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Schaefer K.M.,Inter American Tropical Tuna Commission | Fuller D.W.,Inter American Tropical Tuna Commission | Aldana G.,Instituto Nacional Of Pesca
Fisheries Oceanography | Year: 2014

The movements, behavior, and habitat utilization of yellowfin tuna, Thunnus albacares, following capture and release with archival tags in the Revillagigedo Islands Archipelago Biosphere Reserve (RIABR), Mexico, are described from analyses of 16 578 days of time-series data, downloaded from 52 archival tags recovered from yellowfin (78-173 cm in length and 1.7-8.0 yr of age) at liberty from 93 to 1773 days (x- = 411 days), collected during 2006-2012. An unscented Kalman filter model with sea-surface temperature measurements integrated (UKFsst) was used to process the archival tag data sets to obtain improved estimates of geographic positions, most probable tracks (MPTs), and movement parameters. The MPTs indicate restricted movements, low levels of dispersion, and fidelity of yellowfin tuna to the RIABR. The median parameter estimates from the UKFsst model for errors in longitude (σx) and latitude (σy) were 0.46° and 1.84°, respectively, for directed movements (u and v) -0.05 NM day-1 and -0.05 NM day-1, respectively, and for dispersive movement (D) 117.99 NM2 day-1. Analyses of daily timed depth and temperature records resulted in the classification of the data into four distinct behaviors. There are significant differences among ages in the durations of Type I and Type II diving behaviors and in the daytime and nighttime vertical habitat utilization distributions. The oceanography surrounding the RIABR appears to have a profound influence on the movements, behavior, and habitat utilization of yellowfin in this area. © 2013 John Wiley & Sons Ltd.


Maunder M.N.,Inter American Tropical Tuna Commission | Punt A.E.,University of Washington
Fisheries Research | Year: 2013

Limited data, and the requirement to provide science-based advice for exploited populations, have led to the development of statistical methods that combine several sources of information into a single analysis. This approach, " integrated analysis" was first formulated by Fournier and Archibald in 1982. Contemporary use of integrated analysis involves using all available data, in as raw a form as appropriate, in a single analysis. Analyses that were traditionally carried out independently are now conducted simultaneously through likelihood functions that include multiple data sources. For example, the traditional analysis of converting catch-at-length data into catch-at-age data for use in an age-structured population dynamics models can be avoided by including the basic data used in this conversion, length-frequency and conditional age-at-length data, in the likelihood function. This allows for consistency in assumptions and permits the uncertainty associated with both data sources to be propagated to final model outputs, such as catch limits under harvest control rules. The development of the AD Model Builder software has greatly facilitated the use of integrated analyses, and there are now several general stock assessment models (e.g., Stock Synthesis) that allow many data types and model assumptions to be analyzed simultaneously. In this paper, we define integrated analysis, describe its history and development, give several examples, and describe the advantages of and problems with integrated analysis. © 2012 Elsevier B.V.


Maunder M.N.,Inter American Tropical Tuna Commission | Maunder M.N.,University of California at San Diego | Piner K.R.,Southwest Fisheries Science Center
ICES Journal of Marine Science | Year: 2014

Interpretation of data used in fisheries assessment and management requires knowledge of population (e.g. growth, natural mortality, and recruitment), fisheries (e.g. selectivity), and sampling processes. Without this knowledge, assumptions need to be made, either implicitly or explicitly based on the methods used. Incorrect assumptions can have a substantial impact on stock assessment results and management advice. Unfortunately, there is a lack of understanding of these processes for most, if not all, stocks and even for processes that have traditionally been assumed to be well understood (e.g. growth and selectivity). We use information content of typical fisheries data that is informative about absolute abundance to illustrate some of the main issues in fisheries stock assessment. We concentrate on information about absolute abundance from indices of relative abundance combined with catch, and age and length-composition data and how the information depends on knowledge of population, fishing, and sampling processes. We also illustrate two recently developed diagnostic methods that can be used to evaluate the absolute abundance information content of the data. Finally, we discuss some of the reasons for the slowness of progress in fisheries stock assessment. © 2014 © International Council for the Exploration of the Sea 2014. All rights reserved.


Maunder M.N.,Quantitative Resource Assessment LLC | Maunder M.N.,Inter American Tropical Tuna Commission | Deriso R.B.,Inter American Tropical Tuna Commission
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2011

Multiple factors acting on different life stages influence population dynamics and complicate the assessment and management of populations. To provide appropriate management advice, the data should be used to determine which factors are important and what life stages they impact. It is also important to consider density dependence because it can modify the impact of some factors. We develop a state-space multistage life cycle model that allows for density dependence and environmental factors to impact different life stages. Models are ranked using a two-covariates-at-a-time stepwise procedure based on AICc model averaging to reduce the possibility of excluding factors that are detectable in combination, but not alone. Impact analysis is used to evaluate the impact of factors on the population. The framework is illustrated by application to delta smelt (Hyposmesus transpacificus), a threatened species that is potentially impacted by multiple anthropogenic factors. Our results indicate that density dependence and a few key factors impact the delta smelt population. Temperature, prey, and predators dominated the factors supported by the data and operated on different life stages. The included factors explain the recent declines in delta smelt abundance and may provide insight into the cause of the pelagic species decline in the San Francisco Estuary.


Maunder M.N.,Inter American Tropical Tuna Commission | Harley S.J.,British Petroleum
Fisheries Research | Year: 2011

We used hold-out cross validation model selection to determine the most appropriate form of the selectivity curve, using a nonparametric approach to represent selectivity. The cross-validation method is based on setting aside a portion of the catch-at-age (or catch-at-length) data to use as a test data set. The remaining catch-at-age data, along with other data (e.g. relative indices of abundance) are used to estimate the parameters of the stock assessment model, including the selectivity parameters. These parameter estimates are then used to predict the catch at age for the test data set. The selectivity model that produces the closest predictions to the test data set is chosen as the selectivity model to use in the assessment. The selectivity model we use is nonparametric, based on estimating an individual selectivity parameter for each age and then applying smoothness penalties to constrain how much the selectivity can change from age to age. The smoothness penalties we consider are the first, second, and third differences, a length-based penalty, and a monotonic penalty. The penalties are applied on the logarithm of selectivity to avoid scale-related problems and improve stability. The method was applied to the assessment of bigeye tuna in the eastern Pacific Ocean. We found that the estimated management quantities were relatively robust within the set of smoothness penalties that gave low cross-validations scores. We also found that poor choices for the smoothness penalties could give very different results. Poor choices include both under-smoothing (e.g. no penalties) and over-smoothing (penalties that are too large). The most influential factor was the inclusion of a monotonic penalty. © 2011 Elsevier B.V.


Navarro J.,CSIC - Institute of Marine Sciences | Coll M.,CSIC - Institute of Marine Sciences | Somes C.J.,Leibniz Institute of Marine Science | Olson R.J.,Inter American Tropical Tuna Commission
Deep-Sea Research Part II: Topical Studies in Oceanography | Year: 2013

Cephalopods are an important prey resource for fishes, seabirds, and marine mammals, and are also voracious predators on crustaceans, fishes, squid and zooplankton. Because of their high feeding rates and abundance, squids have the potential to exert control on the recruitment of commercially important fishes. In this review, we synthesize the available information for two intrinsic markers (δ15N and δ13C isotopic values) in squids for all oceans and several types of ecosystems to obtain a global view of the trophic niches of squids in marine ecosystems. In particular, we aimed to examine whether the trophic positions and trophic widths of squid species vary among oceans and ecosystem types. To correctly compare across systems, we adjusted squid δ15N values for the isotopic variability of phytoplankton at the base of the food web provided by an ocean circulation-biogeochemistry-isotope model. Studies that focused on the trophic ecology of squids using isotopic techniques were few, and most of the information on squids was from studies on their predators. Our results showed that squids occupy a large range of trophic positions and exploit a large range of trophic resources, reflecting the versatility of their feeding behavior and confirming conclusions from food-web models. Clear differences in both trophic position and trophic width were found among oceans and ecosystem types. The study also reinforces the importance of considering the natural variation in isotopic values when comparing the isotopic values of consumers inhabiting different ecosystems. © 2013 Elsevier Ltd.


Ten separate experiments monitoring the simultaneous behaviors of 26 skipjack (Katsuwonus pelamis), 26 bigeye (Thunnus obesus), and 33 yellowfin (T. albacares) tunas within large multi-species aggregations associated with drifting fish aggregating devices (FADs) were investigated using ultrasonic telemetry in the equatorial eastern Pacific Ocean. Experiments were conducted during a research cruise aboard a chartered purse seine vessel. Purse seine sets were made on the tuna aggregations associated with FADs at the termination of six of the ten experiments. Seventeen of the 44 tagged tunas were not recaptured indicating the transient nature of the associative behavior of tunas with FADs. Although there was considerable overlap in the depths of the three species, by day and night, there were some species-specific differences and diel differences within species. While we documented spatial and temporal differences in the schooling behavior of the three tuna species, the differences do not appear sufficient such that modifications in purse seine fishing practices could effectively avoid the capture of small bigeye and yellowfin tunas, while optimizing the capture of skipjack tuna in purse seine sets on FADs. © 2013 Springer-Verlag Berlin Heidelberg.


Schaefer K.M.,Inter American Tropical Tuna Commission | Fuller D.W.,Inter American Tropical Tuna Commission
Marine Biology | Year: 2010

The results presented in this report are based on analyses of 16,721 days of data downloaded from 96 archival tags recovered from bigeye tuna (Thunnus obesus; 54-159 cm in length, 0.97-5.44 years of age) at liberty from 31 to 1,508 days in the equatorial eastern Pacific Ocean. Analyses of daily timed depth and temperature records resulted in the classification of the data into three daily behavior types: characteristic, associative (associated with floating objects), and other. There is a significant positive correlation between the proportion of time fish exhibit characteristic behavior and increasing length, and significant negative correlations between the proportion of time bigeye exhibit associative and other behavior with increasing length. For the smallest (54-80 cm) to largest (100-159 cm) length classes, the vertical habitats utilized when exhibiting non-associative behaviors were 99 and 98% of the time above the thermocline depth (60 m) during the night, at the same average depth of 34 m, and 60 and 72% of the time below the thermocline during the day at average depths of 163 and 183 m, respectively. For the same smallest to largest length classes, when exhibiting associative behavior, the average nighttime and daytime depths were 25 and 21, and 33 and 37 m, respectively. The apparent effects of the environment on the behavior of the fish are discussed. © 2010 Springer-Verlag.


Schaefer K.M.,Inter American Tropical Tuna Commission | Fuller D.W.,Inter American Tropical Tuna Commission | Block B.A.,Stanford University
Fisheries Research | Year: 2011

The movements, behavior, and habitat utilization of yellowfin tuna, Thunnus albacares, in the eastern Pacific Ocean off Baja California, Mexico, are described from analyses of 31,357 days of day-log and 28,835 days of time-series data, downloaded from 126 archival tags recovered from yellowfin (57-162cm in length and 1.2-5.2 years of age) at liberty from 90 to 1161 d (x̄=273.2 d), collected during 2002-2010. An unscented Kalman filter model with sea-surface temperature measurements integrated (UKFsst) was used to process the archival tag data sets in order to obtain improved estimates of geographic positions and most probable tracks (MPTs) and parameters. The median parameter estimates from the UKFsst model for errors in longitude (σ x) and latitude (σ y) were 0.32° and 1.36°, respectively, for directed movements (u and v) were 0.27 and 0.77nm/d, respectively, and for dispersive movement (D) was 144.3nm 2/d. The MPTs for 120 (95%) of the yellowfin remained within 1358km of their release locations, indicating restricted horizontal utilization distributions, and fidelity to this area of high biological productivity. There are observed differences in the movement patterns and parameters for fish released in different areas. Analyses of daily timed depth and temperature records resulted in the classification of the data into four distinct behaviors. When exhibiting type-1 diving behavior (82.9% of all days at liberty) the fish remained at depths of less than 50m at night and did not dive to depths greater than about 100m during the day. Type-2 diving behavior (17.1% of all days at liberty) was characterized by 10 or more dives in excess of 150m during the day. Spatial and temporal patterns are evident in the distributions of type-1 and type-2 diving behaviors. Surface-oriented behavior, defined as the time fish remained at depths less than 10m for more than 10min, was also evaluated. The mean number and duration of daytime surface-oriented events per day, for all fish, were 7.6 and 24.2min, respectively. There are significant differences among ages in the percentages of days classified as type-1 and type-2 behaviors, durations of those events, and in the numbers and durations of surface-oriented events. Yellowfin tuna exhibited occasional deep-diving behavior, and some dives were to depths exceeding 1000m, where ambient temperatures were less than 5°C. There are significant differences among ages in the nighttime and daytime average depths. The differences are the result of the fish of ages greater than 3 years showing greater daytime average depths and lesser nighttime average depths. © 2011 Elsevier B.V.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 32.55K | Year: 2010

Evidence increasingly demonstrates that selective removal of marine life can induce restructuring of marine food webs. Trophic structure is the central component of mass balance models, widely used tools to evaluate fisheries in an ecosystem context. Food web structure is commonly determined by stomach contents or by bulk tissue stable isotope analyses, both of which are limited in terms of resolution and versatility. The investigators will refine a tool, Amino Acid Compound-Specific Isotopic Analyses (AA-CSIA), which can be broadly applicable for quantifying the time-integrated trophic position (TP) of consumers. Differences in source and trophic nitrogen isotopic composition for specific amino acids will provide an unambiguous and integrated measure of fractional trophic TP across multiple phyla, regardless of an animals physiological condition or of the biogeochemical cycling at the base of the food web. AA-CSIA will allow testing of the efficacy of trophic position estimates derived from ecosystem-based models and promote the evolution of these models into decision-support tools. This project has three goals: 1. To validate the application of AA-CSIA across multiple marine phyla under differing physiological conditions. 2. To compare the application of AA-CSIA across systems with contrasting biogeochemical cycling regimes. 3. To develop the use of AA-CSIA TP estimates for validating trophic models of exploited ecosystems. The investigators will test and refine the approach using a combination of laboratory feeding experiments and field studies across regions with differing biogeochemical cycling regimes. They will determine the applicability of the AA-CSIA approach in a variety of marine organisms assessed in controlled studies. Subsequently, ecosystem components will be sampled from the eastern tropical Pacific, coastal California and the subtropical Pacific gyre. They will also test the effects of sample preservation on the isotopic composition of individual AA to determine whether the approach can be used on archived samples. This tool will allow testing of the efficacy of ecosystem-based models currently used to gain insight into the ecological effects of fisheries removals and improve the reliability of future models required to manage marine resources. In addition to the goal of developing AA-CSIA for use as a TP indicator, the information obtained through this project will provide important species-specific biological data on the feeding behavior of marine organisms that could have implications for their resilience to anthropogenic pressures and climate change.

This project will have direct application to evaluating ecosystem effects of fisheries by providing an unbiased, integrated and independent approach to
estimating trophic structure, and a method by which to validate existing ecosystem-based model outputs and predictions. In addition, the project will have outreach benefits through the involvement of graduate and undergraduate students, and exposure of younger students through K-12 programs. This research will contribute to the greater understanding of the biology of locally important fish species as well as globally important shrimp and endangered marine turtles.

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