John R. Sibert

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

Many criteria for statistical parameter estimation, such as maximum likelihood, are formulated as a nonlinear optimization problem. Automatic Differentiation Model Builder (ADMB) is a programming framework based on automatic differentiation, aimed at highly nonlinear models with a large number of parameters. The benefits of using AD are computational efficiency and high numerical accuracy, both crucial in many practical problems. We describe the basic components and the underlying philosophy of ADMB, with an emphasis on functionality found in no other statistical software. One example of such a feature is the generic implementation of Laplace approximation of high-dimensional integrals for use in latent variable models. We also review the literature in which ADMB has been used, and discuss future development of ADMB as an open source project. Overall, the main advantages of ADMB are flexibility, speed, precision, stability and built-in methods to quantify uncertainty.

Biomass, Size, and Trophic Status of Top Predators in the Pacific Ocean

Fisheries have removed at least 50 million tons of tuna and other top-level predators from the Pacific Ocean pelagic ecosystem since 1950, leading to concerns about a catastrophic reduction in population biomass and the collapse of oceanic food chains. We analyzed all available data from Pacific tuna fisheries for 1950–2004 to provide comprehensive estimates of fishery impacts on population biomass and size structure. Current biomass ranges among species from 36 to 91% of the biomass predicted in the absence of fishing, a level consistent with or higher than standard fisheries management targets. Fish larger than 175 centimeters fork length have decreased from 5% to approximately 1% of the total population. The trophic level of the catch has decreased slightly, but there is no detectable decrease in the trophic level of the population. These results indicate substantial, though not catastrophic, impacts of fisheries on these top-level predators and minor impacts on the ecosystem in the Pacific Ocean.

Electronic Tagging and Tracking in Marine Fisheries

Sea water is nearly opaque to electromagnetic radiation. It is, therefore, difficult to track marine animals visually over significant distances, and radio tracking is rendered impractical by antennae and power requirements. Marine biologists have been laboring for over 40 years to develop alternative electronic systems to understand the behavior and physiology of marine animals in their natural environment. The pace of development accelerated in the 1990s motivated by new fishery management imperatives and propelled by rapid advances in electronics. By the late 1990s, a wide variety of electronic tagging and tracking devices were being applied in every ocean, in all marine habitats, and to an astonishing array of animals. Behaviorists, physiologists, engineers, modelers, fishery managers, and equipment manufacturers converged in Honolulu in February 2000 to participate in the Symposium on Tagging and Tracking Marine Fish with Electronic Devices. This volume reviews the history and presents the state-of-the-art of electronic tags used in the marine environment, as described in presentations at the symposium.

Tagging and tracking of marine animals with electronic devices

Behavioural Insights Based on the Use of Electronic Tags.- Using Telemetry to Monitor Movements and Habitat Use of Cultured and Wild Juvenile Winter Flounder in a Shallow Estuary.- Comparative Behavior of Wild and Hatchery Reared White Sea Bream (Diplodus sargus) Released on Artificial Reefs Off the Algarve (Southern Portugal).- Survival, Migration Speed and Swimming Depth of Atlantic Salmon Kelts During Sea Entry and Fjord Migration.- Small Scale Vertical Behaviour of Juvenile Albacore in Relation to Their Biotic Environment in the Bay of Biscay.- A Review of Acoustic Telemetry Technology and a Perspective on its Diversification Relative to Coastal Tracking Arrays.- The Ocean Tracking Network - Adding Marine Animal Movements to the Global Ocean Observing System.- Observations of the Behaviour of European Sea Bass (Dicentrarchus labrax) in the North Sea.- Vertical Movements and Habitat Utilization of Skipjack (Katsuwonus pelamis), Yellowfin (Thunnus albacares), and Bigeye (Thunnus obesus) Tunas in the Equatorial Eastern Pacific Ocean, Ascertained Through Archival Tag Data.- Investigations of Horizontal Movements of Atlantic Swordfish Using Pop-up Satellite Archival Tags.- Vertical Behavior and the Observation of FAD Effects on Tropical Tuna in the Warm-Pool of the Western Pacific Ocean.- Effects of T-bar and DST Tagging on Survival and Growth of European Hake.- Body Temperature of the Atlantic Bluefin Tuna (Thunnus thynnus L.) in the Western Mediterranean.- Multi-Channel Data-Logging: Towards Determination of Behaviour and Metabolic Rate in Free-Swimming Sharks.- Harnessing the Sun: Testing a Novel Attachment Method to Record Fine Scale Movements in Ocean Sunfish (Mola mola).- An Archival Tag for Monitoring Key Behaviours (Feeding and Spawning) in Fish.- Geolocation Methods.- Lessons from a Prototype Geolocation Problem.- Geolocating Fish Using Hidden Markov Models and Data Storage Tags.- State Space Model for Light Based Tracking of Marine Animals: Validation on Swimming and Diving Creatures.- Removing Bias in Latitude Estimated from Solar Irradiance Time Series.- Positioning Pelagic Fish from Sunrise and Sunset Times: Complex Observation Errors Call for Constrained, Robust Modeling.- Summary Report of aWorkshop on Geolocation Methods for Marine Animals.- Applications of Electronic Tags to Fisheries Management.- Developing Integrated Database Systems for the Management of Electronic Tagging Data.- Electronic Tagging Data Supporting Flexible Spatial Management in an Australian Longline Fishery.- Correction Factors Derived from Acoustic Tag Data for a Juvenile Southern Bluefin Tuna Abundance Index in SouthernWestern Australia.- A Multi-Scale Study of Red Porgy Movements and Habitat Use, and Its Application to the Design of Marine Reserve Networks.- Erratum.

Fisheries: Decline of Pacific tuna populations exaggerated?

industrial fisheries in the Pacific Ocean and elsewhere since the 1950s. In their analysis of Japanese longline-fishery catchper-unit-effort (CPUE) data, Myers and Worm conclude that the community (species-aggregated) biomass of large pelagic fish, mainly tunas, was reduced by 80% during the first 15 years of exploitation and is now at 10% of pre-industrial levels. We show here that an assumption critical to this conclusion — namely, that Japanese longline CPUE acts as an accurate index of community biomass — is invalid. Our results indicate that biomass decline and fishing impacts are much less severe than is claimed by Myers and Worm. Interpretation of the species-aggregated CPUE as an index of community biomass rests on the assumption that catchability (a coefficient specifying the proportionality between CPUE and abundance) is constant across species and over time. The former is unrealistic because, among other things, the species have different depth distributions and hence different vulnerability to longline gear. The evolution of tuna longline fisheries in all oceans has seen changes in fishing strategies (and hence catchability) as different species have been targeted. In the early 1960s, Japanese longliners changed from targeting albacore (Thunnus alalunga) and yellowfin (T. albacares) for the canned-tuna market to bigeye (T. obesus) and yellowfin tuna for the Japanese sashimi market. Japanese longline CPUE for albacore declined rapidly not because of declining albacore abundance, but because of this change in species targeting. By contrast, Taiwanese longliners have consistently targeted albacore in subequatorial waters of all oceans, and their CPUE provides a better index of albacore abundance. These results show that CPUE has declined by 50% over 40 years in the South Pacific, but they do not replicate the rapid and much larger decline in CPUE in the 1960s evident in the Japanese data (Fig.1a). The Myers and Worm analysis excludes data from the equatorial Pacific, where the highest catches are taken and which is the core habitat for tropical tunas. When these data are included, yellowfin-tuna CPUE in the western Pacific is seen to decline by 70% over 50 years, during which time annual catches by longline and other methods increase from insignificant levels in the early 1950s to more than 400,000 tonnes by the late 1990s (Fig. 1b). By contrast, the CPUE for bigeye tuna has been stable for over 40 years, despite continuously increasing catch (Fig. 1c). Changes in fishing strategies designed to target the deeper-swimming and higher-value bigeye tuna occurred during the 1970s (ref. 3), making it unlikely that CPUE accurately reflects changes in abundance for either species unless it is adjusted to account for the shift in targeting. Unadjusted Japanese longline CPUE tends to overestimate abundance decline for yellowfin tuna and underestimate abundance decline for bigeye tuna. Stock assessments rely on a range of data in addition to CPUE, including catch, size composition, tagging and biological data. When stock-assessment models 6 that consider all the available data are applied to Pacific tunas, fishery-induced declines in abundance during the 1950s and 1960s of the magnitude proposed by Myers and Worm are found to be extremely unlikely. Moreover, where declines do occur, they are not, as claimed by Myers and Worm, due exclusively to fishing. It is impossible, for example, under conventional populationdynamics theory to attribute the pre-1970 decline in yellowfin CPUE to fishing at a time when the total catches were less than one-tenth of today’s catches. In summary, the trends in catches and CPUE (Fig. 1) and the results of stock-assessment modelling show that the basic assumption of Myers and Worm that CPUE is proportional to brief communications arising

Mobility of tropical tunas and the implications for fisheries management

We apply an advection-diffusion reaction model to data from three different tuna tagging experiments in the western and central Pacific Ocean (WCPO) to reexamine the question of to what extent the population dynamics and spatial characteristics of tropical tunas require international cooperation for effective management. The median lifetime displacement of skipjack ranges from 420 to 470 nautical miles. The lifetime displacement of yellowfin is about 20% less. The median half-life, a measure of residence time, of skipjack and yellowfin in WCPO exclusive economic zones (EEZs) is 3-6 months. Fishing decreases the lifetime displacement and decreases the half-life. We conclude that international arrangements between neighboring EEZs are essential for effective conservation, but that Pacific Island countries can achieve benefits from domestic conservation and fishery development policies.

Shifting from marine reserves to maritime zoning for conservation of Pacific bigeye tuna (Thunnus obesus)

Over 50% of the total bigeye tuna (BET) landed in the Western Central Pacific Ocean is caught incidentally in the purse seine fishery and sold for canning at prices less than US

Possible Models for Combining Tracking Data with Conventional Tagging Data

2/kg. The remainder is landed in longline fisheries directed at BET and sold as fresh or frozen tuna at prices greater than US

Population dynamics and movements of skipjack tuna (Katsuwonus pelamis) in the Maldivian fishery: analysis of tagging data from an advection-diffusion-reaction model

10/kg. The combined fishing mortality by all gears will soon reduce the BET biomass in the Pacific Ocean to less than that capable of producing maximum sustainable yield. Closure of the high-seas enclaves in 2009 was hailed as a conservation measure, but was not scientifically evaluated before implementation and appears to have had no beneficial effect on the BET stock. A spatially explicit age-structured ecosystem model, SEAPODYM, is used to simulate alternative area-based fishery management policies to conserve bigeye tuna in the Western Central Pacific Ocean. Closing the high-seas enclaves to purse seine fishing has negligible effect on the BET biomass. Fishery management policies that control mortality on both juveniles and adults, through prohibition of fish aggregation devices in the purse seine fishery and restrictions on longline fishing in spawning areas, are the most efficient conservation policies. Large-scale benefits from bigeye conservation measures will become apparent only in the 2030s, assuming timely implementation and minimal effects of climate change.

Comparative Performance of MULTIFAN and Shepherd's Length Composition Analysis (SRLCA) on Simulated Length-Frequency Distributions

Advection-diffusion models have been used successfully to describe the time and place of recapture of tuna tagged with conventional dart tags. Such models are the continuous analogs of a biased random walk. This paper demonstrates how biased random walks can be used to simulate large scale movements of tunas as recorded by archival tags in a way that captures all of the major characteristics of the tracks. The parameters of the biased random walk model are identical to the parameters of the advection diffusion model, suggesting that a joint parameter estimation procedure might be feasible. Finally, the potential application of the Kalman filter to the analysis of tracking data is discussed. This statistical model has the potential to increase the accuracy of geoposition estimates from tracking devices as well as to estimate biased random walk parameters from tracking data.