Sustainable fisheries management of swordfish Xiphias gladius in the Atlantic and Indian Oceans: biology, population dynamics, stock structure, habitat use, and evaluation of alternative management options.

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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, Axel

Permeable 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.

2023Journal article

Open access

A review of reported effects of pelagic longline fishing gear configurations on target, bycatch and vulnerable species

Publication . Casaca Santos, Catarina; Rosa, Daniela; Gonçalves, Jorge Manuel Santos; Coelho, Rui

1. 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.

2023Journal article

Open access

Management strategy evaluation operating model conditioning: a swordfish case study

Publication . Mosqueira, Iago; Fu, Dan; Coelho, Rui; Rosa, Daniela

Evaluation of fish stock status is a key step for fisheries management. Tuna Regional Fisheries Management Organizations (t-RFMOs) are moving towards management strategy evaluation (MSE), a process that combines science and policy and depends on technical aspects, developed by scientists, designed to meet management objectives established by managers and other stakeholders. In the Indian Ocean, the current management advice for swordfish (Xiphias gladius) is based on an ensemble of 24 models considering four areas of uncertainty about the stock dynamics. There is an ongoing MSE process for swordfish, and this paper describes the methodology being applied for the conditioning of the operating model (OM), including model selection and validation. In the MSE, nine sources of uncertainty were considered, each being characterized by 2-3 levels. A partial factorial design was employed to reduce the number of models from a full factorial design to those needed to encompass the overall uncertainty. A selection and validation process was carried out, filtering models that converged, showed good predictive skills, and provided plausible estimates. Overall, the estimated spawning stock biomass (SSB) relative to SSB at maximum sustainable yield (MSY), and fishing mortality (F) relative to F-MSY encompasses the estimates of the stock assessment ensemble at the most optimist area of the distribution. The MSE for swordfish is an ongoing process that is expected to provide more robust management advice in the future. Further developments to the OM can still occur, but the methods presented herein can be applied to this, or other species, MSE processes.

2024-06-23Journal article

Open access

Leader material and bait effects on target and bycatch species caught in an Atlantic Ocean pelagic longline fishery

Publication . Casaca Santos, Catarina; Santos, Miguel N.; Rosa, Daniela; Coelho, Rui

The influence of bait type and leader material on target and bycatch species was assessed through fishing experiments in the Portuguese shallow pelagic longline fishery in the Atlantic Ocean. Wire leaders were found to decrease catch rates of commercially valuable species such as bigeye tuna and yellowfin tuna, while increasing catch rates of elasmobranchs, including the blue shark and shortfin mako. The odds ratios of capture swordfish and tunas also decrease when using wire leaders, while elasmobranchs have higher odds ratios of capture and athaulback mortality when using wire leaders. Squid bait led to higher catches of targeted tuna species, however it also resulted in higher catches of marine turtles. For most of the taxa caught at-haulback mortality risk was found to be higher on squid bait, which may be related with increased deep-hooking events. While bait type and leader material did not significantly affect size selectivity for most species, wire leaders were found to retain larger blue sharks and fish bait attracted smaller-sized swordfish. This study showed that banning wire leaders on pelagic longline fisheries is an effective measure for reducing the retention of pelagic shark species, particularly of large size blue sharks.

2024-10Journal article

Open access

Spatial and temporal size distribution of swordfish in the Atlantic Ocean: implications for conservation and management

Publication . Rosa, Daniela; Schirripa, Michael; Gillespie, Kyle; Macías, David; Forselledo, Rodrigo; Mourato, Bruno; Kai, Mikihiko; Arocha, Freddy; Su, Nan-Jay; Kerwath, Sven; Bahou, Laurent; Pappalardo, Luigi; Diaz, Guillermo A.; Lino, Pedro G.; Salmeron, Francisca; Urbina, Josetxu Ortiz de; Cardoso, Luis Gustavo; Sant’Ana, Rodrigo; Travassos, Paulo; Santos, Miguel N.; Erzini, Karim; Domingo, Andrés; Báez, Jose Carlos; Hanke, Alex; Brown, Craig; Coelho, Rui

Swordfish (Xiphias gladius) is a common target species of surface pelagic longline fisheries. In the Atlantic Ocean and Mediterranean Sea, swordfish is managed as three separate stocks, all having management measures in place to rebuild or conserve the stocks, including minimum landing sizes. The objective of this study was to review size data for swordfish in the Atlantic Ocean, model the sex-specific size distribution and determine areas where there is higher likelihood of capturing undersized fish. The size distribution differed between males and females and varied by quarter, indicating movements of large fish between temperate and tropical waters. Undersized fish seems to occur in association with coastal waters, with higher proportions in the Northwest Atlantic and tropical areas. This study provides a better understanding of the temporal and spatial size and sex distribution of swordfish and presents insights into the distribution of undersized swordfish that is subject to management measures.

2025-03-07Journal article

Restricted access