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A genotyping-by-sequencing approach was used to discover SNPs throughout the Atlantic Bluefin tuna genome while simultaneously analyzing population structure in the Gulf of Mexico, Atlantic and Mediterranean, including several previously uncharacterized sites. Genotyping revealed temporally persistent differentiation among baseline, early life stage samples from the western Atlantic and Mediterranean using panels of 80 and 25 SNPs (FST = 0.0091, p

Effective sustainable management of marine fisheries requires that assessed management units (that is, fish stocks) correspond to biological populations. This issue has long been discussed in the context of Atlantic bluefin tuna (ABFT, Thunnus thynnus) management, which currently considers two unmixed stocks but does not take into account how individuals born in each of the two main spawning grounds (Gulf of Mexico and Mediterranean Sea) mix in feeding aggregations throughout the Atlantic Ocean. Using thousands of genome-wide molecular markers obtained from larvae and young of the year collected at the species’ main spawning grounds, we provide what is, to the best of our knowledge, the first direct genetic evidence for “natal homing” in ABFT. This has facilitated the development of an accurate, cost-effective, and non-invasive tool for tracing the genetic origin of ABFT that allows for the assignment of catches to their population of origin, which is crucial for ensuring that ABFT management is based on biologically meaningful stock units rather than simply on catch location., Sí

Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen's perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: "habitat and refuge," "biodiversity preservation" and "food production." Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs in other areas. MARE program, within the project "Implantacao e estudo integrado de sistemas recifais" PROMAR program "Elaboracao de estudos de caracterizacao do estado de colonizacao e impacto socioeconomico do recife artificial da Nazare" - 02-PE/2011/GJ info:eu-repo/semantics/publishedVersion

International audience; Productivity and Susceptibility Analysis (PSA) is a methodology for evaluating the vulnerability of a stock based on its biological productivity and susceptibility to fishing. In this study, we evaluated the vulnerability of 60 stocks of tuna, billfishes and other teleosts caught by the tuna longline fleets operating in the South Atlantic and Indian Ocean using a semi-quantitative PSA. We (a) evaluated the vulnerability of the species in the study areas; (b) compared the vulnerability of target and non-target species and oceans; (c) analyzed the sensitivity of data entry; and (d) compared the results of the PSA to other fully quantitative assessment methods. Istiophoridae exhibited the highest scores for vulnerability. The top 10 species at risk were: Atlantic Istiophorus albicans; Indian Ocean Istiompax indica; Atlantic Makaira nigricans and Thunnus alalunga; Indian Ocean Xiphias gladius; Atlantic T. albacares, Gempylus serpens, Ranzania laevis and X. gladius; and Indian Ocean T. alalunga. All species considered at high risk were targeted or were commercialized bycatch, except for the Atlantic G. serpens and R. laevis which were discarded, and may be considered as a false positive. Those species and others at high risk should be prioritized for further assessment and/or data collection. Most species at moderate risk were bycatch species kept for sale. Conversely, species classified at low risk were mostly discarded. Overall, species at high risk were overfished and/or subjected to overfishing. Moreover, all species considered to be within extinction risk (Critically Endangered, Endangered and Vulnerable) were in the high-risk category. The good concordance between approaches corroborates the results of our analysis. PSA is not a replacement for traditional stock assessments, where a stock is assessed at regular intervals to provide management advice. It is of importance, however, where there is uncertaintyabout catches and life history parameters, since it can identify species at risk, and where management action and data collection is required, e.g. for many species at high and most at moderate risk in the South Atlantic and Indian oceans.

Recent coastal planning measures in south-east Portugal (Algarve), where offshore aquaculture developments were set up in fishing areas aiming to maximize expected utility of seafood production activities, raised some discontentment. Public policies created to safeguard offshore aquaculture (OSA) producers and limit small-scale fishing (SSF) activities must be adjusted accordingly in order to maximize income and keep discontentment at a minimum. We collected primary data from stakeholders, fishers (n = 18) and offshore aquaculture operators (n = 3) through participatory workshops and interviews by eliciting problematic issues derived from the offshore area creation and their relative relevance. We used these data to populate conditional probability tables and construct a related influence diagram (Bayesian belief networks) to model the affected system. We selected nine scenarios based on navigability and aquaculture area size with the aim of finding the best expected utility combinations for the OSA SSF system. The inferred results show that maximizing employment and keep pollution at low levels were the most influential factors to keep the system at a satisfactory level. The best decision was not to enlarge the aquaculture area, but to condition the access to other operational stakeholders, namely SSF operators from nearby areas. The overall results of the Bayesian belief network can be used to recommend coastal planners and decision-makers to deal with the interaction between OSA and SSF activities.(c) 2017 Elsevier Ltd. All rights reserved. FEDER Program through the project IAPAA "Avaliacao do impacto da area de producao aquicola da Armona no ecossistema costeiro e comunidades locais" (Portugal) [31-03-01-FEP-0014] info:eu-repo/semantics/publishedVersion

International audience; The difficulty of ensuring adequate statistical coverage of whole fleets is a challenge for the implementation of observer programmes and may reduce the usefulness of the data they obtain for management purposes. This makes it necessary to find cost-effective alternatives. Electronic monitoring (EM) systems are being used in some fisheries as an alternative or a complement to human observers. The objective of this study was to test the use and reliability of EM on the tropical tuna purse-seine fishery. To achieve this objective, seven trips of tuna purse seiners operating in the three Oceans were closely monitored to compare the information provided by EM and on-board observers to determine if EM can reliably document fishing effort, set type, tuna catch, and bycatch. Total tuna catch per set was not significantly different between EM and observer datasets; however, regarding species composition, only main species matched between EM and observers. Success on set-type identification using EM varied between 98.3 and 56.3%, depending on the camera placement. Overall, bycatch species were underestimated by EM, but large bodied species, such as billfishes, were well documented. The analyses in this study showed that EM can be used to determine the fishing effort (number of sets) and total tuna catch as reliably as observers can. Set-type identification also had very promising results, but indicated that refinement of the methods is still needed. To be fully comparable with observer data, improvements for accurately estimating the bycatch will need to be developed in the application and use of the EM system. Operational aspects that need to be improved for an EM programme to be implemented include standardizing installation and on-board catch handling methodology as well as improvements in video technology deployment.

International audience; In spite of its pivotal role in future implementations of the Ecosystem Approach to Fisheries Management, current knowledge about tuna habitat preferences remains fragmented and heterogeneous, because it relies mainly on regional or local studies that have used a variety of approaches making them difficult to combine. Therefore in this study we analyse data from six tuna species in the Pacific, Atlantic and Indian Oceans in order to provide a global, comparative perspective of habitat preferences. These data are longline catch per unit effort from 1958 to 2007 for albacore, Atlantic bluefin, southern bluefin, bigeye, yellowfin and skipjack tunas. Both quotient analysis and Generalised Additive Models were used to determine habitat preference with respect to eight biotic and abiotic variables. Results confirmed that, compared to temperate tunas, tropical tunas prefer warm, anoxic, stratified waters. Atlantic and southern bluefin tuna prefer higher concentrations of chlorophyll than the rest. The two species also tolerate most extreme sea surface height anomalies and highest mixed layer depths. In general, Atlantic bluefin tuna tolerates the widest range of environmental conditions. An assessment of the most important variables determining fish habitat is also provided.

Ecological risk assessment is a useful methodology for assisting the management of fisheries from an ecosystem perspective. Atlantic tuna fisheries, managed by the International Commission for the Conservation of Atlantic Tunas (ICCAT), are economically important and interact with several bycatch species. In spite of these interactions, no comprehensive ecological risk assessment has been conducted for bycatch species caught in ICCAT fisheries. In this paper, we followed a two stage approach with the objective of assessing the relative risk of species being negatively impacted by Atlantic tuna fisheries. An analysis of the ICCAT bycatch species list (which includes all species reported to have interacted with different tuna fishing gears operating in the Atlantic) revealed that most of these species are caught in longline fisheries, followed by gillnets and purse seines. According to the IUCN red list, 7 species of the ICCAT bycatch list (3 coastal sharks, 3 sea turtles and one seabird) are categorized as critically endangered. In our study, and based on their life history characteristics, marine mammals and coastal sharks caught in ICCAT fisheries showed the highest intrinsic vulnerability values. A productivity susceptibility analysis for the European Union (EU) tropical tuna purse seine fleet and the United States (US) pelagic longline fleet revealed two groups with high relative risk scores. The first one included pelagic and coastal sharks, characterized by relatively low productivities, and the second one included teleosts, characterized by higher productivities but high susceptibility to purse seine and longline gears. Some alternative approaches to conduct productivity susceptibility analyses in the context of ecological risk assessments are discussed.

The tagging data base compiled since the 1960s by the secretariat of ICCAT was used to assess the effects of several release factors on the recovery rate of bigeye tuna (Thunnus obesus). The release factors considered were the length of the fish, the latitude, the longitude, the gear used during the tagging operation, the kind of tag used, the year and the month as well as the interactions between the length and the tag type and the length and the year. It was showed that all of these explanatory variables influenced significantly the probability of return of the fish and were used within a GLM framework to predict the probability of recapture of the fish. Results from this model reinforce previous findings concerning the lower efficiency of Betyp tag compared with Spaghetti tag but also highlighted the fact that this detrimental effect concerns only fish lower than 80 cm (FL). Other aspects related to the presence of interactions and the difficulty to discern from inspection of the coefficients how some factors combine to influence the probability of recapture are also discussed.

Conventional “spaghetti” tags have been used for a long time in Tropical Atlantic Ocean and have been collected by ICCAT secretary with the collaboration of scientists and fishermen. Despite, careful examination of the information provided at release and at recapture some errors may persist into the ICCAT tagging data base. The aim of this short note is to highlight some types of errors existing in the tagging data bases for tropical tunas and to suggest potential clues for corrections.

International audience; This paper describes the model FASST. FASST is a fully structured age, size, space and time stock assessment model. It is expressed as a deterministic system of partial differential equations continuous in age, size and time. Space is represented using large discrete zones interconnected by exchange rates. All the parameterizations used to represent recruitment, growth, mortality and movements are chosen to be size-dependent and age independent. Consequently, for simplicity purposes, the age dimension can be simplified. The model is integrated numerically to simulate the stock dynamics. A complex process-and observationerror framework is used to estimate the model parameters, and hence the past stock status, in a Bayesian context. The model uses simultaneously most fishery data currently available for tuna stock assessment such as catch by fleet in number and weight, length-frequency samples, otolith analysis, tag-recapture data. It provides a new way to integrate that information into a consistent stock assessment framework.

Tuna fisheries have been identified as one of the major threats to populations of other marine vertebrates, including sea turtles, sharks, seabirds and marine mammals. The development of technical mitigation measures (MM) in fisheries is part of the code of conduct for responsible fisheries. An in-depth analysis of the available literature regarding bycatch mitigation in tuna fisheries with special reference to elasmobranchs was undertaken. Studies highlighting promising MMs were reviewed for four tuna fisheries (longline, purse seine, driftnets and gillnet, and rod and line – including recreational fisheries). The advantages and disadvantages of different MMs are discussed and assessed based on current scientific knowledge. Current management measures for sharks and rays in tuna Regional Fishery Management Organizations (t-RFMOs) are presented. A review of relevant studies examining at-vessel and postrelease mortality of elasmobranch bycatch is provided. This review aims to help fisheries managers identify pragmatic solutions to reduce mortality on pelagic elasmobranchs (and other higher vertebrates) whilst minimizing impacts on catches of target tuna species. Recent research efforts have identified several effective MMs that, if endorsed by t-RFMOs, could reduce elasmobranchs mortality rate in international tropical purse seine tuna fisheries. In the case of longline fisheries, the number of operational effective MMs is very limited. Fisheries deploying driftnets in pelagic ecosystems are suspected to have a high elasmobranchs bycatch and their discard survival is uncertain, but no effective MMs have been field validated for these fisheries. The precautionary bans of such gear by the EU and by some t-RFMOs seem therefore appropriate. Recreational tuna fisheries should be accompanied by science-based support to reduce potential negative impacts on shark populations. Priorities for research and management are identified and discussed., SI

This report details the operations carried out by the authors during the first leg of the SY002 expedition of the Japanese research vessel Shoyo Maru of the National Research Institute of Far Seas Fisheries in the central Atlantic, within the framework of the ICCAT BETYP research program on bigeye tuna Thunnus obesus. Water samples were collected at different depths to measure nitrite concentration; stomachs of tuna caught by the horizontal longline, as well as those of associated species, were recovered to be examined in the laboratory; potential tuna prey was searched for by day and night trawling using an IKMT micronekton trawlnet in the deep scattering layer; otoliths from bigeye tuna and yellowfin tuna T. albacares were extracted. The mission was also an opportunity to collect tissue samples from mesopelagic species, including bigeye tuna and blue shark Prionace glauca, for future genetic analysis. During trips at sea, six hours a day were devoted, on average, to the observation of marine fauna (seabirds and cetaceans)., Le présent rapport détaille les opérations de recherche effectuées par les auteurs lors du premier leg de la campagne SY002 du navire de recherche japonais Shoyo Maru du National Research Institute of Far Seas Fisheries dans l'Atlantique central dans le cadre du programme BETYP de l'ICCAT sur le patudo Thunnus obesus. Des échantillons d'eau ont été récoltés à différentes profondeurs afin de mesurer les concentrations de nitrites ; des estomacs des thons capturés par la palangre horizontale, ainsi que ceux des espèces associées ont été récupérés pour être examinés au laboratoire ; les proies potentielles des thons ont été recherchées par chalutage de jour et de nuit dans la couche diffusante profonde à l'aide d'un filet à micronecton IKMT ; des otolithes de patudo et de thon à nageoires jaunes T. albacares ont été extraits. La mission a aussi été l'occasion de collecter des échantillons de tissus d'espèces mésopélagiques, dont le patudo et le requin bleu Prionace glauca, en vue de futures analyses génétiques. Lors des trajets en mer, six heures par jour ont été consacrées, en moyenne, à l'observation de la faune marine (oiseaux marins et cétacés).