Biology subjects

Valente, R.

Publications and source records attributed to Valente, R..

10 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

Gene Loss DB: A curated database for gene loss in vertebrate species.

Molecular databases are essential resources for both experimental and computational biologists. The rapid increase in high-quality genome assemblies has led to a surge in publications describing secondary gene loss events associated with lineage-specific adaptations across diverse vertebrate groups. This growing volume of information underscores the urgent need for organized, searchable, and curated resources that facilitate data discovery, allow detection of broad evolutionary patterns, and support downstream analyses. Currently, no existing database compiles manually curated and validated information on published secondary gene loss events. Here, we introduce the Gene Loss Database (GLossDB), a platform designed to centralize and present this data in an easy-to-search and user-friendly format (https://geneloss.org/). GLossDB compiles gene loss events alongside supporting evidence, including the inferred mechanism of gene loss (exon deletion, gene deletion, loss of function mutation), the type of data used to support inactivation (genomic, transcriptomic, single/multiple individual sequence reads, synteny maps) and, when available, whether the event is shared across all lineages within a taxon. Each entry also includes a short excerpt from the original publication to provide context. This information is structured in the database to be searchable by species, gene, taxa, or by GO-terms linked to the gene in question. The initial release of GLossDB focuses on cetaceans, a lineage with numerous gene loss events linked to aquatic adaptations. This first collection comprises 1866 gene loss events identified across 57 cetacean species. In addition, the database includes 1321 gene loss events from other taxa, which were also reported in the same studies and collected simultaneously.

bioinformatics↗

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↗

bioRxiv2024

Alterations of Pleiotropic Neuropeptide-Receptor gene couples in Cetacea

BackgroundHabitat transitions have considerable consequences in organism homeostasis, as they require the adjustment of several concurrent physiological compartments to maintain stability and adapt to a changing environment. Within the range of molecules with a crucial role in the regulation of different physiological processes, neuropeptides are key agents. Here, we examined the coding status of several neuropeptides and their receptors with pleiotropic activity in Cetacea. ResultsAnalysis of 202 mammalian genomes, including 41 species of Cetacea, exposed an intricate mutational landscape compatible with gene sequence modification and loss. Specifically for Cetacea, in the twelve genes analysed we have determined patterns of loss ranging from species-specific disruptive mutations (e.g., Neuropeptide FF-Amide Peptide Precursor; NPFF) to complete erosion of the gene across the cetacean stem lineage (e.g., Somatostatin Receptor 4; SSTR4). ConclusionsImpairment of some of these neuromodulators, may have contributed to the unique energetic metabolism, circadian rhythmicity and diving response displayed by this group of iconic mammals.

evolutionary biology↗

bioRxiv2022

Convergent Decay of Skin-specific Gene Modules in Pangolins

The Mammalia skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation - Awat1/2, show patterns of inactivation in the stem pangolin branch; while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function, is intact and expressed in the skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated, convergent and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes.

evolutionary biology↗

bioRxiv2022

Regeneration of Starfish Radial Nerve Cord restores animal mobility and unveils a new coelomocyte population

The potential to regenerate a damaged body part is expressed to a different extent in animals. Echinoderms, in particular starfish, are known for their outstanding potential to regenerate cell, tissue, organ, and body parts. For instance, humans have restricted abilities to restore organ systems being dependent on limited sources of stem cells. In particular, the potential to regenerate the central nervous system is extremely limited, explaining the lack of natural mechanisms that could overcome the development of neurodegenerative diseases and the presence of traumatisms. Therefore, understanding the molecular and cellular mechanisms of regeneration in starfish could lead to the development of new therapeutic approaches in humans. In this study, we tackle the problem of starfish central nervous system regeneration by examining anatomical and behavioral traits, including external anatomic anomalies, the dynamics of coelomocytes populations and neuronal tissue architecture. We noticed that several anatomic anomalies were evident and detected that the injured arm could not be used anymore to lead the starfish movement. Those seem to be related to defense mechanisms and protection of the wound. In particular, histology showed that tissue patterns during regeneration resemble those described in holothurians and in starfish arm tip regeneration. Flow cytometry coupled with imaging flow cytometry unveiled a new coelomocyte population during the late phase of the regeneration process. Morphotypes of previously characterized coelomocytes populations were described based on IFC data. Further studies of this new coelomocyte population might provide insights on their involvement in radial nerve cord regeneration.

zoology↗

bioRxiv2021

Functional or vestigial? The genomics of the pineal gland in Xenarthra

Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e. Linnaeuss two-toed sloth) but undetected in other closely related species (i.e. brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were lost independently. Additionally, by expanding our analysis to 157 mammal genomes we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy, and endorse the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.

genomics↗

bioRxiv2021

A drastic shift in the energetic landscape of toothed whale sperm cells

Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm motility, and is known to vary among species. Here we describe an extreme example of spermatozoa-energetics adaptation. We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends uniquely on endogenous fatty acid {beta}-oxidation, but not carbohydrates. Our findings substantiate the observation of large mitochondria in spermatozoa, possibly boosting ATP production from endogenous fatty acids. This unique energetic rewiring emphasizes the physiological body reorganisation imposed by the carbohydrate-depleted marine environment.

evolutionary biology↗