Biology subjects

Sousa-Pinto, I.

Publications and source records attributed to Sousa-Pinto, I..

5 recordsLinked to original sources

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↗

bioRxiv2026

Time to Potential Collision: A Dynamic Approach To Study Vessel-Whale Close Encounters

Vessel-whale collisions are a growing global concern and remain challenging to quantify. Therefore, the use of proxies, such as Close Encounters (CEs) that comprise Surprise Encounters (SEs) and Near-Miss Events (NMEs), has been proposed and widely employed to assess collision risk. To better understand this risk in the Eastern North Atlantic, where maritime traffic is intensive, this study aimed to redefine and quantify CEs, and to assess detectability-related variables that may affect CE identification. CEs were assessed using a cetacean occurrence dataset collected between 2012 and 2024 on board cargo ships and oceanographic vessels. CEs thresholds were redefined based on Time to Potential Collision (TPC), rather than distance alone (as described in literature), to allow a more dynamic, risk-based, and speed-sensitive approach. In total, 1226 sightings of whales (baleen, sperm, and beaked whales) were recorded, of which 37.4% were classified as SEs and 2.0% as NMEs. The sperm whale, Physeter macrocephalus, was the species most frequently involved in CEs (13.9% of all CEs), followed by the Cuviers beaked whale, Ziphius cavirostris (11.8%). A Generalized Additive Model was used to assess the influence of detectability-related variables (i.e., meteorological conditions, whale taxa, vessel characteristics, and Marine Mammals Observers (MMOs) experience) on TPC. Significantly lower TPC values were observed with beaked whales, cargo ships, poor visibility conditions, and less experienced MMOs. The results of this study provide an CEs assessment in this region and contribute to the ongoing efforts to standardize CE quantification, by using TPC as a metric. This work also highlights the importance of decreased speeds and the presence of experienced MMOs on board to increase detection probability and TPC, thereby potentially minimizing collision risk.

ecology↗

bioRxiv2025

Parallel erosion of a testis-specific Na+/K+ ATPase in three mammalian lineages sheds light into the evolution of spermatozoa energetics

Understanding how extant physiological landscapes arise from novel genetic interactions is key to elucidating phenotypic evolution. Sperm cells exemplify a striking case of functional compartmentalization shaped by molecular adjustments, notably regarding energy metabolism. Here, we examine the impact of gene duplication and loss on the evolution of sperm energetics in mammals. Our findings reveal that the acquisition of an exclusive mechanism controlling the sperm plasma membrane Na+ gradient, critical for glucose uptake, emerged in the ancestor of mammals through gene duplication, which originated the Na+/K+ ATPase transporting subunit alpha 4 transporter (Atp1a4). Furthermore, we demonstrate that testis-specific expression of Atp1a4 was acquired after the divergence from monotremes. Notably, we identify three independent pseudogenization events of Atp1a4, including in pangolins, the naked mole-rat (Heterocephalus glaber) and toothed whales. The recurrent loss of function in Atp1a4 coincides with the erosion of the testis-specific glycolytic pathway in these lineages. Furthermore, enrichment analysis of striped dolphin (Stenella coeruleoalba) and naked mole-rat testis transcriptomes also suggests significant alterations in sperm capacitation processes. Overall, we show that the elaboration of a sodium-dependent glucose uptake wiring was a key innovation in the energetic landscape governing mammalian spermatozoa, with secondary gene loss in three separate lineages pointing to drastic alterations in motility and capacitation processes. Our findings illustrate how metabolic pathways co-shaped by gene duplication and erosion define extant physiological phenotypes. SignificanceThe sperm cell exhibits a distinct morphology, characterized by exceptional functional and energetic compartmentalization between the midpiece and the flagellum. Here, we demonstrate that the evolution of a sodium-dependent glucose uptake mechanism, driven by gene duplication and giving rise to Atp1a4, was a key innovation promoting efficient glucose usage in mammalian sperm. Additionally, we identify independent losses of Atp1a4 in three lineages--pangolins, naked mole-rats, and toothed whales--coinciding with the reduction of glucose-dependent pathways, such as glycolysis. Our findings highlight how gene expansion and erosion shape metabolic pathways, offering insights into the genetic innovations underlying physiological diversity in reproductive biology.

evolutionary biology↗

bioRxiv2024

Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

The use of environmental DNA (eDNA) to assess the presence of biological communities has emerged as a promising monitoring tool in the marine conservation landscape. Moreover, advances in Next-Generation Sequencing techniques, such as DNA metabarcoding, enable multi-species detection in mixed samples, allowing the study of complex ecosystems such as oceanic ones. We aimed at using these molecular-based techniques to characterise cetacean communities, as well as potential prey in the northern coast of Mainland Portugal. During seasonal campaigns, we collected seawater samples, along with visual records of cetacean occurrence. The eDNA extracted from 64 environmental samples was sequenced in an Illumina platform, with universal primers targeting marine vertebrates. Five cetacean species were identified by molecular detection: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), Rissos dolphin (Grampus griseus), harbour porpoise (Phocoena phocoena) and fin whale (Balaenoptera physalus). Overall, except for the fin whale (not sighted during the campaigns), this cetacean community composition was similar to that obtained through visual monitoring, and the complementary results suggest their presence in the region all year round. In addition, the positive molecular detections of B. physalus are of special relevance since there are no visual records reported in the area. The detection of multiple known preys of the identified dolphins indicates they use these coastal areas for feeding purposes. While this methodological approach remains in a development stage, the present work highlights the benefits of using eDNA to study marine communities, with specific applications for research on cetacean distribution and feeding ecology, ultimately serving as the baseline of a methodological approach for biodiversity monitoring and marine conservation.

ecology↗

bioRxiv2020

Differential Cetacea Circadian Rhythmicity is associated with the molecular erosion of Cortistatin

The ancestors of Cetacea underwent profound morpho-physiological alterations. By displaying an exclusive aquatic existence, cetaceans evolved unique patterns of locomotor activity, vigilant behaviour, thermoregulation and circadian rhythmicity. Deciphering the molecular landscape governing many of these adaptations is key to understand the evolution of phenotypes. Here, we investigate Cortistatin (CORT), a neuropeptide displaying an important role mammalian biorhythm regulation. This neuropeptide is a known neuroendocrine factor, stimulating slow-wave sleep, but also involved in the regulation of energy metabolism and hypomotility inducement. We assessed the functional status of CORT in 139 mammalian genomes (25 orders), including 30 species of Cetacea. Our findings indicate that cetaceans and other mammals with atypical biorhythms, thermal constraints and/or energy metabolism, have accumulated deleterious mutations in CORT. In light of the pleiotropic action of this neuropeptide, we suggest that this inactivation contributed to a plethora of phenotypic adjustments to accommodate adaptive solutions to specific ecological niches.

evolutionary biology↗