Rui Coelho

• PhD
• Researcher at Portuguese Sea and Atmosphere Institute

The objective of this project was to obtain scientific advice for the purpose of implementing the EUPOA on sharks as regards the facilitation of monitoring fisheries and shark stock assessment on a species-specific level in the high seas. The study was focused on major elasmobranch species caught by both artisanal and industrial large pelagic fishe...

Knowledge of the spatiotemporal behavior and interactions with fishing gear of bycatch species is essential to improve conservation and fisheries management strategies. We analyze fine-scale data from onboard observers, covering 25 fishing fleets from 2002 through 2018, to assess temporal trends and spatial variation in sea turtle bycatch in longli...

This paper presents data from 128 tags used to determine the post-release mortality (PRM) of the shortfin mako (Isurus oxyrinchus). The tags include 14 sPATs, 21 Mk10-PATs, and 63 miniPATs from Wildlife Computers; 16 PSATLIFE tags from Lotek Wireless; and 14 X-Tags from Microwave Telemetry. Sharks were tagged during multiple research and commercial...

As part of the ongoing and cooperative Shark Research and Data Collection Program (SRDCP), carried out by the ICCAT Sharks Species Group, information on the size distribution of shortfin mako shark was collected and analyzed. The data came mostly from fishery observers and scientific projects conducted by several fishing nations in the Atlantic tha...

Basking shark Cetorhinus maximus and white shark Carcharodon carcharias are both species of low productivity. Whilst life-history data are limited for both species are limited, published estimated rates of population growth are low (r = 0.1346 year-1 for basking shark, and 0.026 to 0.074 year-1 for white shark). Both species are of conservation con...

Biological information for mobulid rays is summarised for the ICCAT area. At least five valid species occur in this area, although taxonomic uncertainties means that the number of accepted species may change over time. Management regulations applying to mobulids would be applied most effectively at the family-level. Whilst life-history data are lim...

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 manage...

Tuna Regional Fishery Management Organizations (tRFMOs) are increasingly interested in spatiotemporal management as a tool to reduce interaction rates with vulnerable species. We use blue shark (Prionace glauca) as a case study to demonstrate the critical first steps in the implementation process, highlighting how predictions of global habitat for...

Over the last three decades, the advent and the continuous sophistication of telemetry devices have revolutionized our understanding of how pelagic sharks move and exploit their three-dimensional underwater habitat, with implications for management and conservation. In this study, conventional (4,648) and electronic (18) tags were used to assess th...

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‐s...

Loggerhead sea turtles (Caretta caretta) use both oceanic and neritic habitats depending on their life stage, eventually undertaking an ontogenetic shift. Juveniles likely start foraging in a purely opportunistic manner and later seek resources more actively. In the Indian Ocean, it is still unclear where oceanic-stage individuals go, what they do,...

Vast distances and permeable phylogeographic barriers characterize the open ocean, boosting gene flow and decreasing population structure and speciation of widely distributed and migratory species. However, many widely distributed species are formed by different populations throughout their distribution, evidencing our understanding of how the mari...

1. Substantial global population declines in pelagic sharks have led to the introduction of management and conservation measures, including gear restrictions and no-retention policies, to curb declines and encourage stock recovery. As the rate of discarding sharks increases, there is a growing need to understand prognostic factors that influence th...

The blue shark (Prionace glauca) is one of the most abundant and wide-ranging shark species in the world, and also one of the most heavily fished and traded. However, available information is disproportionately distributed across its range, and many aspects of its biology are still poorly understood, limiting our capacity to assess stock status and...

This study is the first to evaluate the fish provisioning services of a whole transitional landscape (Ria Formosa lagoon, Portugal), in parallel with the enhancement of growth, survival and production of single cohorts of the most important commercial fish species by vegetated and unvegetated sub-tidal habitats. Based on monthly beach seine samples...

The recent benchmark assessment for North-east Atlantic porbeagle Lamna nasus necessitated further consideration of stock identification. The published information reviewed suggests seasonal, ontogenetic and sexual differences in movements and distribution, including (i) northward movements of larger porbeagle (including large females) along the sh...

This paper presents the biological information for most commonly shark species collated by the EU Projects "Provision of scientific advice for the purpose of the implementation of the EUPOA sharks (MARE/2010/11, 2011-2013) (Murua et al., 2013)" and "Improving scientific advice for the conservation and management of oceanic sharks and rays (SC 01 EA...

Monitoring the ecological status of marine coastal lagoons requires the integration of multiple indices. However, the efficacy of monitoring programs is complicated by the diverse array of habitats that conform coastal lagoons. In this study, we compared four sampling methods (25-m and 50-m beach seines, beam trawl and Riley push net) in the Ria Fo...

A Benchmark Workshop for selected elasmobranch stocks (WKELASMO) was convened to evaluate the appropriateness of data and methods to assess and provide short-term forecast of four stocks: Porbeagle in the Northeast Atlantic (por.27.nea), thornback ray in the Bay of Biscay (rjc.27.8), undulate ray in the Channel (rju.27.7de), and cuckoo ray in weste...

Relative abundance indices of bluefin tuna (Thunnus thynnus) caught by the Moroccan and Portuguese traps in the Atlantic area close to the Strait of Gibraltar were estimated for the period 2008-2021. Data from four Moroccan and one Portuguese tuna traps were compiled and used. The trend of the nominal CPUE series shows a relatively low and flat per...

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first globa...

The shortfin mako, Isurus oxyrinchus, is an oceanic pelagic shark species found worldwide in tropical and subtropical waters. It is frequently caught by pelagic longline fisheries, but despite its commercial importance and ecological significance, little is still known about its biology and ecology at the molecular level. Therefore, we combined two...

Tagging studies are a fundamental tool for understanding fish population dynamics. Choosing the right tag type, however, is of major importance, as properties such as shedding rate can affect estimates of mortality, abundance, and movement rates. Here, we provide tag-specific recapture rates for blue sharks (Prionace glauca) and assess the retentio...

One potential problem with applying any Management Procedure that requires an index of abundance is that there is only one potential CPUE series, a Spanish longline series that is likely available in the future for management of the eastern Atlantic porbeagle stock. In this fishery, Porbeagle shark are a bycatch species so that there are concerns a...

Blue shark (Prionace glauca) is amongst the most abundant shark species in international trade, however this highly migratory species has little effective management and the need for spatio-temporal strategies increases, possibly involving the most vulnerable stage or sex classes. We combined 265,595 blue shark observations (capture or satellite ta...

The crocodile shark ( Pseudocarcharias kamoharai ) is a small lamniform shark that is occasionally by-caught in pelagic longline fisheries targeting tunas and swordfish. Due to its biological features, this species is highly vulnerable to overexploitation. However, at present, the crocodile shark is not evaluated for its stock status by any of the...

• Extreme climate changes during the Cenozoic Era strengthened different biogeographical barriers that decreased the connectivity among populations, triggering lineage diversification of different species worldwide. • The mitochondrial DNA control region was employed to explore the phylogeography of Sphyrna zygaena, a globally distributed species t...

The shortfin mako is one of the most important shark species caught in Atlantic Ocean pelagic fisheries. Given increasing concerns for the stock status of the species, the present study was designed to fill gaps in the knowledge of habitat use and movement patterns of shortfin mako in the Atlantic Ocean. From 2015 to 2019, 53 shortfin makos were ta...

Since the Miocene profound climatic changes have influenced the biology and ecology of species worldwide, such as their connectivity, genetic population structure, and biogeography. The goal herein is to evaluate the phylogeography of sailfish Istiophorus platypterus between the Atlantic, Indian, and Pacific oceans. Our results evidenced a high gen...

Accurately characterizing the biology of a pelagic shark species is critical when assessing its status and resilience to fishing pressure. Natural mortality (M) is well known to be a key parameter determining productivity and resilience, but also one for which estimates are most uncertain. While M can be inferred from life history, validated direct...

Here, we outline actions taken by Tuna Regional Fisheries Management Organizations on the science of marine turtle’s conservation. The Inter-American Tropical Tuna Commission (1949), the International Commission for the Conservation of Atlantic Tunas (1966), the Indo-Pacific Tuna Program (prior to 1980) the Indian Ocean Tuna Commission(1993), and t...

The Group reviewed the most up-to-date swordfish (SWO) fishery statistics (T1NC: Task I nominal catches; T2CE: Task II catch & effort; T2SZ: Task II size frequencies; T2CS: Task II catch-at-size reported) and conventional tagging data, available in the ICCAT database system (ICCAT-DB). The three swordfish stocks (SWO-N: North Atlantic; SWO-S: South...

The implementation of an Ecosystem Approach Fisheries Management (EAFM) in ICCAT has been slow and patchy, as it lacks a long-term plan, vision and guidance on how to operationalize it. Ecosystem plans are needed to formalize the process of operationalizing the EAFM by identifying and formalizing ecosystem goals and objectives, planning actions bas...

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 enh...

The perceptions of fishers towards the Arrábida Marine Park, a marine protected area (MPA) in the west coast of Portugal, were studied through face-to-face interviews in two different moments of the MPA life cycle. Fishers' perceptions about the MPA and the impact it had on the fishing activity over time were identified just before the full impleme...

The Northwest Atlantic (NWA) population of porbeagles Lamna nasus is susceptible to capture in rod-and-reel fisheries and most individuals are discarded alive due to catch and size limits. To estimate post-release survival, pop-off satellite archival tags were attached to porbeagles captured with rod-and-reel. Fourteen tags were deployed, of which...

This paper provides an update of the study on post-release mortality of the shortfin mako, Isurus oxyrinchus developed within the ICCAT Shark Research and Data Collection Program (SRDCP). Up to date, 43 tags (14 sPATs and 29 miniPATs) have been deployed by observers on Brazilian, Portuguese, Spanish, Uruguayan, and US vessels in the temperate NE an...

A Sustainability Assessment for Fishing Effects (SAFE) was conducted for the porbeagle shark in the North and South Atlantic oceans. The SAFE approach is a quantitative assessment that computes a proxy for fishing mortality rate as the product of four susceptibility components: availability of the species to the fleets, encounterability of the gear...

This 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....

Modeling and understanding the catch rate dynamics of marine species is extremely important for fisheries management and conservation. For oceanic highly migratory species in particular, usually only fishery‐dependent data is available which has limitations in the assumption of independence and if often zero‐inflated and/or over‐dispersed. We teste...

International trade in vulnerable marine species is regulated once they are listed in CITES Appendices (the Convention on International Trade in Endangered Species of Wild Fauna and Flora). Parties to the Convention submit proposal(s) 150 days prior to the CITES Conference for voting on the inclusion of new species in Appendices I and II, making a...

Species 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, co...

In this working paper, we address the ecosystem component consisted of "non-retained sharks and rays" to support the development of an ecosystem report card in the IOTC region. This group includes sharks and ray species that are not retained due to retention bans or due to their low or no commercial value. The interaction between these non-retained...

Several international legal agreements and guidelines have set the minimum standards and key principles to guide the implementation of an ecosystem approach to fisheries management (EAFM). However, the implementation of an EAFM in tuna Regional Fisheries Management Organizations (RFMOs) has been patchy and lack a long-term plan, vision and guidance...

This paper revises detailed data on hooking (at-haulback) mortality of swordfish captured and discarded by pelagic longlines, using as a case study the shallow night setting Portuguese pelagic longline fishery that targets manly swordfish, in the Atlantic Ocean. The overall at-haulback mortality for swordfish was very high, specifically 85.2% for a...

• The tiger shark (Galeocerdo cuvier) is a common widespread coastal–pelagic shark species whose population genetic structure has only recently been the object of genetic studies. • In this study, the tiger's shark mitochondrial DNA control region was sequenced for a sample of 172 individuals from the western Atlantic and from Australia's east coas...

The smooth hammerhead shark, Sphyrna zygaena, is a pelagic shark occasionally captured as bycatch by industrial pelagic longline fleets in the Atlantic Ocean. Data for this study were collected by fishery observers, between 2003 and 2016. Datasets analyzed included information on catches per unit effort (CPUE), size and sex of smooth hammerhead sha...

UE Framework contract EASME/EMFF/2016/008

Maturity ogives are usually estimated using different methods, including macroscopical and microscopical maturity data. Differences in maturity ogives estimations are found for species and by area/stock. So those differences may be a consequence of the use of different methodological techniques (criteria) or due to different spawning tactics. Takin...

Population 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...

Since there is still a lack of biological information regarding Prionace glauca in the Indian Ocean, specifically in terms of age estimation and growth modelling, the age and growth of this species was studied by analysing vertebral samples. All samples were collected from specimens captured by pelagic longliners between March 2013 and September 20...

Depredation has aroused great interest over the last few decades, mainly due to the expansion of distant fishing, in particular longlines. For this study, captures and depredation records were taken by scientific observers on board Portuguese commercial longline vessels in the Atlantic and Indian Oceans between 2011 and 2016. A total of 1,336 fishi...

Environmental variability changes the distribution, migratory patterns, and susceptibility to various fishing gears for highly migratory marine fish. These changes become especially problematic when they affect the indices of abundance (such as those based on catch-per-unit-effort: CPUE) used to assess the status of fish stocks. The use of simulate...

Recreational fishing is an important socioeconomic activity that needs systematic studies and data monitoring programs. The Pescardata project, coordinated by the Centre for Marine Sciences of the University of Algarve has two goals: (1) fill the gaps with regard the systematic collection of data on the recreational catches of the species included...

Numerous 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...

Barplots of fish abundance and biomass per protection level and substrate Barplots of mean (±standard error) fish abundance (A: CPUE n⋅500 m−1) and biomass (B: BPUE kg⋅500 m−1) per protection level and substrate (sand, mud).

Mean species abundance and biomass for each protection level and period Mean (and standard error - SE) species abundance (CPUE - n⋅500 m−1) and biomass (BPUE - kg⋅500 m−1) according to period (Period 1, Period 2) and protection level (BA - buffer area; PPA - partially protected area; FPA - fully protected area). Only species with frequency of occur...

Discriminant species at each leaf of the multivariate regression tree Discriminant species at each leaf (terminal node) of the multivariate regression tree analysis (Leaf I - Muddy BA & PPA; Leaf II - Muddy FPA; Leaf III - Sandy BA; Leaf IV - Sandy PPA & FPA, Period 1; Leaf V - Sandy PPA & FPA, Period 2). Indicator values (IndVal) are shown (specie...

List of fish species sampled during the experimental fishing surveys List of fish species sampled during the experimental fishing surveys in the Luiz Saldanha Marine Park, and corresponding references (full references in File S1) used for length-weight (L-W) relationships (for all species except pelagics). The environment, maximum length reported (...

Mean species total length for each protection level and period Mean total length (TL - cm) per species according to period (Period 1, Period 2) and protection level (BA - buffer area; PPA - partially protected area; FPA - fully protected area). Only species with frequency of occurrence higher than 15% are shown.

Mean species abundance for each substrate type Mean (and standard error - SE) species abundance (CPUE - n⋅500 m−1) per substrate type. Only species with frequency of occurrence higher than 15% are shown.

Species frequency of occurrence Table with frequency of occurrence of the species included in the analyses (FO%; percentage of samples with presence of each species). Species code (used in Fig. 6) and family are also shown (species ordered according to decreasing FO%).

Mean species abundance in each leaf - multivariate regression tree Mean (and standard error - SE) species abundance (CPUE - n⋅500 m−1) in each leaf of the multivariate regression tree analysis (MRT) (Leaf I - Muddy BA & PPA; Leaf II - Muddy FPA; Leaf III - Sandy BA; Leaf IV - Sandy PPA & FPA, Period 1; Leaf V - Sandy PPA & FPA, Period 2).

Summary table of the ratios analyses and multivariate regression tree Summary table of the ratio (Protected area:Buffer area; After MPA Full Implementation:Before MPA Full Implementation) analyses (N - abundance, B - biomass, L - total length) and multivariate regression tree (MRT) (MRT Ind Spp - cluster where the species was assigned as indicator)...

Table of additional information of species traits: fisheries category and reproduction Additional information of species traits: taxonomic family, environment, maximum length, market price and reproduction (mode, length and age at maturity) (references of length/age at maturity listed). Fisheries category is shown in the ‘price per kg’ column: T -...

Table of additional information of species traits: longevity and movement pattern Additional information of species traits: maximum reported age, theoretical longevity (based on Von Bertalanffy Growth Function - VBGF) and movement pattern. Information on the type of study reporting movement pattern data is shown: FS - fishing surveys, MR - mark-rec...

References used in the Supplemental Information section

Dataset of experimental fishing surveys Raw data of experimental fishing surveys in the Luiz Saldanha Marine Park.

The smooth hammerhead shark, Sphyrna zygaena, is a cosmopolitan semipelagic shark captured as bycatch in pelagic oceanic fisheries, especially pelagic longlines targeting swordfish and/or tunas. From 2012 to 2016, eight smooth hammerheads were tagged with Pop-up Satellite Archival Tags in the inter-tropical region of the Northeast Atlantic Ocean, w...

Dataset considered for this study. (XLSX)

Age and growth studies are fundamental to successful fisheries management. Zapteryx brevirostris (Müller & Henle, 1841) is distributed off the Brazilian continental shelf and this species is assessed as “Vulnerable” in the Red List of the International Union for the Conservation of Nature (IUCN). Thus, the objective of this study was to present pre...

Senghor Seamount is an important fishing ground around the Cape Verde archipelago in the Eastern Central Atlantic. On an experimental field survey in October 2009 and December 2011, a total of 115 deep-sea fishes of 26 species belonging to 18 families were caught on the seamount summit, along the slopes and on the adjacent abyssal plane, using long...

This study provides information on some biological aspects of Euthynnus alletteratus from the western Mediterranean (Spanish coast) and in the Atlantic Ocean (south of Iberian Peninsula). A total of 1266 individuals were measured between 2003 and 2017. The L-W relationship was calculated with W equal to 0.01242 FL 3.058. Histological analysis of th...