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- Population genetics of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans: implications for conservationPublication . Morales, Millke Jasmine Arminini; Mendonça, Fernando Fernandes; Magalhães, Carolina Oliveira; Oliveira, Claudio; Coelho, Rui; Santos, Miguel Neves; Cruz, Vanessa Paes; Piercy, Andrew; Burgess, George; Hazin, Fabio Vieira; Foresti, FaustoPopulation structure and genetic connectivity are pivotal contributions to the establishment of conservation strategies for fisheries management, in particular for highly migratory species that are affected by commercial fisheries. This study used partial sequences of mitochondrial DNA control region to determine the genetic structure of the bigeye thresher shark Alopias superciliosus in the Atlantic and Indian Oceans. A total of 858 base pairs of mtDNA CR from 228 individuals were analyzed. The resulting nucleotide diversity (π) was 0.0011 ± 0.0008 and the haplotype diversity (h) was 0.127 ± 0.030. These are the lowest diversities registered in elasmobranchs with this genetic marker. Two genetically distinct lineages were identified, one of them represented by 3.9% of the analyzed individuals and none restricted to any particular area. Simulated scenarios of population structure, tested with AMOVA and pairwise ΦST did not result in significant values indicating high connectivity among all sampled groups. The absence of population structure, even between Atlantic and Indian Oceans, corroborates the high dispersal ability of this species. The low genetic diversity detected in this species and the identification of two historical lineages occurring in sympatry, one represented by a very small number of individuals, should be considered in the conservation efforts and management plans of A. superciliosus.
- Reproductive aspects of the undulate ray, Raja undulata, from the south coast of PortugalPublication . Coelho, Rui; Erzini, KarimThe maturity of the undulate ray, Raja undulata, one of the most important by-catch elasmobranch species captured in south Portugal, was studied for the first time. Females ranged in total length (TL) from 19.4 to 88.2 cm and males from 23.0 to 83.2 cm. The gonadosomatic index for females was higher during the winter, meaning that this species reproduces during this season. Females matured at significantly larger sizes and older ages than males, with 50% of the females mature at 76.2 cm TL at an age of 8.98 years while 50% maturity for males was achieved at 73.6 cm TL and 7.66 years. Females were mature at 86.3% of the maximum observed size and 69.1% of the maximum observed age while males matured at 88.5% of the maximum observed size and 63.8% of the maximum observed age, making this a very late maturing species, with important consequences in terms of fisheries management and conservation. (c) 2006 Elsevier B.V. All rights reserved.
- Catches in ghost-fishing octopus and fish traps in the northeastern Atlantic Ocean (Algarve, Portugal)Publication . Erzini, Karim; Bentes, L.; Coelho, Rui; Lino, P. G.; Monteiro, P.; Ribeiro, J.; Gonçalves, J. M. S.Ghost fishing is the term used to describe the continued capture of fish and other living organisms after a fisherman has lost all control over the gear. Traps may be lost for a variety of reasons including theft, vandalism, abandonment, interactions with other gear, fouling on the bottom (i.e., traps and ropes are caught on rocky substrate), bad weather, and human error (Laist, 1995). Annual trap loss can be as high as 20% to 50% of fished traps in some fisheries (Al-Masroori et al., 2004). Because lost traps can continue to fish for long periods, albeit with decreasing efficiency over time (e.g., Smolowitz, 1978; Breen, 1987, 1990; Guillory, 1993), ghost fishing is a concern in fisheries worldwide.
- Soft-bottom fishes and spatial protection: findings from a temperate marine protected areaPublication . Sousa, Inês; Gonçalves, Jorge Manuel Santos; Claudet, Joachim; Coelho, Rui; Gonçalves, Emanuel J.; Erzini, KarimNumerous studies over the last decades have focused on marine protected areas (MPAs) and their effects on fish communities. However, there is a knowledge gap regarding how species that live associated with soft-substrates (e.g., sand, mud) respond to spatial protection. We analyzed abundance, biomass and total lengths of the soft-bottom fishes in a multiple-use MPA in the north-eastern Atlantic, the Luiz Saldanha Marine Park (Portugal), during and after the implementation of its management plan. Data were collected by experimental fishing in areas with three different levels of protection, during the implementation period and for three years after full implementation of the MPA. Univariate analysis detected significant biomass increases between the two periods. Fish assemblages were mainly structured by depth and substrate, followed by protection level. Community composition analyses revealed significant differences between protection levels and between the two periods. Species exhibited a broad variation in their response to protection, and we hypothesize that factors such as species habitat preferences, body size and late maturity might be underlying determinants. Overall, this study provides some evidence of protection effectiveness in soft-bottom fish communities, supported by the significant increase in biomass in the protected areas and the positive trends of some species.
- Feeding ecology of the deep-sea lanternshark Etmopterus pusillus (Elasmobranchii: Etmopteridae) in the northeast AtlanticPublication . Xavier, José C.; Vieira, Cátia; Assis, Carlos; Cherel, Yves; Hill, Simeon; Costa, Esmeralda; Borges, Teresa C.; Coelho, RuiThis study provides the first description of the feeding ecology of the smooth lanternshark Etmopterus pusillus based on stomach contents of specimens caught as bycatch in the Algarve (southern Portugal) with bottom trawling and bottom longline. The diet of E. pusillus consists mainly of fish (dry weight (% W)=87.1%; frequency of occurrence (%FO)=28.6%; number (%N)=30.3%), crustaceans (%W=7.7%; %FO=36.7%; %N=3.4%) and cephalopods (%W=4.7%; %FO=11.3%; %N=11.1%). The diet did not vary between sexes. Ontogenic changes were detected: crustaceans decreased in importance as the sharks increased in size and fish became dominant in the diet of adults. Combining two fishing methods provided broad information on the diet of E. pusillus, as bottom trawling caught smaller specimens and longlines caught larger individuals. E. pusillus feeds mainly on non-commercial species, and therefore does not compete directly with commercial fisheries. Finally, E. pusillus feeds in various parts of the water column and thus it can access a wide range of prey; however, this also means that it can be caught by both gears, making it more vulnerable in terms of conservation.
- Towards mitigation of seabird bycatch: Large-scale effectiveness of night setting and Tori lines across multiple pelagic longline fleetsPublication . Jiménez, Sebastián; Domingo, Andrés; Winker, Henning; Parker, Denham; Gianuca, Dimas; Neves, Tatiana; Coelho, Rui; Kerwath, SvenBycatch in pelagic longline fleets remains a considerable source of mortality for threatened seabirds. Despite efforts to implement mitigation measures, the effectiveness of their application across multiple fleets and wide spatio-temporal scales remains poorly understood. We analyse about 15,800 sets and 36.4 million hooks observed during 583 trips aboard 132 vessels from five pelagic longline fleets (Brazil, Portugal, South Africa, Uruguay and foreign charter-vessels) operating in the south Atlantic and southwestern Indian Oceans (2002–2016) to assess the large-scale effect on bycatch rates of the implementation over time of night-setting and Tori (bird-scaring or streamer) lines. There was a highly significant decrease in standardised bycatch rate from 2002 to 2008 to 2009–2011 and a further reduction in 2012–2016, as consequence of an increased use of mitigation measures. This reduction on fleet-wide bycatch rates temporally coincides with the progressive implementation of mitigation measures in the two relevant Regional Fishery Management Organisations. Night-setting significantly reduced bycatch rates under all conditions, particularly for albatrosses. Surprisingly, bycatch rate during daylight was higher when Tori lines were deployed. Inconsistencies in Tori line deployments, entanglements with the fishing gear and the non-use of this measure with low seabird abundance may explain this pattern. At night, relative moon illumination increased bycatch rate, especially of petrels, but Tori lines significantly reduced seabird bycatch. Our results imply that a major reduction in global bycatch of threatened seabirds could be achieved, if night setting and Tori lines are correctly applied and extensively implemented by fleets operating south of 25°S.
- Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus)Publication . Domingues, Rodrigo R.; Mastrochirico-Filho, Vito Antonio; Mendes, Natalia J.; Hashimoto, Diogo T.; Coelho, Rui; da Cruz, Vanessa Paes; Antunes, Agostinho; Foresti, Fausto; Mendonca, Fernando F.The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark found worldwide in tropical and subtropical waters. However, the understanding of its biology at molecular level is still incipient. We sequenced the messenger RNA isolated from eye and liver tissues. De novo transcriptome yielded a total of 705,940 transcripts. A total of 3774 genes were differentially expressed (DEGs), with 1612 in the eye and 2162 in the liver. Most DEGs in the eye were related to structural and signaling functions, including nonocular and ocular opsin genes, whereas nine out of ten most overexpressed genes in the liver were related to tumor suppression, wound healing, and human diseases. Furthermore, DEGs findings provide insights on the monochromatic shark vision and a repertory of cancer-related genes, which may be insightful to elucidate shark resistance to cancer. Therefore, our results provide valuable sequence resources for future functional and population studies.
- Monitoring of hazardous substances at Alcantarilha’s WTP, PortugalPublication . Rosa, Maria João; Cecilio, T.; Ribau Teixeira, Margarida; Viriato, M.; Coelho, R.; Lucas, HelenaA monitoring programme of hazardous substances was implemented in Alcantarilha’s water treatment plant (Algarve, Portugal) since 2002, in addition to the legally established monitoring of standard physical, chemical and microbiological parameters. The objective of this programme was to ensure the drinking water quality regarding the waterborne disease organisms Cryptosporidium, Giardia, Salmonella, Pseudomonas aeruginosa, enterovirus and cyanobacteria, and the potentially harmful chemicals aluminium, cyanotoxins, and disinfection by-products (THM) and their precursors (TOC, DOC, UV254nm, SUVA). Most of these parameters are new and still not regulated by the Portuguese and the European legislation. Data presented in this study refer to the period of August 2002 to October 2003. Results show that, despite the seasonal variations of the raw water quality, concentrations of the hazardous substances in the supplied drinking water were far below the legal standards and the WHO’s and EPA guideline values, demonstrating the high removal efficiencies of this treatment plant.
- Characterization and standardization of Atlantic sailfish (Istiophorus albicans) catch rates in the east Atlantic from the Portuguese pelagic longline fisheryPublication . Coelho, Rui; Lino, Pedro; Santos, MiguelThis document analyzes the catch, effort and standardized CPUE trends for the eastern Atlantic stock of Atlantic sailfish (Istiophorus albicans) captured by the Portuguese pelagic longline fleet from 1999-2015. Nominal annual CPUE were calculated as kg/1000 hooks and were standardized with Generalized Linear Models (GLM) with Tweedie distribution and using year, quarter, area and targeting effects (ratios) as explanatory variables. Model goodness-of-fit was determined with AIC and the pseudo coefficient of determination, and model validation was analyzed with residual analysis. The final standardized CPUE series shows a general decrease in the initial years, between 1999 and 2010, followed by a general increase in the more recent years, until 2015, with some inter-annual oscillations. This paper presents the first index of abundance for Atlantic sailfish estimated from captures from the Portuguese pelagic longline fleet in the east Atlantic and can be used for future stock assessments of the species
- Updates on habitat use and migrations patterns for shortfin mako in the Atlantic using satellite telemetryPublication . Casaca Santos, Catarina; Domingo, Andrés; Carlson, John; Natanson, Lisa; Travassos, Paulo; Macias, David; Cortés, Enric; Miller, Philip; Hazin, Fábio H. V.; Mas, Federico; Ortiz de Urbina, Josetxu; Coelho, RuiThis paper provides an update of the study on habitat use for shortfin mako, developed within the ICCAT Shark Research and Data Collection Program (SRDCP). A total of 43 tags (29 miniPATs and 14 sPATs) have been deployed by observers on Portuguese, Uruguayan, Brazilian, Spanish and US vessels in the temperate NE and NW, Equatorial and SW Atlantic. Data from 41 tags/specimens are available, and a total of 1656 tracking days have been recorded. Results showed shortfin mako moved in multiple directions, travelling considerable distances. Shortfin mako sharks spent most of their time above the thermocline (0-90 m), between 18 and 22 °C. The main plan for the next phase of the project is to continue the tag deployment during 2019 in several regions of the Atlantic.