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16 results on '"Instituto Português de Investigação do Mar e da Atmosfera (IPMA)"'

1. Contrasting impacts of climate change on connectivity and larval recruitment to estuarine nursery areas

Author

Maud Pierre, Henrique N. Cabral, Susanne E. Tanner, Ana Teles-Machado, Patrick Reis-Santos, Mario Lepage, Jérémy Lobry, Hilaire Drouineau, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), University of Adelaide, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), Universidade de Lisboa (ULISBOA), and Fundaçao para a Ciencia e a Tec-nologia (FCT) via strategic (UID/MAR/04292/2020)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Population structure, Nurseries, Temperature salinity diagrams, Climate change, Aquatic Science, Larval dispersal, 01 natural sciences, 14. Life underwater, Marine-estuarine, 0105 earth and related environmental sciences, geography, Larva, Connectivity, geography.geographical_feature_category, biology, Iberian coast, Soleá, 010604 marine biology & hydrobiology, fungi, North Atlantic, Geology, Estuary, biology.organism_classification, Fishery, Oceanography, opportunist fishes, Estuarine recruitment, 13. Climate action, Biological dispersal, Dicentrarchus
Abstract

International audience; Connectivity between spawning grounds and recruitment areas of marine fish species drives population structure and dynamics, and may be affected by climate-induced changes in oceanographic processes. We analysed the variability in recruitment success of larvae to estuarine nursery areas along the Iberian Atlantic coast of four fish species with distinct spawning grounds and periods (Solea solea, Solea senegalensis, Platichthys flesus and Dicentrarchus labrax). Concomitantly, we explored the variations in connectivity patterns between "cold" and "warm" year archetypes. We used a three-dimensional Lagrangian transport particle-tracking model integrating time series of velocity, temperature and salinity fields archived from the Regional Ocean Modelling System. We simulated individual larval dispersal, over extended spawning periods, from multiple coastal spawning areas to estuarine recruitment areas over 20 years (1989-2008). Overall, high inter-and intra-annual variation were found for all species. Nonetheless, highest overall average recruitment estimates were obtained for S. solea and D. labrax (with 7.3% and 5.7% of the particles released in spawning areas reaching a recruitment area, respectively) compared to S. senegalensis and P. flesus (3.4% and 1.7%, respectively). Recruitment estimates were overall higher at earlier spawning dates but peak values occurred at later spawning events. Regarding spawning origin, particles that recruited to the northern part of the Iberian coast were mainly from southern source areas. For estuarine systems located in southern Portugal, the relative contributions of northern and southern coastal spawning areas were more balanced, or with a preponderance of northern spawning areas (namely for S. senegalensis and D. labrax). Recruitment was higher in "warm" years compared to "cold" years, except for P. flesus for which nil recruitment was registered in the southern Iberian coast during "warm" years. Larvae also travelled farther in "warm" years compared to "cold" years. Ultimately, understanding how oceanographic conditions govern larval recruitment to estuarine nursery areas is pivotal to forecast the potential impacts of climate change on species with segregated life histories, and will underpin long term management and safeguarding of estuarine nursery role.

Published
2021
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2. Historical Data in the CoastNet Geoportal: Documenting Fish Assemblages in Portuguese Estuaries

Author

Susana França, Vanessa F. Fonseca, Susanne E. Tanner, Rita P. Vasconcelos, Patrick Reis-Santos, Anabela Maia, Miguel Ruano, Inês Cardoso, Sofia Henriques, Miguel Pessanha Pais, Pedro Brandão, Ana C. Brito, Paola Castellanos, Paula Chainho, Bernardo Quintella, Luís da Costa, Maria José Costa, José Lino Costa, Henrique N. Cabral, UNIVERSIDADE DE LISBOA MARE LISBOA PRT, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Universidad de Concepción - University of Concepcion [Chile], Faculdade de Ciências [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA), Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project, and Universidade de Lisboa (ULISBOA)

Subjects
0106 biological sciences, CoastNet research infrastructure, global changes, Science, Estuarine ecosystems, Ocean Engineering, QH1-199.5, Aquatic Science, estuarine fish communities, Oceanography, 010603 evolutionary biology, 01 natural sciences, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Water Science and Technology, Global and Planetary Change, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, General. Including nature conservation, geographical distribution, Estuary, language.human_language, Fishery, estuarine ecosystems, historical data, [SDE]Environmental Sciences, language, %22">Fish , Portuguese, Geoportal
Abstract

International audience

Published
2021
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3. Determining natal origin for improved management of Atlantic bluefin tuna

Author

Jean-Marc Fromentin, John F. Walter, David E. Richardson, Fambaye N Sow, Matthew V. Lauretta, Işık Oray, Joseph M. Quattro, Noureddine Abid, José Luis Varela, Leif Nøttestad, Francisco Alemany, Simeon Deguara, Molly Lutcavage, Pedro J Pascual-Alayón, Miguel N. Santos, Nicolas Goñi, Yohei Tsukahara, Natalia Díaz-Arce, F. Saadet Karakulak, Jay R. Rooker, Alex Hanke, Naiara Rodríguez-Ezpeleta, Piero Addis, Haritz Arrizabalaga, Tomoyuki Itoh, James S. Franks, Igaratza Fraile, AZTI - Tecnalia, NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Texas A&M University [College Station], Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Fisheries and Oceans Canada (DFO), Gulf Coast Research Laboratory, University of Southern Mississippi (USM), AquaBioTech Ltd, Universita degli Studi di Cagliari [Cagliari], Department of Biology [Univ. of Cadiz], University of Cadiz, Acadia University, Institut National de Recherche Halieutique de Tanger (INRH), Centro Oceanografico de Baleares (IEO), Centro Oceanografico de Baleares, Istanbul University, University of South Carolina [Columbia], Centre de Recherche Océanographique de Dakar-Thiaroye (CRODT), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), National Research Institute of Far Seas Fisheries, National Research Institut of Far Seas Fisheries, Centro Oceanográfico de Canarias, IEO, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), International Commission for the Conservation of Atlantic Tunas (ICCAT), ICCAT, University of Massachusetts [Boston] (UMass Boston), University of Massachusetts System (UMASS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), AquaBioTech Group [Malta], and Università degli Studi di Cagliari = University of Cagliari (UniCa)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Population, Sede Central IEO, Fish stock, 010603 evolutionary biology, 01 natural sciences, Mediterranean sea, Marine fisheries, 14. Life underwater, Population-structure, education, Ecology, Evolution, Behavior and Systematics, Stock (geology), 0105 earth and related environmental sciences, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, Fishery, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Natal homing, Geography, Sustainable management, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna
Abstract

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

Published
2019
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4. Food-web dynamics in the Portuguese continental shelf ecosystem between 1986 and 2017: Unravelling drivers of sardine decline

Author

Henrique N. Cabral, T. Veiga-Malta, Alexandra Silva, Susana Garrido, Corina Chaves, M.A. Torres, Maria Manuel Angélico, Pedro Ré, L. Sobrinho-Gonçalves, B. Alcoforado, Dorota Szalaj, Instituto Dom Luiz, Universidade de Lisboa (ULISBOA), Instituto Espagňol de Oceanografia (IEO), DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), Ecosystèmes aquatiques et changements globaux (UR EABX), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Ecosystem modelling, Sardine fisheries, Aquatic Science, Centro Oceanográfico de Cádiz, Oceanography, 01 natural sciences, Hindcast analysis, Chub mackerel, Ecosystem model, Ecosystem, 14. Life underwater, Medio Marino, 0105 earth and related environmental sciences, Trophic level, fish, Biomass (ecology), geography, geography.geographical_feature_category, biology, Continental shelf, 010604 marine biology & hydrobiology, food, Sardine, Food webs, dynamics, biology.organism_classification, Food web, Fishery, continental shelves, 13. Climate action, [SDE]Environmental Sciences, rights, Ecopath with ecosim, Portuguese shelf
Abstract

The Ecopath food web model that describes the Portuguese continental shelf ecosystem was fitted to available time series to investigate the ecosystem dynamics and decline of the Portuguese sardine stock. Our results showed that the Portuguese continental shelf ecosystem model is a good predictor of biomass and catch time series trends for many species. Moreover, our results suggested that the main factors that drove the ecosystem dynamics were trophic interactions, fishing and environmental forcing (sea surface temperature). The same drivers were important in explaining sardine decline among which the largest contribution was observed when incorporating sea surface temperature forcing on adult sardine, followed by fishing. Moreover, sardine eggs predators (i.e., chub mackerel, horse mackerel and bogue) were emphasised as the most important among trophic interactions in explaining sardine trend between 1986 and 2017. Furthermore, a flow control hypothesis test, showed that model parametrization allows explaining sardine behaviour through wasp-waist control mechanism, characteristic for upwelling systems. This study represents an important step forward in understanding the changes that occurred in the Portuguese continental shelf ecosystem and provides helpful insights to explain Portuguese sardine decline., SI

Published
2021
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5. Effects of scale on the assessment of fish biodiversity in the marine strategy framework directive context

Author

Teresa Moura, Inês Machado, Ivone Figueiredo, Henrique N. Cabral, José Lino Costa, Corina Chaves, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Fundação para a Ciência e a Tecnologia, I.P., under the project UIDB/04292/2020, granted to MARE – Marine and Environmental Sciences Centre, and under the project UIDB/50019/2020, granted to IDL – Instituto Dom Luiz. The leading author has received funding support from the FCT through a PhD fellowship (PD/BD/135065/2017).

Subjects
0106 biological sciences, Spatial scales, Ecology (disciplines), Population, Biodiversity, General Decision Sciences, Context (language use), Biodiversity Environmental, 010501 environmental sciences, Marine Strategy, 010603 evolutionary biology, 01 natural sciences, Marine Strategy Framework Directive, Framework Directive, Status Breakpoint and Trend Analysis, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Non-commercial fish species, Biomass (ecology), education.field_of_study, Ecology, business.industry, Environmental resource management, 15. Life on land, Trend analysis, [SDE]Environmental Sciences, business, Scale (map)
Abstract

International audience; The Marine Strategy Framework Directive is undergoing its second implementation cycle while work is ongoingto promote further harmonization, especially regarding the European Commission standards on datasets, metrics, and thresholds. Even though spatial scales for Biodiversity descriptor criteria concerning fish are set by theDirective at subdivision of region, subregion or region level (depending on the fish species group), the scales ofthe assessment have never been confirmed across the multiple metrics, taxons and regions. In this work,Descriptor 1 – Biodiversity and Criterion 2 – Population abundance of the species (D1C2) was evaluated andcompared for six non-commercial fish species, at five geographical scales in the Portuguese Continental waters,to understand if scales used in the assessment affect species group status and hinder the establishment of adequate monitoring or management measures. For comparability purposes, the methods used were identical to theMSFD; a Breakpoint analysis combined with a Trend analysis of the last five years. Results showed that assessments at Portuguese continental Economic Exclusive Zone level mask local population patterns that were visible when smaller size scales were used, and that each species had different scale requirements. Argentyna sphyraena had low biomass index in the northern region of Aveiro, and species analysed in the Algarve region presented distinct patterns. Downsizing scales revealed that Microchirus variegatus was not in good status – i.e., below threshold - in the southern coastal area, requiring further attention to understand how pressures are impacting populations locally. Although the overall status of the species was maintained, when species assessment was integrated, smaller sized assessment scales are required to understand how populations respond to pressures locally and therefore how monitoring and management of status and pressures should be implemented. Results highlight the need to consider species biology, ecology and population dynamics to define precise scales of assessment and to identify areas of risk at locally relevant scales.

Published
2020
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6. Species richness in North Atlantic fish: Process concealed by pattern

Author

Jón Sólmundsson, Didier Gascuel, Jónas P. Jonasson, Luis Gil de Sola, Jakov Dulčić, Jákup Reinert, Melita Peharda, Jan G. Hiddink, Heino O. Fock, Henrik Gislason, Mark R. Payne, Sanja Matić-Skoko, Lilja Stefansdottir, Nedo Vrgoč, F. Velasco, Corina Chaves, Cristina Silva, Remment ter Hofstede, Igor Isajlović, Andrey V. Dolgov, Hicham Masski, Gudrun Marteinsdottir, Maria de Fátima Borges, Anders Nielsen, Jeremy S. Collie, Teresa Bottari, Ole A Jørgensen, Kristján Kristinsson, Daniel E. Duplisea, Brian R. MacKenzie, DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Graduate School of Oceanography [Narragansett], University of Rhode Island (URI), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Institute for Biological Resources and Marine Biotechnology (IRBIM), RUSSIAN FEDERAL RESEARCH INSTITUTE OF FISHERIES AND OCEANOGRAPHY MOSCOW RUS, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institute of Oceanography, Fisheries, Maurice-Lamontagne Institute, Fisheries and Oceans Canada (DFO), Thünen-Institute of Sea Fisheries, Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Español de Oceanografía (IEO). Centro Costero de Málaga, Muelle Pesquero s/n. 29.640 Fuengirola (Málaga), Spain, School of Ocean Sciences [Menai Bridge], Bangor University, MARINE AND FRESHWATER RESEARCH INSTITUTE REYKJAVIK ISL, Institute of Life and Environmental Sciences, University of Iceland, INRH, Faroe Marine Research Institute, INSTITUTO ESPANOL DE OCEANOGRAFIA SANTANDER ESP, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Centro Oceanográfico de Santander, abundance, biodiversity, density, marine fish, species size, temperature, Biodiversity, 010603 evolutionary biology, 01 natural sciences, Latitude, Abundance (ecology), SDG 14 - Life Below Water, 14. Life underwater, Pesquerías, Ecology, Evolution, Behavior and Systematics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Global and Planetary Change, Extinction, Ecology, 010604 marine biology & hydrobiology, Generalized additive model, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Environmental science, Species richness, Neutral theory of molecular evolution, Global biodiversity
Abstract

Aim: Previous analyses of marine fish species richness based on presence-absence data have shown changes with latitude and average species size, but little is known about the underlying processes. To elucidate these processes we use metabolic, neutral and descriptive statistical models to analyse how richness responds to maximum species length, fish abundance, temperature, primary production, depth, latitude and longitude, while accounting for differences in species catchability, sampling effort and mesh size. Data: Results from 53,382 bottom trawl hauls representing 50 fish assemblages. Location: The northern Atlantic from Nova Scotia to Guinea. Time period: 1977–2013. Methods: A descriptive generalized additive model was used to identify functional relationships between species richness and potential drivers, after which nonlinear estimation techniques were used to parameterize: (a) a ‘best’ fitting model of species richness built on the functional relationships, (b) an environmental model based on latitude, longitude and depth, and mechanistic models based on (c) metabolic and (d) neutral theory. Results: In the ‘best’ model the number of species observed is a lognormal function of maximum species length. It increases significantly with temperature, primary production, sampling effort, and abundance, and declines with depth and, for small species, with the mesh size in the trawl. The ‘best’ model explains close to 90% of the deviance and the neutral, metabolic and environmental models 89%. In all four models, maximum species length and either temperature or latitude account for more than half of the deviance explained. Main conclusions: The two mechanistic models explain the patterns in demersal fish species richness in the northern Atlantic almost equally well. A better understanding of the underlying drivers is likely to require development of dynamic mechanistic models of richness and size evolution, fit not only to extant distributions, but also to historical environmental conditions and to past speciation and extinction rates, Sí

Published
2020
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7. Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection

Author

Maria Sofia Costa, Vitor Ramos, Bárbara Frazão, João Morais, Pedro N. Leão, Vitor Vasconcelos, Rosário Martins, Raquel Castelo-Branco, Ângela Maria Vieira Pinheiro, Sébastien Brûle, Ana Luísa Pereira, Ana Regueiras, Cristiana Moreira, Viviana R. Lopes, Joana Martins, Martin L. Saker, Silvia Maria Mathes Faustino, Joana Osswald, Dina Gomes, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Faculdade de Ciências da Universidade do Porto (FCUP), Uppsala University, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Université de Bretagne Sud - Lorient (UBS Lorient), Université de Bretagne Sud (UBS), Universidade Federal do Amapà (UNIFAP), Instituto Politécnico do Porto = Polytechnic Institute of Porto, Alpha Environmental Solutions [Dubai], VR gratefully acknowledges financial support from a Fundação para a Ciência e a Tecnologia (FCT) fellowship SFRH/BD/80153/2011. The Project NOMORFILM has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 634588. Structured Program of R&D&I INNOVMAR-Innovation and Sustainability in the Management and Exploitation of Marine Resources (reference NORTE-01-0145-FEDER-000035, Research Line NOVELMAR), funded by the Northern Regional Operational Program (NORTE2020) through the European Regional Development Fund (ERDF). PNL acknowledges funding from FCT through contract (IF/01358/2014)., European Project: 634588,H2020,H2020-BG-2014-2,NOMORFILM(2015), Centro Interdisciplinar de Investigação Marinha e Ambiental, Repositório Científico do Instituto Politécnico do Porto, Universidade do Porto, and Instituto Politécnico do Porto = Oporto Polytechnic Institute

Subjects
0106 biological sciences, 0301 basic medicine, Biodiversity, Strains, Plant Science, Aquatic Science, Biology, Biological resource centers, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Cyanobacteria, Microbiology, 01 natural sciences, Article, 03 medical and health sciences, Teknik och teknologier, Botany, 14. Life underwater, Culture collection, Bioprospecting, Synechococcales, Phylogenetic tree, 010604 marine biology & hydrobiology, Strain (biology), 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mikrobiologi, Phylogenetic diversity, Chemodiversity, 030104 developmental biology, GenBank, Engineering and Technology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC. © 2018, The Author(s). Acknowledgements VR gratefully acknowledges financial support from a Fundação para a Ciência e a Tecnologia (FCT) fellowship SFRH/BD/ 80153/2011. The Project NOMORFILM has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 634588. Structured Program of R&D&I INNOVMAR-Innovation and Sustainability in the Management and Exploitation of Marine Resources (reference NORTE-01-0145-FEDER-000035, Research Line NOVELMAR), funded by the Northern Regional Operational Program (NORTE2020) through the European Regional Development Fund (ERDF). PNL acknowledges funding from FCT through contract (IF/01358/2014).

Published
2018
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8. Conflicts in the coastal zone : Human impacts on commercially important fish species utilizing coastal habitat

Author

Olivier Le Pape, Elliot John Brown, Francesco Colloca, Rita P. Vasconcelos, Karen E. van de Wolfshaar, Giacomo Millisenda, Josianne Støttrup, Ulf Bergström, Håkan Wennhage, Repositório da Universidade de Lisboa, DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Department of Aquatic Resources, Swedish University of Agricultural Sciences (SLU), Wageningen Marine Research [The Netherlands], Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche (CNR), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Mapping fish habitats, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], habitat loss, Fishing, coastal, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Invasive species, Onderzoeksformatie, ecosystem-based management, Anthropogenic pressure, Ecosystem, SDG 14 - Life Below Water, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, 010604 marine biology & hydrobiology, fungi, Cumulative effects, habitat degradation, human activity, 15. Life on land, Fishery, Geography, Habitat, 13. Climate action, fisheries, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Water quality, Fisheries management, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Eutrophication
Abstract

Fundacao para a Ciencia e a Tecnologia (FCT) [IF/00058/2013, PTDC/AAG-GLO/5849/2014, UID/MAR/04292/]; European Commission via National Programme for Biological Sampling (PNAB) integrated in the Data Collection Framework; Wageningen Marine Research This work was developed within the context of the ICES Working Group on the Value of Coastal Habitats for Exploited Species (WGVHES). We thank both ICES and all participants of the Working Group during 2014-2017. Contributors to this research were independently funded and supported: EJB was funded by the Danish Recreational Fishers Fund - Marine Fiskepleje and the Otto Monsted Fund; RPV was financed through Fundacao para a Ciencia e a Tecnologia (FCT) via Investigador FCT Programme 2013 (IF/00058/2013), project PTDC/AAG-GLO/5849/2014 and project UID/MAR/04292/, and through European Commission via National Programme for Biological Sampling (PNAB) integrated in the Data Collection Framework, and KvdW was supported by Wageningen Marine Research.; International audience; Coastal ecosystems are ecologically, culturally, and economically important, and hence are under pressure from diverse human activities. We reviewed the literature for existing evidence of effects of human-induced habitat changes on exploited fish utilizing coastal habitats. We focused on fish species of the Northeast Atlantic for which fisheries advice is provided by International Council for the Exploration of the Sea (ICES) and which utilize coastal habitats for at least one life-history stage (LHS). We found that 92% of these species are impacted by human activity in at least one LHS while utilizing coastal habitat and 38% in multiple stages. Anthropogenic pressures most commonly shown to impact these fish species were toxicants and pollutants (75% of species). Eutrophication and anoxia, invasive species, and physical coastal development affected about half of the species (58, 54, and 42% of species, respectively), while indirect fishing impacts affected a minority (17% of species). Moreover, 71% of the ICES advice species that utilize coastal habitats face impacts from more than one pressure, implying cumulative effects. Given that three-fourths of the commercial landings come from fish species utilizing coastal habitats, there is an obvious need for a better understanding of the impacts that human activities cause in these habitats for the development of ecosystem-based fisheries management.

Published
2018
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9. Local fishermen's perceptions of the usefulness of artificial reef ecosystem services in Portugal

Author

Amber Himes-Cornell, Miguel N. Santos, Jorge Ramos, Pedro G. Lino, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), Universidade do Algarve (UAlg), Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), International Commission for the Conservation of Atlantic Tunas (ICCAT), ICCAT, 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], FCT-Foundation for Science and Technology [UID/SOC/04020/2013], Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Artificial reefs, Resource (biology), 010504 meteorology & atmospheric sciences, Fishing, Biodiversity, lcsh:Medicine, Ecosystem Science, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Ecosystem services, Stakeholders, Local fishermen, 14. Life underwater, Direct use value, 0105 earth and related environmental sciences, Indirect use value, Portugal, business.industry, 010604 marine biology & hydrobiology, General Neuroscience, Environmental resource management, lcsh:R, General Medicine, Geography, Habitat, Software deployment, [SDE]Environmental Sciences, Aquaculture, Fisheries and Fish Science, Perception, Artificial reef, General Agricultural and Biological Sciences, business, Null hypothesis, Likert scales
Abstract

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

Published
2019
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10. Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations

Author

Henrique N. Cabral, Bronwyn M. Gillanders, Susanne E. Tanner, Montse Pérez, Maria Ana Aboim, Patrick Reis-Santos, Grégory Charrier, Pablo Presa, Jean Laroche, Rita P. Vasconcelos, Marine and Environmental Sciences Centre [Portugal] (MARE), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida (ISPA), School of Biological Sciences [Adelaïde], University of Adelaide, Faculdade de Ciências [Lisboa], Universidade de Lisboa (ULISBOA), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidade de Vigo, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Instituto Universitário de Ciências Psicológicas, Sociais e da Vida = University Institute of Psychological, Social and Life Sciences (ISPA), Universidade de Lisboa = University of Lisbon (ULISBOA), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Repositório da Universidade de Lisboa

Subjects
0106 biological sciences, Environmental change, lcsh:Medicine, Flounder, 01 natural sciences, Gene flow, baltic sea, lcsh:Science, 3105 Peces y Fauna Silvestre, Atlantic Ocean, Otolith, education.field_of_study, Principal Component Analysis, Multidisciplinary, biology, Ecology, integrated approach, medicine.anatomical_structure, cod gadus-morhua, Biocomplexity, 3105.10 Dinámica de las Poblaciones, Microsatellite, Genetic Markers, Genotype, Population, chemistry, 010603 evolutionary biology, Article, quality-assurance, medicine, Animals, 14. Life underwater, EUROPEAN FLOUNDER, education, otolith reference material, ACL, 010604 marine biology & hydrobiology, lcsh:R, Genetic Variation, Bayes Theorem, biology.organism_classification, Genetic marker, physiological influences, 2409.03 Genética de Poblaciones, northeast atlantic, flounder platichthys-flesus, lcsh:Q, stock delineation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microsatellite Repeats
Abstract

Processes regulating population connectivity are complex, ranging from extrinsic environmental factors to intrinsic individual based features, and are a major force shaping the persistence of fish species and population responses to harvesting and environmental change. Here we developed an integrated assessment of demographic and genetic connectivity of European flounder Platichthys flesus in the northeast Atlantic (from the Norwegian to the Portuguese coast) and Baltic Sea. Specifically, we used a Bayesian infinite mixture model to infer the most likely number of natal sources of individuals based on otolith near core chemical composition. Simultaneously, we characterised genetic connectivity via microsatellite DNA markers, and evaluated how the combined use of natural tags informed individual movement and long-term population exchange rates. Individual markers provided different insights on movement, with otolith chemistry delineating Norwegian and Baltic Sea sources, whilst genetic markers showed a latitudinal pattern which distinguished southern peripheral populations along the Iberian coast. Overall, the integrated use of natural tags resulted in outcomes that were not readily anticipated by individual movement or gene flow markers alone. Our ecological and evolutionary approach provided a synergistic view on connectivity, which will be paramount to align biological and management units and safeguard species’ biocomplexity Fundação para a Ciência e a Tecnologia | Ref. UID/MAR/04292/2013 Fundação para a Ciência e a Tecnologia | Ref. PTDC/AAG-GLO/5849/2014 Fundação para a Ciência e a Tecnologia | Ref. PTDC/MAR-EST/2098/2014

Published
2017
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11. Stakeholders' conceptualization of offshore aquaculture and small-scale fisheries interactions using a Bayesian approach

Author

Miguel Caetano, Jorge Ramos, Amber Himes-Cornell, Miguel N. Santos, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Universidade do Algarve (UAlg), Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), International Commission for the Conservation of Atlantic Tunas (ICCAT), ICCAT, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Artificial reefs, Economic-analysis, Fishing, 010501 environmental sciences, Management, Monitoring, Policy and Law, Aquatic Science, Oceanography, 01 natural sciences, Livelihood, Stakeholders, Aquaculture, Influence diagram, 14. Life underwater, Expected utility hypothesis, 0105 earth and related environmental sciences, Resource-management, Belief networks, River, Small-scale fisheries, Southern Portugal, Offshore aquaculture, Sea, business.industry, 010604 marine biology & hydrobiology, Natural-resource, Environmental resource management, Bayesian approach, Bayesian network, Fish, Scale (social sciences), [SDE]Environmental Sciences, Navigability, business
Abstract

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

Published
2017
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12. Image Analysis as a Tool to Age Estimations in Fishes: An Approach Using Blue Whiting on ImageJ

Author

Vitor Vaz da Silva, Patrícia Gonçalves, António Ávila de Melo, Alberto G. Murta, Henrique N. Cabral, Repositório da Universidade de Lisboa, Faculty of Sciences of the University of Lisbon (OI-FCUL), Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Department of Electronics, Telecommunications and Computers Engineering [ISEL, Lisbon], Instituto Superior de Engenharia de Lisboa (ISEL), Centre of Technology and Systems (CTS), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Luis M. Camarinha-Matos, Mafalda Parreira-Rocha, Javaneh Ramezani, TC 5, and WG 5.5

Subjects
0106 biological sciences, Stock assessment, 010603 evolutionary biology, 01 natural sciences, Image analysis, Image processing, Abundance (ecology), Statistics, medicine, [INFO]Computer Science [cs], 14. Life underwater, Mathematics, Otolith, Fisheries science, biology, Blue whiting and fisheries science, 010604 marine biology & hydrobiology, Effective management, Blue whiting, biology.organism_classification, Slow growth, Otoliths, Oceanography, medicine.anatomical_structure, Age estimation, Fish ageing
Abstract

Part 5: Smart Sensorial Systems; International audience; Otoliths are the fish bones that allow it to hear sounds and achieve balance. The otolith grows in size as fish grows; ring bands are formed in the otoliths’ surface registering periods of rapid and slow growth, opaque bands appear alternating with translucent bands. Age classification was made considering the number of translucent rings in the otolith; one translucent ring was equivalent to one year. The modeling of fish species abundance on the majority of fisheries assessment use age based models. The task of ring counting and ageing is time consuming and may introduce errors that can have a strong impact in stock assessment results. Thus, accurate and precise age estimates are crucial for the effective management and understanding of fisheries resources because recruitment dynamics, growth and mortality estimates relies on these data. The main goal of this study is to produce automatic reading procedures to help researchers, ageing blue whiting fish, minimize ring error count and improve accuracy and precision on age estimation.

Published
2017
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13. Asynchrony in settlement time between the closely related oysters Crassostrea angulata and C. gigas in Ria Formosa lagoon (Portugal)

Author

Francisco Ruano, Pierre Boudry, Vera G. Fonseca, Frederico M. Batista, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], Zoologisches Forschungsmuseum Alexander Koenig, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)

Subjects
0106 biological sciences, 0301 basic medicine, Oyster, animal structures, MICROSATELLITE, INVASION, Hybrids, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, MITOCHONDRIAL, CLASSIFICATION, Gene flow, 03 medical and health sciences, Invasion, HYBRIDS, biology.animal, SEQUENCE VARIATION, Seasonal breeder, Pacific oyster, 14. Life underwater, Hybridization, PACIFIC OYSTER, Ecology, Evolution, Behavior and Systematics, Larva, Sequence variation, Ecology, biology, ACL, Populations, fungi, Microsatellite, biology.organism_classification, Classification, Mitochondrial, 030104 developmental biology, Taxon, DIFFERENTIATION, Differentiation, Crassostrea, POPULATIONS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, HYBRIDIZATION, Portuguese oyster
Abstract

The Portuguese oyster Crassostrea angulata and the Pacific oyster Crassostrea gigas are very closely related species originating from Asia that were introduced in Europe. The objectives of the present study were to determine if there is asynchrony in settlement time of C. angulata and C. gigas larvae in an area where both taxa coexist and if hybridization between the two species occurs throughout the breeding season. Oyster collectors were deployed every two weeks during one year in two different sites in Ria Formosa lagoon (Portugal) and the oysters that settled were genotyped with nuclear and mitochondrial markers. Settlement of Crassostrea sp. was observed from April to November 2004 (n = 694), with two distinct periods. In the first period (April), when 19% of the oysters settled, the haplotypes and alleles characteristic of C. gigas were mainly observed. In the following settlement period (July to November), the frequency of haplotypes and alleles of C. gigas decreased over time while those characteristics of C. angulata reached high frequencies by the end of the settlement period. Our results suggest that C. gigas was able to reproduce at lower temperatures than C. angulata in spring. However, the non-significant allelic disequilibrium observed during almost all settlement periods suggests that hybridization is widespread in time. The results obtained in the present study show that there are differences in the reproductive behavior between C. angulata and C. gigas that may limit gene flow between the two species. Fundacao para a Ciencia e a Tecnologia (FCT) [SFRH/BD/8972/2002] info:eu-repo/semantics/publishedVersion

Published
2017
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14. Investigating stock structure and trophic relationships among island-associated dolphins in the oceanic waters of the North Atlantic using fatty acid and stable isotope analyses

Author

Jeremy J. Kiszka, Irma Cascão, Sophie Quérouil, Ana Dinis, Luís Freitas, Ricardo S. Santos, Filipe Alves, Ana Rita Cordeiro, Narcisa M. Bandarra, Instituto do Mar & Department of Oceanography and Fisheries - University of the Azores (IMAR-DOP), IMAR, Caractérisation et valorisation de la diversité ichtyologique pour une aquaculture raisonnée (CAVIAR), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences [Miami], Florida International University [Miami] (FIU), Museau de Baleia da Madeira, museu da Baleia, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), University of the Azores, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, MADEIRA, Common dolphin, Population, Delphinus delphis, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, biology.animal, Blubber, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, Apex predator, Trophic level, Ecological niche, education.field_of_study, Ecology, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 010604 marine biology & hydrobiology, ACORES, biology.organism_classification, Stenella, ATLANTIQUE ILES, OCEAN ATLANTIQUE
Abstract

International audience; Short-beaked common dolphins (Delphinus delphis) and Atlantic spotted dolphins (Stenella frontalis) are the two most abundant cetacean species in the oceanic waters of Madeira and the Azores. They are of similar size, occur in similar habitats and are regularly observed in mixed-species groups to forage together. Genetic analyses suggested that, within each species, dolphins ranging around both archipelagos belong to the same panmictic population. We tested the hypotheses that (1) within each species, individuals from the two archipelagos belong to a single ecological stock; (2) between species, common and spotted dolphins have distinct trophic niches; using fatty acid (FA) and stable isotope (SI) analyses. Fatty acids and stable isotopes were analysed from 86 blubber and 150 skin samples of free-ranging dolphins, respectively. Sex-related differences were not significant, except for common dolphin FA profiles. In S. frontalis, FA and SI differences between archipelagos suggested that individuals belonged to different ecological stocks, despite the existence of gene flow between the two archipelagos. In D. delphis, differences were more pronounced, but it was not possible to distinguish between stock structure and a seasonal effect, due to differential sampling periods in the Azores and Madeira. Inter-specific comparisons were restricted to the Azores where all samples were collected during summer. Differences in FA proportions, noticeably for FA of dietary origin, as well as in nitrogen SI profiles, confirmed that both species feed on distinct resources. This study emphasizes the need for an integrated approach including both genetic and biochemical analyses for stock assessment, especially in wide-ranging marine top predators.

Published
2013
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15. The Ocean Sampling Day Consortium

Author

Oleksandra Bobrova, Petra ten Hoopen, Rodrigo Costa, Rania Siam, Rehab Z. Abdallah, Jorge A. Herrera Silveira, Catarina Magalhães, Nedime Serakinci, Marie E. DeLorenzo, Riccardo Rosselli, Paul Malthouse, Lise Øvreås, Eyjólfur Reynisson, Susan Gebbels, Francesca Malfatti, Frank Oliver Glöckner, Federico M. Lauro, Hans Erik Karlsen, David Wallom, Christian Jeanthon, Mark J. Costello, Fergal O'Gara, Nadezhda Todorova, Ana C. Costa, Monia El Bour, Paul D. van Ruth, Ivaylo Kostadinov, Martin Ostrowski, Jed A. Fuhrman, Viggo Marteinsson, Thierry Cariou, Hiroyuki Ogata, Maria Luiza Pedrotti, Emilie Villar, Federico Baltar, Sandi Orlić, Valentina Turk, Katja Lehmann, Dawn Field, Renzo Kottmann, Florence Jude-Lemeilleur, Daniel Vaulot, Alessandro Vezzi, Neil M Davies, Mahrous M. Kandil, Véronique Berteaux-Lecellier, Christopher D. Sinigalliano, Timothy W. Davis, Peter N. Golyshin, Stéphane L'Haridon, Jonathan A. Martinez, Sandra Ramos, Pascal Conan, Ma. Leopoldina Aguirre-Macedo, Antonio Fernandez-Guerra, Soumya Essayeh, Clara Loureiro, Edvardsen Bente, Noureddine Boukhatem, Rachelle M. Jensen, Sophie Pitois, Bouchra Chaouni, Kate Munnik, Anke Kremp, Stephane Pesant, Roberto Danovaro, Cecilia Alonso, Said Barrijal, Jodie van de Kamp, Michail M. Yakimov, Nicole J. Poulton, Zackary I. Johnson, Adriana Zingone, Bernardo Duarte, Ilkay Salihoglu, Paraskevi N. Polymenakou, Jack A. Gilbert, Melody S. Clark, Ian Salter, Hassan Ghazal, Julie LaRoche, J. Mortelmans, Ranjith Edirisinghe, Grazia Marina Quero, Dion Matthew Frederick Frampton, Isabel Caçador, Georgios Tsiamis, Declan C. Schroeder, Jamie Hinks, Ana Martins, Noga Stambler, Rachel Collin, João Canning-Clode, Tinkara Tinta, Mesude Bicak, Scott Jones, Valentina Amaral, Matthias S. Ullrich, Gunnar Gerdts, Klaas Deneudt, Michael Steinke, Mohamed Bennani, Rafael Santana, Fabio De Pascale, Jennifer Tolman, Juan Iriberri, Levente Bodrossy, Abderrahim Bouali, Antonella Penna, Bruno Cataletto, Josep M. Gasol, Florencia Biancalana, Maribeth L. Gidley, Stephen A. Jackson, Mahmut Cerkez Ergoren, Carolin R. Löscher, Antje Wichels, Ventzislav Karamfilov, R. Eric Collins, Sara Ettamimi, Riccardo Schiavon, Mohammed Timinouni, Christina Bienhold, Julia Schnetzer, Marc E. Frischer, Wayne J. Fuller, Simon Claus, Ibon Cancio, Guy Cochrane, Patrick Martin, Gian Marco Luna, Snejana Moncheva, Linda A. Amaral-Zettler, Eva C. Sonnenschein, Paul Anders Fronth Nyhus, Shiao Y. Wang, Antonina Dos Santos, Eyal Rahav, Eileen Bresnan, Anna Kopf, Barker Katherine, Michèle Barbier, Naiara Rodríguez-Ezpeleta, Kemal Can Bizsel, Tim Ingleton, Patricia Wecker, Julia A. Busch, Kelly D. Goodwin, El Houcine Zaid, Rajaa Chahboune, Takashi Yoshida, Fatima El Otmani, Marianna Mea, Nina Dzhembekova, Anne-Lise Ducluzeau, Christopher P. Meyer, Georgios Kotoulas, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Jacobs University [Bremen], University of Oxford, Centre for Ecology & Hydrology, Oxfordshire UK, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Israel Oceanographic and Limnological Research (IOLR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Hellenic Centre for Marine Research (HCMR), American University in Cairo, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Institut Ruder Boskovic, Institut Ruđer Bošković (IRB), University of Essex, Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Universidade de Lisboa = University of Lisbon (ULISBOA), Smithonian Environmental Research Center, Research Center, Odessa National I.I.Mechnikov University, Matis Ltd, Universidade dos Açores, Istituto di Science Marine (ISMAR ), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Finnish Environment Institute (SYKE), National Oceanic and Atmospheric Administration (NOAA), University of Bergen (UiB), Dalhousie University [Halifax], Università di Urbino, Skidaway Institute of Oceanography, Smithsonian Institution, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mississippi State University [Mississippi], Bigelow Laboratory for Ocean Sciences, Smithsonian Marine Station, Smithsonian Tropical Research Institute, University of Southern California (USC), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Universidad de la República [Montevideo] (UDELAR), Bar-Ilan University [Israël], The Interuniversity Institute for marine Science in Eilat, IAMC-CNR, Istituto per l'Ambiente Marino Costiero &ndash, University of Otago [Dunedin, Nouvelle-Zélande], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Macquarie University, South Australian Research and Development Institute (SARDI), South Australian Research and Development Institute, Flanders Marine Institute, VLIZ, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), University of Algarve [Portugal], Marine Biological Association of the UK, Department of Chemistry, Alexandria University [Alexandrie], Argentine Institute of Oceanography, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of Tasmania [Hobart, Australia] (UTAS), Waters, wetlands & coasts Sydney, Lwande technologies Cape Town, AZTI (AZTI), AZTI, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Université Mohammed Premier [Oujda], Université Mohammed V de Rabat [Agdal] (UM5), Université Sidi Mohamed Ben Abdellah (USMBA), Université Abdelmalek Essaâdi (UAE), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), Faculty of Sciences, Rabat, Morocco., Bulgarian Academy of Sciences (BAS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Université de Brest (UBO), Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Università degli Studi di Padova = University of Padua (Unipd), Singapore centre for environmental life sciences engineering, Nanyang Technological University [Singapour], Indigo V Expeditions, Newcastle University [Newcastle], Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universität Bremen, Istituto Nazionale di Geofisica e di Oceanografia Sperimentale (OGS), Rajarata University of Sri-Lanka (RUSL), University of Southern Mississippi (USM), Mediterranean Science Commission, National institute of biology Fornace, Near East University, Marine Scotland Marine Laboratory, Kind of Blue Project ABS, University of Oslo (UiO), Marine biology research station, Bangor University, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Fridtjof Nansen Institute of oceanology, Duke University [Durham], Miami University, Miami University [Ohio] (MU), Stazione Zoologica Anton Dohrn (SZN), Polytechnic University of Marche, University of Patras, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), INSTIM, University of Alaska [Fairbanks] (UAF), University of Hawaii, University of Auckland [Auckland], Marine Biological Laboratory (MBL), University of Chicago, Brown University, Zhejiang University, Argonne National Laboratory [Lemont] (ANL), Department of Mathematics [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Repositório da Universidade de Lisboa, Kopf, A, Bicak, M, Kottmann, R, Schnetzer, J, Kostadinov, I, Lehmann, K, Fernandez-Guerra, A, Jeanthon, C, Rahav, E, Ullrich, M, Wichels, A, Gerdts, G, Polymenakou, P, Kotoulas, G, Siam, R, Abdallah, Rz, Sonnenschein, Ec, Cariou, T, O'Gara, F, Jackson, S, Orlic, S, Steinke, M, Busch, J, Duarte, B, Cacador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, Cm, Luna, Gm, Quero, Gm, Loscher, Cr, Kremp, A, Delorenzo, Me, Ovreas, L, Tolman, J, Laroche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, Cp, Ramos, S, Magalhaes, C, Jude-Lemeilleur, F, Aguirre-Macedo, Ml, Wang, S, Poulton, N, Jones, S, Collin, R, Fuhrman, Ja, Conan, P, Alonso, C, Stambler, N, Goodwin, K, Yakimov, Mm, Baltar, F, Bodrossy, L, Van De Kamp, J, Frampton, Dmf, Ostrowski, M, Van Ruth, P, Malthouse, P, Claus, S, Deneudt, K, Mortelmans, J, Pitois, S, Wallom, D, Salter, I, Costa, R, Schroeder, Dc, Kandil, Mm, Amaral, V, Biancalana, F, Santana, R, Pedrotti, Ml, Yoshida, T, Ogata, H, Ingleton, T, Munnik, K, Rodriguez-Ezpeleta, N, Berteaux-Lecellier, V, Wecker, P, Cancio, I, Vaulot, D, Bienhold, C, Ghazal, H, Chaouni, B, Essayeh, S, Ettamimi, S, Zaid, E, Boukhatem, N, Bouali, A, Chahboune, R, Barrijal, S, Timinouni, M, El Otmani, F, Bennani, M, Mea, M, Todorova, N, Karamfilov, V, ten Hoopen, P, Cochrane, G, L'Haridon, S, Bizsel, Kc, Vezzi, A, Lauro, Fm, Martin, P, Jensen, Rm, Hinks, J, Gebbels, S, Rosselli, R, De Pascale, F, Schiavon, R, dos Santos, A, Villar, E, Pesant, S, Cataletto, B, Malfatti, F, Edirisinghe, R, Silveira, Jah, Barbier, M, Turk, V, Tinta, T, Fuller, Wj, Salihoglu, I, Serakinci, N, Ergoren, Mc, Bresnan, E, Iriberri, J, Nyhus, Paf, Bente, E, Karlsen, He, Golyshin, Pn, Gasol, Jm, Moncheva, S, Dzhembekova, N, Johnson, Z, Sinigalliano, Cd, Gidley, Ml, Zingone, A, Danovaro, R, Tsiamis, G, Clark, M, Costa, Ac, El Bour, M, Martins, Am, Collins, Re, Ducluzeau, Al, Martinez, J, Costello, Mj, Amaral-Zettler, La, Gilbert, Ja, Davies, N, Field, D, Glockner, Fo, European Commission, University of Oxford [Oxford], Israel Oceanographic and Limnological Research - IOLR (ISRAEL), Danmarks Tekniske Universitet (DTU), Carl Von Ossietzky Universität Oldenburg, Universidade de Lisboa (ULISBOA), Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Universidad de la República [Montevideo] (UCUR), Kyoto University [Kyoto], Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), University of Mohammed V, Sidi Mohammed Ben Abdellah University, Universita degli Studi di Padova, Rajarata University of Sri-Lanka, University of Patras [Patras], University of California [Berkeley], and University of California-University of California

Subjects
0106 biological sciences, Biodiversity, Marine life, 01 natural sciences, Bacteria, Genomics, Health Index, Marine, Metagenomics, Micro B3, Microorganism, OSD, Ocean sampling day, Standards, 11. Sustainability, Data and Information, Ocean Sampling Day, biodiversity, genomics, health index, bacteria, microorganism, metagenomics, marine, standards, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, Environmental resource management, Geology, Computer Science Applications, Interdisciplinary Natural Sciences, Microbial biodiversity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ocean sampling day, OSD, Biodiversity, Genomics, Health Index, Bacteria, Microorganism, Metagenomics,Marine, Micro B3, Standards, Oceans and Seas, Microorganisms, Marine Biology, Health Informatics, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Ecology and Environment, Metagenomic, 03 medical and health sciences, Health index, Medisinske Fag: 700 [VDP], SDG 14 - Life Below Water, 14. Life underwater, 030304 developmental biology, business.industry, 010604 marine biology & hydrobiology, Ocean sampling, 13. Climate action, Commentary, Genomic, Database Management Systems, Global Ocean, business
Abstract

Kopf, Anna ... et. al.-- 5 pages, 1 figure.-- This manuscript is NOAA-GLERL contribution number 1763, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits, This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589

Published
2015
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16. Technical mitigation measures for sharks and rays in fisheries for tuna and tuna-like species: turning possibility into reality

Author

Maria Korta, Hilario Murua, Miguel N. Santos, Jim R. Ellis, Pierre Chavance, Rui Coelho, Bach Pascal, Javier Ariz, Bernard Séret, Francois Poisson, Francisco Abascal Crespo, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre for Environment, Fisheries and Aquaculture Science [Lowestoft] (CEFAS), Institut de Recherche pour le Développement (IRD), International Commission for the Conservation of Atlantic Tunas (ICCAT), ICCAT, Instituto Português de Investigação do Mar e da Atmosfera (IPMA), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Mitigation, [SDE.MCG]Environmental Sciences/Global Changes, Aquatic Science, Biology, bycatch, 010603 evolutionary biology, 01 natural sciences, Recreational fishing, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Centro Oceanográfico de Canarias, Pesquerías, 14. Life underwater, marine mammals, Recreation, fish, tuna regional fishery management organizations, 010604 marine biology & hydrobiology, tuna fisheries, Pelagic zone, pelagic, mortality, Great barrier reef, sustainable fishing, Bycatch, Fishery, Current management, Fisheries management, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna, elasmobranch, exploitation
Abstract

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

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