Biology subjects

Ruivo, R.

Publications and source records attributed to Ruivo, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Cldn18 evolution reveals pleiotropic constraints in vertebrate stomach loss

Understanding the origins of anatomical innovations is central to elucidate the evolution of phenotypic diversity, as novel body plans often underpin the colonization of new ecological niches. The stomach, with its acid-secreting glands, evolved in the gnathostome ancestor and has been lost repeatedly. Claudin 18 (CLDN18) is a tight-junction protein that preserves gastric epithelial integrity against extreme H gradients and, in mammals, also acts in the lung through alternative first-exon isoforms. This dual role suggests that pleiotropy may shape the fate of CLDN18 after stomach loss. Here, we provide a detailed analysis of CLDN18 evolution across jawed vertebrates. CLDN18 originated in the gnathostome ancestor and is expressed in the stomach of elasmobranchs. We found no evidence of the gene in chimaeras or lungfishes, two additional agastric lineages, extending the loss of cldn18a previously described in agastric teleosts. Exon 1 architecture indicates a tandem duplication in the Euteleostomi ancestor, whereas stomach- and lung-associated isoforms are partitioned in most tetrapods examined. Monotremes, although agastric, retain only the lung-associated exon 1, consistent with lung function sustaining selection on the locus. Together, these findings reveal a complex evolutionary history involving gene loss, alternative splicing, tissue-specific regulation, and secondary exon loss, highlighting how pleiotropy and regulatory partitioning shaped the evolution of epithelia in jawed vertebrates.

evolutionary biology↗

bioRxiv2026

Convergent gene erosion in the chemical defensome of marine mammals

To preserve homeostasis in the face of continual chemical insult, animals evolved dedicated molecular systems that detect, detoxify, and eliminate foreign compounds. Collectively, these enzymes, transporters, and regulatory pathways constitute the chemical defensome. In cetaceans, the loss of two key nuclear receptors (NR1I2/PXR and NR1I3/CAR) suggests a profound rearrangement of the chemical defense systems. Therefore, we investigated the gene inventory of the chemical defensome in Cetacea and two other major marine mammal lineages (Pinnipedia and Sirenia), using their closest terrestrial relatives to understand the extent and patterns of chemical defensome remodelling. We demonstrate large-scale gene loss in chemical defensome genes of cetaceans, as well as smaller scale gene loss in the other two marine mammal lineages, indicating possible convergent evolution. Gene loss occurred predominantly in phase I and phase II biotransformation enzymes, including CYPs, FMOs, SULTs, and GSTs. Many of the lost genes in cetaceans are known to be regulated by PXR and/or CAR, while genes lost in multiple marine mammal lineages are often not regulated by these transcription factors. We hypothesize that the transition to aquatic environments, often accompanied by corresponding changes in feeding habits, led to convergent loss of chemical defensome genes, and loss of PXR and CAR in cetaceans accelerated these losses. These findings reveal systematic erosion of chemical defense capabilities across marine mammal lineages, suggesting that adaptation to marine life involves trade-offs in detoxification capacity that may have significant implications for these species responses to increasing chemical pollution in present-day ocean environments.

genomics↗

bioRxiv2026

Eco-Friendly Antifouling Solutions: Hazard Assessment of Synthetic Derivatives of Natural Compounds

The accumulation of microorganisms and macroorganisms on aquatic surfaces poses economic and ecological challenges, particularly in maritime transport. Traditional antifouling methods, such as biocidal coatings containing toxic compounds like tributyltin (TBT) and copper, are effective but harmful to the environment. This study investigates eco-friendly antifouling alternatives, focusing on nature-inspired compounds (NIAFs) GBA 26 (GBA) and DPC345DHC (DH345), derived from polyphenols and flavonoids, respectively. The ecotoxicity of these compounds was evaluated using standardized assays with various species, including embryos of Danio rerio (zebrafish) (OECD TG 236), the algae Raphidocelis subcapitata (OECD TG 201), and the bacteria Vibrio fischeri (ISO 11348-2), along with nuclear receptor transactivation assays in Mytilus galloprovincialis (Mediterranean mussel). Gallic acid derivative GBA and 24h-transformation products showed low toxicity in zebrafish embryos, while dihydrochalcone DH345 inflicted developmental toxicity in zebrafish at 1 mg/L and above. Comparatively, tralopyril, a commercial biocide, exhibited significant toxicity at lower concentrations. Transcriptomic analysis of zebrafish embryos treated with GBA revealed selective gene modulation related to stress response, ion transport, and protein synthesis. Both, GBA and DH345, were shown to inhibit algae growth at 0.1 mg/L. Vibrio fischeri assay showed no toxic effects for any of the tested compounds. Nuclear receptor transactivation assays conducted with GBA revealed no activation of PPAR or PXR receptors. These findings suggest GBA and DH345 as potential eco-friendly antifouling agents with lower environmental risks than established antifoulants such as tralopyril. However, further research is needed to evaluate their potential long-term ecological impacts, particularly chronic toxicity across various organisms. This study advances the pursuit of sustainable antifouling solutions that prioritize environmental protection.

ecology↗

bioRxiv2025

Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel

Unraveling how adaptive traits originate and evolve is key to understanding the mechanisms shaping species diversity and their adaptive potential. Seasonal color molts, from summer-brown to winter-white, evolved in at least 21 mammals and birds to maintain camouflage in environments with seasonal snow, but the occurrence of winter-brown morphs reflects seemingly convergent local adaptation to distinct snow conditions. In the least weasel (Mustela nivalis), alternative winter morphs map to the pigmentation gene MC1R, but the evolutionary history and functional basis of this variation remain unknown. Using in vitro cellular assays, we show that winter-brown coats are caused by a derived protein-coding amino acid substitution that reduces MC1R affinity to its ligands, ASIP and -MSH. Using targeted enrichment and sequencing, we find that this mutation arose de novo within the species, around one million years ago, and was maintained across the geographically structured populations generated during its evolution in Europe. Using simulations, we show that genetic drift cannot explain the long-term maintenance of this variant, which is likely driven by spatially varying selection acting on the phenotypic polymorphism, anchoring local adaptive responses. Our results underscore how long-standing adaptive variation can fuel recurrent adaptation to heterogeneous environments through time.

evolutionary biology↗

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

Ghrelin and Mboat4 are lost in Serpentes

Exploring the evolution of gene networks associated with metabolic/energetic homeostasis can yield key insights into the adaptive landscapes governing the physioology of extant lineages. Here, we investigate a key hormonal module of energy metabolism in reptiles. Ghrelin (GHRL), also known as the "hunger hormone", is a multifunctional gastric peptide, involved in appetite, food intake and body weight regulation. We examined the genomes of 112 species comprising members of the Squamata, Testudines, Crocodilia and Rhynchocephalia and provide ample evidence that GHRL was independently lost in snakes, chameleons and toadhead agamas. In accordance, the enzyme responsible for ghrelin acylation and essential for its activity (membrane bound O-acyltransferase domain containing 4), is also eroded in these lineages. We suggest that the loss of this hormonal signalling system parallels critical modifications in energy metabolism, including a lower need to stimulate fatty acid oxidation during fasting in the locomotor muscles of snakes compared to other groups.

evolutionary biology↗

bioRxiv2025

PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era

High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic mutational events such as premature stop codons, deletions and insertions. It enables the investigation of cross-species genomic datasets through: (i) integration into automated workflows, (ii) multiprocessing capability, and (iii) creation of a functional reference from annotation files. In addition, we introduce PseudoViz, a novel graphical interface designed to help interpret the results of PseudoChecker2 with intuitive visualizations. These tools combine the versatility and automation of a command-line tool with the user-friendliness of a graphical interface to tackle the challenges of the Genome Era. Availability and implementationPseudoChecker2 and PseudoViz are fully available at https://github.com/rresendepinto/PseudoChecker2 and https://github.com/rresendepinto/PseudoViz.

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

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

A de novo transcriptome assembly of the annelid worm Hediste diversicolor

The development of Next-Generation Sequencing (NGS) technologies has revolutionized multiple fields of Biology. The ability to sequence DNA and RNA in an automated, parallel and low-cost approach, was key to boost the applicability and acquisition efficiency of omics resources. In this context, the availability of these tools has become indispensable towards our understanding of biodiversity, deepening our knowledge on the distinct complexity levels, from cells to ecosystems. In this study we comprehensively characterised and annotated a whole-body transcriptome of Hediste diversicolor. This annelid worm species belongs to the family Nereididae and inhabits estuarine and lagoon areas on the Atlantic coasts of Europe and North America. Ecologically, this species plays an important role in benthic food webs. The ability of rework sediments through bioturbation activity makes this species essential to the estuarine mechanisms. Here, we used Illumina next-generation sequencing technology, to sequence a total 105 million (M) paired-end (PE) raw reads and produce the first multi-tissue transcriptome assembly of an adult of H. diversicolor. This transcriptome contains 69,335 transcripts with a N50 transcript length of 2,313 bp and a BUSCO gene completeness of 97.7% and 96% (S: 88.2%; D: 7.8%) in Eukaryota and Metazoa lineage-specific profile libraries. Our findings offer a valuable resource for multiple biological studies using this species.

genomics↗

bioRxiv2021

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource

The Atlantic chub mackerel, Scomber colias Gmelin, 1789, is a medium-size pelagic fish with substantial importance in the fisheries of the Atlantic Ocean and the Mediterranean Sea. Over the past decade, this species has gained special relevance being one of the main targets of pelagic fisheries in the NE Atlantic. Here, we sequenced and annotated the first high-quality draft genome assembly of S. colias, produced with Pacbio HiFi long reads and Illumina Paired-End short reads. The estimated genome size is 814 Mb distributed into 2,028 scaffolds and 2,093 contigs with an N50 length of 4,19 and 3,34 Mb, respectively. We annotated 27,675 protein-coding genes and the BUSCO analyses indicated high completeness, with 97.3 % of the single-copy orthologs in the Actinopterygii library profile. The present genome assembly represents a valuable resource to address the biology and management of this relevant fishery. Finally, this is the fourth high-quality genome assembly within the Order Scombriformes and the first in the genus Scomber.

genomics↗

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↗

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↗

bioRxiv2019

The dopamine receptor D5 gene shows signs of independent erosion in Toothed and Baleen whales

To compare gene loci considering a phylogenetic framework is a promising approach to uncover the genetic basis of human diseases. Imbalance of dopaminergic systems is suspected to underlie some emerging neurological disorders. The physiological functions of dopamine are transduced via G-protein-coupled receptors, including DRD5 which displays a relatively higher affinity towards dopamine. Importantly, DRD5 knockout mice are hypertense, a condition emerging from an increase in sympathetic tone. We investigated the evolution of DRD5, a high affinity receptor for dopamine, in mammals. Surprisingly, among 124 investigated mammalian genomes, we found that Cetacea lineages (Mysticeti and Odontoceti) have independently lost this gene, as well as the burrowing Chrysochloris asiatica (Cape golden mole). We suggest that DRD5 inactivation parallels hypoxia-induced adaptations, such as peripheral vasoconstriction required for deep-diving in Cetacea, in accordance with the convergent evolution of vasoconstrictor genes in hypoxia-exposed animals. Our findings indicate that Cetacea are natural knockouts for DRD5 and might offer valuable insights into the mechanisms of some forms of vasoconstriction responses and hypertension in humans.

evolutionary biology↗

bioRxiv2019

Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution

The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine receptor (CCR10), which interacts with an epidermal CC chemokine, the skin-specific C-C motif chemokine ligand 27 (CCL27). CCL27 is selectively produced in the skin by keratinocytes, particularly upon inflammation, mediating the adhesion and homing of skin-infiltrating T cells. Here, we examined the evolution and coding condition of Ccl27 in 112 placental mammalian species. Our findings reveal that a number of open reading frame inactivation events such as insertions, deletions, start and stop codon mutations, independently occurred in Cetacea, Pholidota, Sirenia, Chiroptera, and Rodentia, totalizing 18 species. The diverse habitat settings and life-styles of Ccl27-eroded lineages probably implied distinct evolutionary triggers rendering this gene unessential. For example, in Cetacea the rapid renewal of skin layers minimizes the need for an elaborate inflammatory mechanism, mirrored by the absence of epidermal scabs. Our findings suggest that the convergent and independent loss of Ccl27 in mammalian evolution concurred with unique adaptive roads for skin physiology.

evolutionary biology↗

bioRxiv2018

The singularity of Cetacea behaviour parallels the complete inactivation of melatonin gene modules

Melatonin, the hormone of darkness, is a peculiar molecule found in most living organisms. Emerging as a potent broad-spectrum antioxidant, melatonin was repurposed into extra roles such as the modulation of circadian and seasonal rhythmicity: affecting numerous aspects of physiology and behaviour, including sleep entrainment and locomotor activity. Interestingly, the pineal gland--the melatonin synthesising organ in vertebrates--was suggested to be absent or rudimentary in some mammalian lineages, including Cetacea. In Cetacea, pineal regression is paralleled by their unique bio-rhythmicity, as illustrated by the unihemispheric sleeping behaviour and long-term vigilance. Here, we examined the genes responsible for melatonin synthesis (Aanat and Asmt) and signalling (Mtnr1a and Mtnr1b) in 12 toothed and baleen whale genomes. Based on an ample genomic comparison, we deduce that melatonin-related gene modules are eroded in Cetacea.

evolutionary biology↗