Haritz Arrizabalaga

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.

Standardization of bluefin tuna, Thunnus thynnus, catch per unit effort in the baitboat fishery of the Bay of Biscay (Eastern Atlantic)

Relative indices of abundance by age class for bluefin tuna from 1975 to 2000 were estimated using generalized linear mixed models. Age class was included as a fixed factor within the model specifications, with the Year×Age interaction as a fixed factor component in order to obtain annual indices by age. Catch and effort data on bluefin tuna were available from two sources, catches by trip, and daily catches from logbooks. Catches were modelled using the delta-lognormal model. The model finally selected included the following explanatory factors: Year, Age, Year×Age, Month, number of Crew, number of Bait Tanks, and with the Year×Month interaction as a random component. Overall, year trends and coefficients of variation were similar from both datasets by age class. In general, the standardization procedure showed that vessel characteristics and technological advances related to fishing have a relatively minor explanatory effect on the observed catch rates of bluefin tuna in the fishery. Neither geographical distribution nor type of bait had an explanatory effect on the observed catch rates. The 1994 cohort stands out as an exceptionally large year class; it can be followed through the standardized series. This standardized catch rate index at age of bluefin tuna is the most complete yet available and is the only one currently used for juvenile fish in calibrating population models to evaluate the Eastern Atlantic and Mediterranean stock. It is particularly valuable because, apart from improvements in electronic technology, there are no changes in the method of exploitation during the entire series.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

Small Scale Vertical Behaviour of Juvenile Albacore in Relation to Their Biotic Environment in the Bay of Biscay

The goal of the present study is to analyze the small scale vertical behaviour of juvenile albacore tuna (Thunnus alalunga) in relation to the abundance and distribution of their main prey, which has particular importance regarding catchability by surface fishing gears, such as trolling. A total of six juvenile albacore were tracked in the south east Bay of Biscay in July and August 2005, using ultrasonic transmitters. Two echosounders working at 38 and 120 kHz on the tracking vessel were used to collect data on the biotic environment (krill, small pelagic fish and planktonic layers) between the surface and 200 m depth. These data were echo-integrated in order to relate tuna vertical movements to food availability. The stomach contents of 97 albacore caught during the surveys were analyzed, the comparison of prey occurrences respectively in the stomachs and on the echograms showed selectivity for blue whiting. However, the biotic factors considered in this study had no significant influence on the depth of albacore, which possibly feed during night-time in surface waters. The tracked albacore had a shallow depth distribution and did not exhibit any regular deep-diving behaviour. A significant effect of time of day and body size on albacore depth was shown, all fish remaining deeper during daytime, and smaller fish having a shallower vertical distribution.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.

Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data.

Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids.

The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases.

Misidentification of bluefin tuna larvae: a call for caution and taxonomic reform

The international effort to prevent the collapse of Atlantic bluefin tuna (BFT, Thunnus thynnus, Scombridae) stocks exemplifies the challenges associated with modern marine resource conservation. Rampant mismanagement, under-reporting and illegal, unreported and unregulated fishing led to decades of over-exploitation in the BFT fishery. Surveys of larval abundance in the Gulf of Mexico and the Mediterranean Sea have been used as a proxy for both spawning biomass and recruitment by researchers working to improve estimates of stock abundance. Recent genetic barcoding studies have revealed that species identification errors are common among larvae surveys that use morphology-based taxonomy alone. Misidentification of larvae can lead to uncertainty about the spatial distribution of a species, confusion over life history traits and population dynamics, and potentially disguise the collapse or recovery of localized spawning sites. In an effort to identify the source of these errors, we review several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials. Recent advances in molecular techniques useful for specimen identification and population studies are discussed at length. We advocate a more constructive integration of morphology-based taxonomy and barcoding in order to add confidence to larval surveys and to strengthen associated fisheries management.

Review of albacore tuna, Thunnus alalunga, biology, fisheries and management

Albacore is one of the most important commercially harvested species in the world’s oceans. Despite a long history of scientific research, there is no global review or synthesis of knowledge about the species across all oceanic regions. We analysed 613 published studies that report on albacore and summarize the current state of knowledge on biology, stock structure, fisheries and management. To describe the trends in albacore fisheries, we examined the catch and effort databases of Regional Fisheries Management Organisations. The stocks of albacore are generally largest in the Pacific Ocean and smallest in the Mediterranean Sea. The biology of Atlantic and Pacific Ocean stocks are well documented, while the Indian Ocean and the Mediterranean Sea stocks are more data deficient. These two latter areas should be considered as priorities for future research and data collection in order to better understand the state of global stocks of albacore tuna. Improved information would also assist with delineating stock boundaries needed for sustainable management of this species.

Otolith shape variation provides a marker of stock origin for north Atlantic bluefin tuna (Thunnus thynnus)

Two stocks of bluefin tuna (Thunnus thynnus) inhabit the north Atlantic; the western and eastern stocks spawn in the Gulf of Mexico and the Mediterranean Sea respectively. Trans-Atlantic movements occur outside spawning time whereas natal homing maintains stock structure. Commercial fisheries may exploit a mixed assemblage of both stocks. The incorporation of mixing rates into stock assessment is precluded by uncertainties surrounding stock discrimination. Otolith shape descriptors were used to characterise western and eastern stocks of Atlantic bluefin tuna in the present study and to estimate stock composition in catches of unknown origin. Otolith shape varied with length and between locations and years. Within a restricted size range (200–297-cm fork length (FL)) the two stocks were distinguished with an accuracy of 83%. Bayesian stock mixture analysis indicated that samples from the east Atlantic and Mediterranean were predominantly of eastern origin. The proportion assigned to the eastern stock showed slight spatial variation; however, overlapping 95% credible intervals indicated no significant difference (200–297cm FL: central Atlantic, 73–100%; Straits of Gibraltar, 73–100%; Morocco, 50–99%; Portugal 64–100%). Otolith shape could be used in combination with other population markers to improve the accuracy of mixing rate estimates for Atlantic bluefin tuna.

Otolith chemistry as an indicator of movements of albacore (Thunnus alalunga) in the North Atlantic Ocean

Albacore (Thunnus alalunga) in the North Atlantic Ocean is currently managed as a single well-mixed stock, although this assumption remains contentious. We measured stable isotopes (δ13C and δ18O) and trace elements (Mg, Mn, Sr, Ba) in otoliths of albacore collected from two feeding grounds, namely the Bay of Biscay and Atlantic offshore waters, and compared them among sampling locations and life history stages. Measurements in otolith core, post-core and edge were used to determine whether albacore from these two regions have the same nursery origin and migratory patterns. We found no clear evidence of distinct nursery grounds based on otolith core chemistry, but Sr:Ca and Mg:Ca were different in the post-core portions of albacore from the two locations, suggesting residency in different regions during the early juvenile stage. Otolith edge chemistry, particularly stable isotopes and Sr:Ca, proved to be a valuable tool for classifying individuals to their capture locations. Annual cycles of Sr:Ca ratios were visible along life history transects, likely reflecting migratory patterns between water masses of differing salinity, but the timing of Sr:Ca cycles differed between the two groups. Differentiation in trace element concentrations in the otolith post-core and the timing of Sr:Ca cycles suggest the occurrence of two migratory contingents of albacore in the north-east Atlantic Ocean.