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- A review of reported effects of pelagic longline fishing gear configurations on target, bycatch and vulnerable speciesPublication . Casaca Santos, Catarina; Rosa, Daniela; Gonçalves, Jorge Manuel Santos; Coelho, Rui1. A meta-analysis of 40 publications totalling 59 experiments was undertaken to review and assess the effects of changing the hook (circle vs. J-hooks or tuna hooks), bait (fish vs. squid) and leader (wire vs. nylon) type on retention and at haulback mortality rates of teleosts (tunas and billfishes), elasmobranchs and sea turtles caught on shallow-set and deep-set pelagic longline fisheries. 2. Circle hooks are a promising approach to mitigate the impact of pelagic longline fisheries on sea turtles, as they reduced sea turtle retention rates. The adoption of circle hooks would, however, also lead to a decrease in swordfish retention, the main target species of shallow-set pelagic longlines. 3. Using fish as bait resulted in lower retention rates of sea turtles, highlighting that option as an additional measure to further mitigate sea turtle bycatch. The bait type had non-significant effects on sharks, except for blue shark and shortfin mako, for which at-haulback mortality rates were significantly higher with fish bait. 4. The use of nylon leaders instead of wire leaders could serve as a conservation measure for sharks, as they reduced the retention of blue shark without adversely impacting the catches of swordfish. The results on the effect of the leader material types should, however, be interpreted with caution owing to the limited information available reporting on leader material effects. 5. When considering future research directions, priority should be given to experimental field work on the effects of leader material and on deep-set longlines. Evaluating the post-release survival of species should also be a priority.
- Shark Research and Data Collection Program: progress on the age and growth of the shortfin mako in the Atlantic OceanPublication . Coelho, Rui; Carlson, John; Natanson, Lisa; Rosa, Daniela; Mas, Federico; Mathers, Alyssa; Domingo, Andrés; Santos, Miguel N.This paper presents an update of the age and growth study within the ICCAT Shark Research and Data Collection Program (SRDCP), including the current development status and plans for the 2nd phase of the project. There are currently 469 vertebrae samples (205 females, 257 males and 7 specimens with unidentified sex) collected and processed from both the North and Southern hemispheres. The sample distribution is much more complete in the north, while in the south at this stage there are only samples from the equatorial region. The size range of the samples varies from 52 cm to 366 cm FL. The next steps of this projects is proposing a workshop on age reading and growth in order to prepare a reference set of vertebrae that can be used as a guideline for the readings of the remaining sample, and also discuss aspects of age validation and band deposition periodicity. The final results will be presented to the SCRS sharks working group in 2017, in order to contribute to the 2017 shortfin mako stock assessment.
- Progress on a meta-analysis for comparing hook, bait and leader effects on target, bycatch and vulnerable fauna interactionsPublication . Casaca Santos, Catarina; Rosa, Daniela; Coelho, RuiThis paper describes the progress of an EU Project "Evaluation of the effects of hooks’ shape & size on the catchability, yields and mortality of target and by-catch species, in the Atlantic Ocean and adjacent seas surface longline fisheries". At this stage, a meta-analysis of 36 publications totaling 55 experiments was conducted to assess effects of hook, bait, and leader type on retention and at-haulback mortality rates of swordfish, blue shark, and loggerhead sea-turtle. Using circle hooks significantly lowers retention rates of loggerhead sea-turtles and swordfish. Fish bait significantly reduces the retention of loggerhead sea-turtles but does not significantly affect the retention of swordfish or blue shark. The effects of using wire leaders could not be assessed for the loggerhead turtle and significantly increased retention of blue sharks. As for at-haulback mortality, it was significantly reduced for swordfish when using circle hooks. Fish bait increased at-haulback mortality of blue shark and was not significant for the other taxa. The effects of using wire leaders on at-haulback mortality were only possible to calculate for blue shark and were not significant.
- Seascape genomics and phylogeography of the sailfish (Istiophorus platypterus)Publication . Ferrette, Bruno Lopes da Silva; Coimbra, Raphael T F; Winter, Sven; De Jong, Menno J; Williams, Samuel Mackey; Coelho, Rui; Rosa, Daniela; Rotundo, Matheus Marcos; Arocha, Freddy; Mourato, Bruno Leite; Mendonça, Fernando Fernandes; Janke, AxelPermeable phylogeographic barriers characterize the vast open ocean, boosting gene flow and counteracting population differentiation and speciation of widely distributed and migratory species. However, many widely distributed species consists of distinct populations throughout their distribution, evidencing that our understanding of how the marine environment triggers population and species divergence are insufficient. The sailfish is a circumtropical and highly migratory billfish that inhabits warm and productive areas. Despite its ecological and socioeconomic importance as a predator and fishery resource, the species is threatened by overfishing, requiring innovative approaches to improve their management and conservation status. Thus, we presented a novel high-quality reference genome for the species and applied a seascape genomics approach to understand how marine environmental features may promote local adaptation and how it affects gene flow between populations. We delimit two populations between the Atlantic and Indo-Western Pacific oceans and detect outlier loci correlated with sea surface temperature, salinity, oxygen, and chlorophyll concentrations. However, the most significant explanatory factor that explains the differences between populations was isolation by distance. Despite recent population drops, the sailfish populations are not inbred. For billfishes in general, genome-wide heterozygosity was found to be relatively low compared to other marine fishes, evidencing the need to counteract overfishing effects. In addition, in a climate change scenario, management agencies must implement state-of-the-art sequencing methods, consider our findings in their management plans, and monitor genome-wide heterozygosity over time to improve sustainable fisheries and the long-term viability of its populations.
- Shark Research and Data Collection Program: progress on the satellite tagging of shortfin mako for post-release survival and habitat use studiesPublication . Coelho, Rui; Domingo, Andrés; Carlson, John; Cortés, Enric; Rosa, Daniela; ller, Philip; Santos, Miguel N.This paper provides an update of two projects developed within the ICCAT Shark Research and Data Collection Program (SRDCP) using satellite telemetry, specifically a study on habitat use and other on post-release survival. At the time of this paper, 10 tags (6 miniPATs and 4 sPAT) had been deployed from observers on Portuguese fishing vessels in the temperate NE Atlantic. The remaining tags are being deployed by USA in the temperate NW and Uruguay in the SW. The preliminary analysis shows that specimens tagged in the temperate NE moved to southern areas, while specimens tagged in the tropical NE close to the Cabo Verde archipelago moved easterly to the African continent. Three tags were deployed in equatorial waters and one moved to the NE while the other moved SE. In terms of post-release survivorship, 2 specimens tagged with sPATs survived and 2 died. For the 2nd year of the project we will acquire additional miniPATs to be deployed preferably in equatorial waters, in the mixing zone for the stocks.
- Standardized CPUE and size distribution of the shortfin mako shark in the portuguese pelagic longline fishery in the AtlanticPublication . Coelho, Rui; Rosa, Daniela; Lino, PedroThis document provides fishery indicators for the shortfin mako shark captured by the Portuguese pelagic longline fishery in the Atlantic (standardized CPUEs and size distribution). The analysis was based on data collected from fishery observers, port sampling and skippers logbooks (self sampling), between 1995 and 2015. The mean sizes were compared between years, seasons (quarters), stocks (north and south) and sampling areas. The CPUEs were analyzed for the North Atlantic and compared between years, and were standardized with Tweedie and Delta GLM approaches. In general, there was a large variability in the nominal CPUE trends in the North Atlantic, and the final standardized series was flatter than the nominal. For the size distribution there were no major trends in the time series, with the sizes tending to be larger in the South Atlantic. The data presented in this document can be considered for use in the upcoming 2017 shortfin mako stock assessment, specifically the standardized CPUE for the North Atlantic and the size distribution for both hemispheres.
- Hook, bait and leader type effects on surface pelagic longline retention and mortality rates: a meta-analysis with comparisons for target, bycatch and vulnerable fauna interactionsPublication . Casaca Santos, Catarina; Rosa, Daniela; Coelho, RuiA meta-analysis of 24 publications was conducted to assess effects of hook, bait and leader type on retention and at-haulback mortality rates of target, bycatch and vulnerable species of the pelagic longline fishery. Turtles and swordfish had lower retention rates with circle hooks. In contrast, retention rates of 3 sharks and 2 tuna species were greater with circle hooks. Bait type did not seem to significantly influence the retention rates of most of the species examined. Wire leader lead to a decrease in retention rates of bony fishes and a mix for elasmobranchs. For athaulback mortality, hook type was the most influential, with 5 elasmobranch species and 6 bony fishes having a significantly lower at-haulback mortality rates when using circle hooks. Bait type and leader type did not have a significant effect on at-haulback mortality rates for most species. The results presented here should be considered preliminary. Future work will consider expanded information on fishery characteristics.
- Local indicators for global species: Pelagic sharks in the tropical northeast Atlantic, Cabo Verde islands regionPublication . Coelho, Rui; Macías, David; Ortiz de Urbina, Josetxu; Martins, Albertino; Monteiro, Carlos; Lino, Pedro G.; Rosa, Daniela; Casaca Santos, Catarina; Bach, Pascal; Murua, Hilario; Abaunza, Pablo; Santos, Miguel N.Pelagic sharks are an important bycatch in pelagic fisheries, especially for drifting longlines targeting swordfish. In the Cabo Verde Archipelago (tropical NE Atlantic), pelagic shark catches can reach a significant proportion of the total catches. Due to the increased concern on the status of pelagic shark species, this study was developed to enhance the current knowledge of those sharks in the Cabo Verde region in comparison to the adjacent areas, especially associated with European Union (EU) pelagic longline fishing activity. Stock status indicators for the two main species, blue shark (Prionace glauca) and shortfin mako (Isurus oxyrinchus), were developed, based on fisheries data from logbooks and onboard scientific observers, including analysis of size frequency distributions and standardized catch-per-unit-of-effort (CPUE) indexes over time. The standardized CPUEs have been stable or increasing for both species in the past 10 years, indicating no signs of local depletion. In terms of sizes, the blue shark catch is composed mainly of adults, which can be a sign of a stable population. On the contrary, the catch of shortfin mako is composed mainly of juveniles, which in conjunction of a decrease of mean size might be a cause of concern, highlighting possible overfishing on the species in the region. Thirty satellite tags, 25 archival miniPATs and 5 SPOT GPS, were deployed in the Cabo Verde Exclusive Economic Zone (EEZ), showing that those species are highly mobile. The biomass and size distributions were modeled with spatial and seasonal models (GAMs) identifying locations where juveniles are predominantly concentrated and that should be prioritized for conservation. This work presents new information on the status of pelagic sharks in the Cabo Verde region in the context of those highly migratory species, and can now be used to promote more sustainable fisheries in the region.
- Are shifts in species distribution triggered by climate change? A swordfish case studyPublication . Erauskin-Extramiana, Maite; Arrizabalaga, Haritz; Cabré, Anna; Coelho, Rui; Rosa, Daniela; Ibaibarriaga, Leire; Chust, GuillemSpecies shifts due to climate change are being recorded and reported worldwide. However, the accurate estimation and causal attribution of species shifts using spatial distribution indicators, such as the center of gravity, is challenging. This is particularly problematic for commercially exploited marine species with data from research surveys, commercial fisheries or other data collection methods that are not recorded homogeneously over time and space. Here, we propose a new framework to ascertain whether the changes in the spatial distribution of species are due to changes in habitat conditions, fishing activity or other factors. This approach is developed to help elucidate the main drivers of species shifts and it is based upon the comparison of historical trends in species distribution shifts among raw data and modeled: i) fishing effort, ii) population occurrence and abundance, iii) habitat, and iv) spatio-temporal reconstruction of the species distribution. We apply this new methodology to the case study of swordfish populations worldwide. On a global scale, 2 out of 6 stocks of swordfish shifted latitudinally during 1958–2004. Of those two, only the Mediterranean stock was associated with a linear trend change of its habitat. In two other stocks, the latitudinal center of gravity of populations occurrence varies following their habitats’ interannual variability; however, this shift is not linear. We further developed a worldwide habitat suitability model for swordfish and projected its distribution and abundance into the future under the RCP8.5 climate change scenario, the highest greenhouse gas concentration scenario, by the end of the century. Future projections estimate an overall swordfish decrease of 22% in CPUE (catch per unit of effort), with substantial decreases in most tropical areas, and a slight increase in its distribution range limits, both in the north and southern hemispheres.
- Fishery indicators for the shortfin mako (Isurus oxyrinchus) caught by the portuguese pelagic longline fishery in the Atlantic: nominal CPUEs, catch-at-size and at-haulback mortalityPublication . Coelho, Rui; Rosa, Daniela; Lino, PedroThis paper provides an overview of fishery indicators for the shortfin mako shark captured by the Portuguese pelagic longline fishery in the Atlantic, in terms of catch-at-size, nominal CPUEs and at-haulback mortality. The analysis is based on data from fishery observers, port sampling and skippers logbooks (self sampling), from 1997-2015. In general, there was a large variability in the nominal CPUE trends for the north Atlantic, with a slight increase during the period. For the catch-at-size there were no major trends in the time series, but the sizes tended to be larger in the South Atlantic and with a larger variability. The at-haulback mortality was similar between sexes, with a trend for decreasing mortality rates with increasing specimen size. The data presented in this working document should be considered preliminary and is presented in preparation for the 2017 shortfin mako stock assessment in the Atlantic Ocean.