Biology subjects

Marques, T. A.

Publications and source records attributed to Marques, T. A..

6 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↗

bioRxiv2025

Spatiotemporal data integration for marine megafauna SDMs in dynamic environments: A point process approach

Species distribution models (SDMs) are widely used to predict where and when species occur, but the data available to fit them often resolve space and time unevenly. Designed surveys, such as line-transect distance-sampling surveys, provide structured spatial coverage and the detection information needed to estimate detectability, but logistical and funding constraints often limit them to short, infrequent periods. Opportunistic or citizen-science records are collected more frequently across the year, but from areas shaped by observer access and interest rather than survey design, and usually without comparable detection information. As a result, models built from either source alone tend to capture spatial structure or temporal dynamics well, but not both, limiting predictions for mobile species in dynamic environments. Here, we present a general framework, based on a log-Gaussian Cox process (LGCP) fitted using integrated nested Laplace approximations (INLA), that links multiple data sources to a shared spatiotemporal measure of species density through source-specific observation models: a detection function for survey transects, and spatial constraints reflecting the footprint of opportunistic effort. We apply the framework to cetacean line-transect surveys and whale-watching records. In a simulation with one month of survey data and twelve months of opportunistic data, the integrated model recovered spatiotemporal distribution patterns well (median correlation with the true pattern = 0.91) and estimated monthly abundance with a mean error of +10.7%, outperforming single-source models. In a case study of common dolphins (Delphinus delphis) off mainland Portugal, integration improved the spatial accuracy of predictions, although weak covariate effects limited the temporal variation the model could resolve. These results show that integration adds the most value when the two data sources resolve complementary aspects of distribution, in this case broad spatial structure from the survey and temporal replication from whale-watching, while temporal predictions remain limited when covariates carry weak seasonal signal. The framework is general and can be extended to other taxa, systems, and combinations of structured and opportunistic data by substituting the relevant observation models.

ecology↗

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↗

bioRxiv2025

Climate-driven warming disrupts the symbiosis of bobtail squid Euprymna scolopes and the luminous bacterium Vibrio fischeri

Under the current climate crisis, marine heatwaves (MHW) are expected to intensify and become more frequent in the future, leading to adverse effects on marine life. Here, we aimed to investigate the impact of environmental warming on the symbiotic relationship between the Hawaiian bobtail squid (Euprymna scolopes) and the bioluminescent bacterium Vibrio fischeri. We exposed eggs of E. scolopes to three different temperatures during the embryogenesis, namely: i) 25 {degrees}C (yearly average), ii) 27 {degrees}C (average summer), or iii) 30 {degrees}C (category IV MHW), followed by a colonisation assay under the same conditions. Decreased hatching success and reduced developmental time were observed across warmer conditions compared to 25 {degrees}C. Moreover, exposure to the category IV MHW led to a significant decrease in survival after 48 hours. With increasing temperature, bobtail squids required more bacteria in the surrounding seawater for successful colonisation. When colonised, the regression of the light organs appendages was not dependent on temperature, but the opposite was found in non-colonised bobtail squids. Furthermore, the capacity to maintain the symbiosis diminished significantly with temperature. Finally, the capacity for crypt 3 formation in the squids light organ, which is crucial for enhancing resilience under stress, also declined with warming conditions. This study emphasises the critical need to study the dynamics of microbial symbiosis under the projected conditions for the ocean of tomorrow.

ecology↗

bioRxiv2023

Narwhal (Monodon monoceros) echolocation click rates to support cue counting passive acoustic density estimation

Estimating animal abundance is fundamental for effective management and conservation. It is increasingly done by combining passive acoustics with knowledge about rates at which animals produce cues (cue rates). Narwhals (Monodon monoceros) are elusive marine mammals for which passive acoustic density estimation might be plausible, but for which cue rates are lacking. Clicking rates in narwhals were investigated using a pre-existing dataset from sound and movement tag records collected in August 2013-2016 and 2019 in East Greenland. Clicking rates were quantified for[~] 1200 one-second-long systematic random samples from 8 different whales. Generalized Additive Models were used to model (1) the probability of being in a clicking state versus depth; and (2) the clicking rate while in a clicking state, versus time and depth. The probability of being in a clicking state increased with depth, reaching[~] 1.0 at[~] 500 meters, while the number of clicks per second (while in a clicking state) increased with depth. The mean cue production rate, weighted by tag duration, was 1.28 clicks per second (se= 0.13, CV= 0.10). This first cue rate for narwhals may be used for cue counting density estimation, but care should be taken if applying it to other geographical areas or seasons.

ecology↗

bioRxiv2022

Fin whale singalong: evidence of song conformity

Mechanisms driving song learning and conformity are still poorly known yet fundamental to understand the behavioural ecology of animals. Broadening the taxonomic range of these studies and interpreting song variation under the scope of cultural evolution will increase our knowledge on vocal learning strategies. Here, we analysed changes in fin whale (Balaenoptera physalus) songs recorded over two decades across the Central and Northeast Atlantic Ocean. We found a rapid (over 4 years) replacement of fin whale song types (different inter-note intervals - INIs) that co-existed with hybrid songs during the transition period and showed a clear geographic pattern. We also revealed gradual changes in INIs and note frequencies over more than a decade with all males adopting both rapid and gradual changes. These results provide evidence of vocal learning of rhythm in fin whale songs and conformity in both song rhythm and note frequencies.

animal behavior and cognition↗