Biology subjects

Marcalo, A.

Publications and source records attributed to Marcalo, A..

4 recordsLinked to original sources

bioRxiv2026

Integrating dedicated and opportunistic surveys to estimate seasonal common dolphin density off mainland Portugal

1. Common dolphins (Delphinus delphis) are the most abundant cetaceans off mainland Portugal and a species of conservation and bycatch concern, so reliable abundance estimates are a management priority. Yet no single survey provides adequate spatiotemporal coverage: dedicated programmes offer sparse snapshots, while opportunistic programmes are spatially constrained by their routes. Integrating them is methodologically demanding, and the existing methods that do so in a single model estimate the density of animal groups, not of the individual animals that management often requires. 2. We develop a spatiotemporal marked log-Gaussian Cox process that integrates four structurally distinct surveys through a shared intensity surface, comprising environmental covariates, a latent spatial field, and survey-specific detection functions. Group size enters as a zero-truncated negative binomial mark with its own spatiotemporal field. We apply it to a dedicated aerial survey and three opportunistic ship-based programmes off mainland Portugal, comprising 162,514 km of on-effort transects and 1,756 sightings of 17,000 animals. We fit the model in a Bayesian framework with integrated nested Laplace approximations, yielding seasonally resolved group and animal density surfaces across the Portuguese Exclusive Economic Zone, and abundance estimates with fully propagated uncertainty. 3. Predicted animal density concentrated over the shelf and upper slope in every season, peaking northwest, and increased in shallower, cooler, more productive waters and over steeper seabed. Abundance nearly doubled from summer (77,000 [95% credible interval: 60,000, 98,000]) to winter (146,000 [99,000, 208,000]). Seasons shared 56% of the spatial field's variance, so effort from any programme in any season informed all others, and the seasonal contrast remained estimable despite uneven coverage. 4. Synthesis and applications. Our framework allows managers to combine dedicated surveys with existing platforms of opportunity to estimate animal density by season. Because group size is modelled explicitly, densities are estimated in animals rather than groups, as required for bycatch risk assessment and marine spatial planning. Because each survey enters through its own observation model, the approach accommodates programmes that differ in platform and protocol and transfers to any species or region where several surveys each cover part of a population.

ecology↗

bioRxiv2026

Exploring the relationship between dolphins and fisheries: uncovering the spatial and temporal patterns that influence potential conflicts along Portugal's north coast

The north coast of mainland Portugal supports a strong dolphin presence and extensive fishing activity, increasing the likelihood of interactions, such as bycatch. This study provides an initial assessment of potential conflict areas, using automatic identification system (AIS) data from Global Fishing Watch. To this end, sighting data from the ATLANTIDA project (2021-2024) on the common dolphin (Delphinus delphis) were used to describe spatiotemporal patterns of occurrence and encounter rates, and to predict their association with fishing effort to identify and map areas of potential overlap. A generalised additive model (GAM) was then applied, integrating environmental, spatial, temporal, and fisheries-related variables to identify the main predictors of species occurrence. Common dolphins were frequently observed during the summer, with an average encounter rate of 3.662 sightings/km. This high encounter rate may be associated with factors such as sea surface temperature, diet, and purse seine fishing activity. The maps showed a spatial overlap between fishing grounds and areas of common dolphin occurrence. Fishing effort was nearly identical between locations with sightings (2.00 h/km{superscript 2}) and those without (1.62 h/km{superscript 2}), suggesting that dolphins are not actively avoiding fishing areas but may instead frequent them due to shared habitat preferences. The best-fitted GAM indicated that encounters were related to year, latitude, fishing effort, depth, sea surface temperature, and season. There was an increase in occurrence over the years and a decrease with increasing fishing effort and sea surface temperature, possibly linked to changes in prey availability, although broad confidence intervals warrant cautious interpretation. Despite some limitations encountered in this study, we believe our findings provide valuable insights into the relationship between dolphin occurrence, environmental conditions, and fishing activities in the area, establishing an important baseline for future conservation and fisheries management efforts.

ecology↗

bioRxiv2025

Assessing fish welfare in small-scale commercial fixed-net fisheries off the southern Portuguese coast

Despite a growing interest in animal welfare in production systems, research on fish welfare remains limited, particularly in commercial fisheries. Fish caught in fixed-net fisheries experience multiple stressors from the time of capture to mortality on deck considered detrimental to their welfare. We examined the impact of bottom-set gill nets and on-board handling on catch welfare using behavioural and physiological indicators. Vitality assessments were performed on four commercially important fish species on-board fishing vessels through a devised vitality scale that included behaviours, morphological condition and reflexes as indicators of welfare. Physiological stress parameters (Cortisol, Glucose, Lactate and Osmolality) were evaluated in blood collected on deck and analysed in relation to the vitality scores. The vitality at arrival on deck as well as the rate of decrease in vitality differed significantly amongst the tested species. Furthermore, Generalised Linear Models predicted that several biological, operational, and environmental variables significantly affect the extent of time the fish shows activity, and hence, on the welfare. Elevated average cortisol levels were found at all the vitality stages highlighting the stress experienced by fish due to the fishing process. The findings of this study enable us to recommend welfare-friendly methods in set-net fisheries to promote better fishing standards.

animal behavior and cognition↗

bioRxiv2025

Seasonal and interannual variation of common dolphin densities in Portuguese waters

Modelling a species ecology and abundance provides important insights into its habitat preferences, population trends and distribution. This can be used to inform conservation efforts, highlighting populations at risk of extinction and regions in need of protection. Here, we studied how environmental factors relate to common dolphins (Delphinus delphis) densities in the waters off mainland Portugal. We analyzed an opportunistic dataset collected using European Seabirds At Sea (ESAS) methodology with distance sampling, spanning from 2004 to 2020. There were 1151 sightings of common dolphins, 737 of which were during effort. Detection functions were fitted to model the dolphins detectability as a function of the distance to the track line. We used smooths of static (depth, slope, and distance to the coast, 200m and 1000m isobaths) and dynamic (sea surface temperature, salinity, chlorophyll-a concentration with and without a time lag, zooplankton, and sardine biomass) environmental factors, relating them to counts corrected for detectability and survey effort, to fit habitat-based Density Surface Models. We then predicted and mapped common dolphin densities seasonally (winter, spring, summer autumn) throughout the sample years. The results show how different environment variables relate to dynamic common dolphin densities. In general, common dolphins had higher densities in coastal environments, especially during the summer due to high productivity and lower sea surface temperature in shelf waters, associated with seasonal upwelling. During the summer, there were predicted local peaks in common dolphin densities, in areas with high zooplankton and chlorophyll-a concentration. In the other seasons, its range expands to more offshore waters, with less local density peaks. The interannual variation of this species densities is mostly explained by the annual sardine biomass. Overall, this brings important insights into this species conservation and potential impacts from anthropogenic activities, such as climate change and overfishing.

ecology↗