Movements of Atlantic halibut in the Gulf of Maine based on geolocation (original) (raw)
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Validation of a hidden Markov model for the geolocation of Atlantic cod
Canadian Journal of Fisheries and Aquatic Sciences, 2017
Models developed to geolocate individual fish from data recorded by electronic tags often require significant modification to be applied to new regions, species, or tag types due to variability in oceanographic conditions, fish behavior, and data resolution. We developed a model for geolocating Atlantic cod off New England that builds upon an existing hidden Markov model (HMM) framework and addresses region-and species-specific challenges. The HMM framework contains a likelihood model which compares tag-recorded environmental data (depth, temperature, tidal characteristics) with those derived from an oceanographic model and a behavior model which constrains the horizontal movement of the fish. Validation experiments were performed on stationary tags, double-electronic-tagged fish (archival and acoustic tags), and simulated tracks. Known data, including fish locations and activity metrics, showed good agreement with those estimated by the modified approach, and improvements in performance of the modified method over the original. The modified geolocation approach will be applicable to additional species and regions to obtain valuable movement information that is not typically available for demersal fishes.
Journal of Northwest Atlantic Fishery Science, 2007
Tagging results from five years of a federal experimental Atlantic halibut fishery in the eastern Gulf of Maine are presented in this paper. These data show both localized movements within the study area and long-distance emigrations of juveniles. Twenty-eight percent of the recoveries from this study were made in Canadian waters, demonstrating an interchange between fish in the Gulf of Maine and those considered part of the Scotian Shelf/Southern Grand Banks stock unit. The predominance of long-distance, northeastward movement of juveniles poses the question of compensatory emigration in response to the predicted southwestward drift of eggs and larvae.
Geolocation of Atlantic cod (Gadus morhua) movements in the Gulf of Maine using tidal information
Fisheries Oceanography, 2007
Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the migration of 11 tagged Atlantic cod (Gadus morhua) during 2001 in Massachusetts Bay, the Gulf of Maine, and Georges Bank. The DST tags continuously recorded time, temperature and depth. To geolocate fish positions during its time at large, we first extracted the tidal signal from the pressure recordings on the DST tags, and then compared the resulting data to data predicted with a Massachusetts Bay tidal model that provided us with geographical coordinates at a given date and time. Using least-squares criteria within an estimated geographical region of confidence that was constrained by biological and statistical information (e.g. swimming speed, known release and recapture location, and bottom depth) we were able to geolocate the fish. The resultant geolocated migration tracks indicate a large degree of movement of Atlantic cod in the region and an elevated importance of the Great South Channel (GSC) migration corridor between Massachusetts Bay and the western Georges Bank and Nantucket Shoals region. This observation contrasts strongly with inferences of limited movements by Atlantic cod based on conventional tag recapture methods (mean of 1200 km traveled versus 44 km traveled as measured by conventional tagging and geolocation, respectively). This study demonstrates that geoloca-tion methodologies applied to archival tag studies hold great promise of becoming an important new tool for fisheries managers to quantify the movements of fishes. It also points out the need for greater collaboration between fisheries scientists and oceanographers, and particularly for the development of improved tidal models to cover stock regions more accurately and with higher precision.
Geolocating Fish Using Hidden Markov Models and Data Storage Tags
Reviews: Methods and Technologies in Fish Biology and Fisheries, 2009
Geolocation of fish based on data from archival tags typically requires a statistical analysis to reduce the effect of measurement errors. In this paper we present a novel technique for this analysis, one based on Hidden Markov Models (HMM's). We assume that the actual path of the fish is generated by a biased random walk. The HMM methodology produces, for each time step, the probability that the fish resides in each grid cell. Because there is no Monte Carlo step in our technique, we are able to estimate parameters within the likelihood framework. The method does not require the distribution to be Gaussian or belong to any other of the usual families of distributions and can thus address constraints from shorelines and other nonlinear effects; the method can and does produce bimodal distributions. We discuss merits and limitations of the method, and perspectives for the more general problem of inference in state-space models of animals. The technique can be applied to geolocation based on light, on tidal patterns, or measurement of other variables that vary with space. We illustrate the method through application to a simulated data set where geolocation relies on depth data exclusively.
HMMoce: An R package for improved geolocation of archival‐tagged fishes using a hidden Markov method
Methods in Ecology and Evolution, 2018
Electronic tagging of marine fishes is commonly achieved with archival tags that rely on light levels and sea surface temperatures to retrospectively estimate movements. However, methodological issues associated with light‐level geolocation have constrained meaningful inference to species where it is possible to accurately estimate time of sunrise and sunset. Most studies have largely ignored the oceanographic profiles collected by the tag as a potential way to refine light‐level geolocation estimates. Open‐source oceanographic measurements and outputs from high‐resolution models are increasingly available and accessible. Temperature and depth profiles recorded by electronic tags can be integrated with these empirical data and model outputs to construct likelihoods and improve geolocation estimates. The R package HMMoce leverages available tag and oceanographic data to improve position estimates derived from electronic tags using a hidden Markov approach. We illustrate the use of th...
Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, using electronic tags
Environmental Biology of Fishes, 2005
Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, is particularly challenging because they occupy a deep, remote environment during the spawning season. To identify spawning events, a method is needed in which direct observation by humans is not employed. Spawning behavior of seven other flatfish species has been directly observed in their natural environment by investigators using SCUBA. All of these flatfish species display almost identical spawning behavior that follows a routine. Therefore, it is reasonable to believe that this spawning behavior occurs in other flatfish species, including Pacific halibut. As part of a larger study, we recaptured two Pacific halibut on which Pop-up Archival Transmitting (PAT) tags had been attached during the winter spawning season. Because the tags were physically retrieved, we were able to collect minute-by-minute depth records for 135 and 155 days. We used these depth data to tentatively identify spawning events. On seven separate occasions between 20 January 2001 and 9 February 2001, one fish displayed a conspicuous routine only seen during the spawning season of Pacific halibut and the routine parallels the actions of other spawning flatfish directly observed by humans using SCUBA. Therefore, we propose this routine represents spawning behavior in Pacific halibut. The second tagged fish did not display the conspicuous routine, thus challenging the assumption that Pacific halibut are annual spawners. PAT tags may prove to be a useful tool for identifying spawning events of Pacific halibut, and that knowledge may be used for improved management in the future.
Ecological Modelling, 2016
Numerous methods have been developed to geolocate fish from data storage tags. Whereas demersal species have been tracked using tide-driven geolocation models, pelagic species which undertake extensive migrations have been mainly tracked using light-based models. Here, we present a new HMM-based model that infers pelagic fish positions from the sole use of high-resolution temperature and depth histories. A key contribution of our framework lies in model parameter inference (diffusion coefficient and noise parameters with respect to the reference geophysical fields-satellite SST and temperatures derived from the MARS3D hydrodynamic model), which improves model robustness. As a case study, we consider long time series of data storage tags deployed on European sea bass for which individual migration tracks are reconstructed for the first time. We performed a sensitivity analysis on synthetic and real data in order to assess the robustness of the reconstructed tracks with respect to model parameters, chosen reference geophysical fields and the knowledge of fish recapture position. Model assumptions and future directions are discussed. Finally, our model opens new 2 avenues for the reconstruction and analysis of migratory patterns of many other pelagic species in relatively contrasted geophysical environments.
Geolocation of North Sea cod (Gadus morhua) using hidden Markov models and behavioural switching
2008
When geolocating fish based on archival tag data, a realistic assessment of uncertainty is essential. Here, we describe an application of a novel Fokker-Planck-based method to geolocate Atlantic cod (Gadus morhua) in the North Sea area. In this study, the geolocation relies mainly on matching tidal patterns in depth measurements when a fish spends a prolonged period of time at the seabed with a tidal database. Each day, the method provides a nonparametric probability distribution of the position of a tagged fish and therefore avoids enforcing a particular distribution, such as a Gaussian distribution. In addition to the tidal component of the geolocation, the model incoporates two behavioural states, either high or low activity, estimated directly from the depth data, that affect the diffusivity parameter of the model and improves the precision and realism of the geolocation significantly. The new method provides access to the probability distribution of the position of the fish that in turn provides a range of useful descriptive statistics, such as the path of the most probable movement. We compare the method with existing alternatives and discuss its potential in making population inference from archival tag data. Résumé : Lorsqu'on fait la géolocalisation de poissons à partir de données provenant d'étiquettes à archivage, il est essentiel d'obtenir une évaluation réaliste de l'incertitude. Nous décrivons ici l'utilisation d'une méthode nouvelle basée sur l'équation de Fokker-Planck pour faire la géolocalisation des morues franches (Gadus morhua) dans la région de l'Atlantique Nord. Dans notre étude, la géolocalisation se base principalement sur l'appariement des patrons de marées dans les mesures de profondeur lorsqu'un poisson passe une période de temps prolongée sur le fond de la mer avec la banque de données sur les marées. Chaque jour, la méthode fournit une distribution non paramétrique de la position du poisson marqué et ainsi elle évite l'imposition d'une distribution particulière, par exemple la gaussienne. En plus de la composante tidale de la géolocalisation, le modèle incorpore deux états comportementaux, soit une activité forte et une activité faible, estimés directement à partir des données de profondeur, qui affectent le paramètre de diffusivité du modèle et améliorent significativement la précision et le réalisme de la géolocalisation. La nouvelle méthode donne accès à la distribution de probabilité de la position du poisson qui, à son tour, fournit une gamme de données statistiques descriptives utiles, telles que la piste la plus probable de déplacement. Nous comparons notre méthode avec les méthodes de rechange actuellement disponibles et discutons de son potentiel pour faire des déductions à partir de données provenant d'étiquettes à archivage.
Locating Historical Fishing Grounds and Tracking Movements of Cod in the Gulf of Maine with GIS
2019
The following report describes a procedure for locating and mapping historical Gulf of Maine fishing grounds on modern digitized charts, the methodology for determining seasonal distribution and relative abundance. These procedures were developed as part of a study to determine the population structure, range, and distribution of cod populations in the Gulf of Maine (GOM) by tracking historic seasonal distribution and abundance. In the “Fishing Grounds of the Gulf of Maine”, Rich identified 250 individual fishing grounds between Ipswich Bay and the Bay of Fundy. (10) Many of these grounds still have vestigial cod populations on them and 92 grounds have been actively fished for more than a century. He described the location of each fishing ground with compass courses and distances from known landmark(s). Rich also described the substrate and bottom characteristics for each fishing ground. Rich’s landmarks for each fishing ground were found by using the appropriate digitized NOAA char...
2004
Archival tags enhance the interpretability and power of tagging studies, as illustrated by results from a mark-recapture study of yellowtail flounder off New England. Until recently, the well-studied yellowtail flounder was thought to be a "sedentary" fish, feeding on epibenthic fauna and limited to relatively shallow, sandy habitats. This strict habitat preference and the discontinuous distributions of such habitats were considered to limit movement among offshore banks and shelves, thereby maintaining geographic stock structure. However, recent information obtained from data-storage tags documents frequent off-bottom movements associated with movement to different habitats. Similar to results from historical tagging studies for yellowtail, a mark-recapture study off New England that began in 2003 confirms a low frequency of movement among stock areas. However, the movement likely involves passive drift in midwater currents, similar to patterns observed for other flatfish...