasa predichas por Ecosim no fueron sensibles, pero la escala fue sensible para varios componentes. Describimos el proceso de revisión al que fue sujeto el modelo, inclusive revisiones por el Grupo de Trabajo sobre Captura Incidental de la CIAT y un grupo de trabajo apoyado por el Centro Nacional para Síntesis y Análisis Ecológicos. Ajustamos el modelo a series de tiempo históricas de capturas por unidad de esfuerzo y tasas de mortalidad de atunes aleta amarilla y patudo en simulaciones que incorporaron esfuerzo de pesca histórico e impulsos climáticos para representar el efecto de variaciones a escala de El Niño-Oscilación del Sur sobre el sistema. El modelo fue diseñado para evaluar las posibles implicaciones ecológicas de la pesca atunera de varias formas. Reconocemos la imposibilidad de que el modelo represente toda la complejidad de un ecosistema oceánico pelágico, pero creemos que el modelo del POT mejora los conocimientos de la estructura y función del POT pelágico.

A review of the Japanese longline fishery for tunas and billfishes in the eastern Pacific Ocean, 1993-1997

English: This report reviews the Japanese longline fishery in the eastern Pacific Ocean during the 1993-1997 period, extending the studies for the 1956-1992 period made by other investigators. The spatial and temporal distributions of fishing effort, catch, apparent abundance, sexual maturity, and size composition are examined for the principal species of tunas and billfishes taken by that fishery. Some information on the catches of sharks by the Japanese longline fishery is given. The interactions between the surface and longline fisheries are discussed. Spanish: En este informe se presenta un análisis de la actividad pesquera de buques palangreros japoneses en el Océano Pacífico oriental durante el período de 1993-1997, extendiendo los estudios del período de 1956-1992 realizados por otros investigadores. Se examinan las distribuciones espacial y temporal del esfuerzo de pesca, la captura, la abundancia aparente, la madurez sexual, y la composición por talla de las principales especies de atunes y picudos capturadas por dicha pesquería. Se presenta cierta información sobre las capturas de tiburones por la pesquería palangrera japonesa. Se describen las interacciones entre las pesquerías de superficie y palangrera.

Bycatches of sharks in the tuna purse-seine fishery of the eastern Pacific Ocean reported by observers of the Inter-American Tropical Tuna Commission, 1993-2004

Information on bycatches of sharks collected by observers of the Inter-American Tropical Tuna Commission (IATTC) between 1993 and 2004 is presented in this data report. This report contains two sections. The first section summarizes information used by the staff of the IATTC to review and revise IATTC observers’ at-sea species identifications of Carcharhinus falciformis, C. limbatus, and C. longimanus. The revisions were based on 1) data collected on species-specific diagnostic characteristics as part of a special sampling program conducted between March 2000, and March 2001 and 2) a review of observers’ archival field notes for the 1993-2004 period. The second section summarizes the shark bycatches reported by IATTC observers between 1993 and 2004, incorporating the revisions of observers’ at-sea identifications. The IATTC-observed shark bycatch data are summarized as tables with annual tallies of observed bycatches and maps of the spatial distributions of the average bycatches per set and size compositions of the bycatches.

Variations in eastern North Pacific demersal fish biomass based on the U.S. west coast groundfish bottom trawl survey (2003–2010)

In response to declining biomass of Northeast Pacific groundfish in the late 1990s and to improve the scientific basis for management of the fishery, the Northwest Fisheries Science Center standardized and enhanced their annual bottom trawl survey in 2003. The survey was expanded to include the entire area along the U.S. west coast at depths of 55–1280 m. Coast-wide biomass and species richness significantly decreased during the first eight years (2003–10) of this fishery-independent survey. We observed an overall tendency toward declining biomass for 62 dominant taxa combined (fishery target and nontarget species) and four of seven subgroups (including cartilaginous fish, flatfishes, shelf rockfishes, and other shelf species), despite increasing or variable biomass trends in individual species. These decreases occurred during a period of reduced catch for groundfish along the shelf and upper slope regions relative to historical rates. We used information from multiple stock assessments to aggregate species into three groups: 1) with strong recruitment, 2) without strong recruitment in 1999, and 3) with unknown recruitment level. For each group, we evaluated whether declining biomass was primarily related to depletion (using year as a proxy) or environmental factors (i.e., variation in the Pacific Decadal Oscillation). According to Akaike’s information criterion, changes in aggregate biomass for species with strong recruitment were more closely related to year, whereas those with no strong recruitment were more closely related to climate. The significant decline in biomass for species without strong recruitment confirms that factors other than depletion of the exceptional 1999 year class may be responsible for the observed decrease in biomass along the U.S. west coast.

Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

Stage-specific vertical distribution of Alaska plaice (Pleuronectes quadrituberculatus) eggs in the eastern Bering Sea

The stage-specific distribution of Alaska plaice (Pleuronectes quadrituberculatus) eggs in the southeastern Bering Sea was examined with collections made in mid-May in 2002, 2003, 2005, and 2006. Eggs in the early stages of development were found primarily offshore of the 40-m isobath. Eggs in the middle and late stages of development were found inshore and offshore of the 40-m isobath. There was some evidence that early-stage eggs occur deeper in the water column than late-stage eggs, although year-to-year variability in that trend was observed. Most eggs were in the later stages of development; therefore the majority of spawning is estimated to have occurred a few weeks before collection—probably April—and may be highly synchronized among local spawning areas. Results indicate that sampling with continuous underway fish egg collectors(CUFES) should be supplemented with sampling of the entire water column to ensure adequate samples of all egg stages of Alaska plaice. Data presented offer new information on the stage-dependent horizontal and vertical distribution of Alaska plaice eggs in the Bering Sea and provide further evidence that the early life history stages of this species are vulnerable to near-surface variations in hydrographical conditions and climate forcing.

Analysis of sex-specific spawning biomass per recruit of the sailfish (Istiophorus platypterus) in the waters off eastern Taiwan

Analyses of sex-specific yield per recruit and spawning stock biomass per recruit were conducted to evaluate the current status of the sailfish (Istiophorus platypterus) fishery in the waters off eastern Taiwan. Natural mortality rates estimated from Pauly’s empirical equation were 0.26/yr for females and 0.27/yr for males. The current fishing mortality rates were estimated as 0.24/yr and 0.43/yr for females and males, respectively, which are much lower than the estimated F0 .1 (0.62/yr and 0.79/yr for females and males, respectively) and FSSB40 (0.46/yr for females) which are commonly used as target reference points in fisheries management. The effects of the fishing mortality, natural mortality, and age at first capture on the estimates of biological reference points were evaluated by using the Monte Carlo simulation. The results indicate that failure to consider the uncertainty in parameters such as natural mortality or age at first capture may lead to the improper estimation of biological reference points. This study indicates the possibility of current fishing mortality exceeding the target biological reference points may be negligible for sailfish in the waters off eastern Taiwan. However, in view of the recent rapid increase in fishing effort, it is evident that the stock status and development of the fishery need to be closely monitore

Multiple stable reference points in oyster populations: implications for reference point-based management

In the second of two companion articles, a 54-year time series for the oyster population in the New Jersey waters of Delaware Bay is analyzed to examine how the presence of multiple stable states affects reference-point–based management. Multiple stable states are described by four types of reference points. Type I is the carrying capacity for the stable state: each has associated with it a type-II reference point wherein surplus production reaches a local maximum. Type-II reference points are separated by an intermediate surplus production low (type III). Two stable states establish a type-IV reference point, a point-of-no-return that impedes recovery to the higher stable state. The type-II to type-III differential in surplus production is a measure of the difficulty of rebuilding the population and the sensitivity of the population to collapse at high abundance. Surplus production projections show that the abundances defining the four types of reference points are relatively stable over a wide range of uncertainties in recruitment and mortality rates. The surplus production values associated with type-II and type-III reference points are much more uncertain. Thus, biomass goals are more easily established than fishing mortality rates for oyster population

Assessment of fish populations and habitat on Oculina Bank, a deep-sea coral marine protected area off eastern Florida

A portion of the Oculina Bank located off eastern Florida is a marine protected area (MPA) preserved for its dense populations of the ivory tree coral (Oculina varicosa), which provides important habitat for fish. Surveys of fish assemblages and benthic habitat were conducted inside and outside the MPA in 2003 and 2005 by using remotely operated vehicle video transects and digital still imagery. Fish species composition, biodiversity, and grouper densities were used to determine whether O. varicosa forms an essential habitat compared to other structure-forming habitats and to examine the effectiveness of the MPA. Multivariate analyses indicated no differences in fish assemblages or biodiversity among hardbottom habitat types and grouper densities were highest among the most complex habitats; however the higher densities were not exclusive to coral habitat. Therefore, we conclude that O. varicosa was functionally equivalent to other hardbottom habitats. Even though fish assemblages were not different among management areas, biodiversity and grouper densities were higher inside the MPA compared to outside. The percentage of intact coral was also higher inside the MPA. These results provide initial evidence demonstrating effectiveness of the MPA for restoring reef fish and their habitat. This is the first study to compare reef fish populations on O. varicosa with other structure-forming reef habitats and also the first to examine the effectiveness of the MPA for restoring fish populations and live reef cover.

Evidence of the selection of tidal streams by northern rock sole (Lepidopsetta polyxystra) for transport in the eastern Bering Sea

Depth data from archival tags on northern rock sole (Lepidopsetta polyxystra) were examined to assess whether fish used tidal currents to aid horizontal migration. Two northern rock sole, out of 115 released with archival tags in the eastern Bering Sea, were recovered 314 and 667 days after release. Both fish made periodic excursions away from the bottom during mostly night-time hours, but also during particular phases of the tide cycle. One fish that was captured and released in an area of rotary currents made vertical excursions that were correlated with tidal current direction. To test the hypothesis that the fish made vertical excursions to use tidal currents to aid migration, a hypothetical migratory path was calculated using a tide model to predict the current direction and speed during periods when the fish was off the bottom. This migration included limited movements from July through December, followed by a 200-km southern migration from January through February, then a return northward in March and April. The successful application of tidal current information to predict a horizontal migratory path not only provides evidence of selective tidal stream transport but indicates that vertical excursions were conducted primarily to assist horizontal migration.

Prevalence of the commensal barnacle Xenobalanus globicipitis on cetacean species in the eastern tropical Pacific Ocean, and a review of global occurrence

Distribution and prevalence of the phoretic barnacle Xenobalanus on cetacean species are reported for 22 cetaceans in the eastern tropical Pacific Ocean (21 million km2). Four cetacean species are newly reported hosts for Xenobalanus: Bryde’s whale (Balaenoptera edeni), long-beaked common dolphin (Delphinus capensis), humpback whale (Megaptera novaeangliae), and spinner dolphin (Stenella longirostris). Sightings of Xenobalanus in pelagic waters are reported for the first time, and concentrations were located within three productive zones: near the Baja California peninsula, the Costa Rica Dome and waters extending west along the 10°N Thermocline Ridge, and near Peru and the Galapagos Archipelago. Greatest prevalence was observed on blue whales (Balaenoptera musculus) indicating that slow swim speeds are not necessary for effective barnacle settlement. Overall, prevalence and prevalence per sighting were generally lower than previously reported. The number of barnacles present on an individual whale was greatest for killer whales, indicating that Xenobalanus larvae may be patchily distributed. The broad geographic distribution and large number of cetacean hosts, indicate an extremely cosmopolitan distribution. A better understanding of the biology of Xenobalanus is needed before this species can be used as a biological tag.