Biology subjects

Pascual, M.

Publications and source records attributed to Pascual, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Urinary extracellular vesicles reveal a sex-specific miRNome profile in alcohol use disorder patients

miRNA-based transcriptomic analysis of extracellular vesicles (EVs) provide a promising strategy for identifying non-invasive biomarkers and understanding complex pathological mechanisms. Recently, however, urinary extracellular vesicles (uEVs) have emerged as a valuable window into molecular alterations. Despite the high morbidity and mortality associated with alcohol use disorder (AUD), the molecular mechanisms underlying its sex-specific differences remain poorly understood. To address this, we characterize for the first time the uEV miRNome in AUD, revealing its sexually dimorphic profile. We employed uEVs from actively drinking AUD patients of both sexes who did not have advanced liver disease, alongside matched controls. Deep sequencing revealed 14 differentially expressed miRNAs in females (e.g., hsa-miR-197-3p, hsa-miR-19b-3p, hsa-miR-505-3p, hsa-miR-625-5p, and hsa-miR-27a-5p) and 6 in males (e.g., hsa-miR-1290, hsa-miR-1246, hsa-miR-450a-5p, and miR-590-5p). Notably, whereas hsa-miR-4787-5p was consistently overexpressed in uEVs from both sexes, it was absent in plasma-derived EVs, highlighting the specificity of the urinary compartment. Remarkably, the miRNA signatures we uncovered reflect the multiorgan impact of AUD. For instance, hsa-miR-1290 and hsa-miR-197-3p point to alcohol-related liver injury and systemic inflammation, whereas hsa-miR-19b-3p and hsa-miR-1246 signal neuroinflammation and neuronal stress. A subset--including hsa-miR-1290, hsa-miR-1246, and hsa-miR-27a-5p--has been implicated in cancer contexts. Collectively, these findings support the uEV miRNome as a promising sex-informed molecular signature of AUD with biomarker and mechanistic relevance.

cell biology↗

bioRxiv2026

Tipping points are typical in ecosystems with higher-order interactions

Whether species-rich communities erode gradually or collapse abruptly under environmental change is a central question in ecology [1]. Classical pairwise theory predicts that coexistence is always lost gradually, through smooth declines to extinction [2], yet real ecological interactions are often strongly state-dependent - shaped by nonlinearities that fixed pairwise coefficients cannot capture [3]. Here we show that higher-order (nonlinear) interactions make abrupt, irreversible loss of coexistence a typical route to community collapse: across diverse random communities, the equilibrium supporting coexistence disappears suddenly at a fold bifurcation. Using polynomial homotopy continuation [4] to track equilibria as environmental conditions change, we find that folds progressively dominate the boundary of the coexistence domain as nonlinearity strengthens, replacing the gradual extinctions of pairwise theory. Furthermore, the sign structure of higher-order interactions controls both the onset of tipping-points and whether biodiversity buffers or amplifies collapse. Because higher-order and nonlinear interactions are intimately linked, tipping points also arise generically in pairwise models with strong nonlinearity. Applying our continuation framework to a canonical model of plant-pollinator collapse [5], we formally resolve its bifurcation structure as fold-mediated, and we show that fold bifurcations are typical across published multispecies models spanning mutualistic, competitive, and consumer-resource interactions. These results challenge the expectation that monitoring abundances suffices to anticipate collapse, and unify structural-stability theory, which delineates the safe operating space for coexistence, with critical transition theory, which characterizes the nature of its boundaries.

ecology↗

bioRxiv2026

Humidity shapes the thermal niche of Anopheles stephensi,an invasive malaria vector

Vector-borne pathogens cause 17% of all human infectious diseases, and rising global temperatures are shifting the distribution and abundance of mosquito vectors. Because mosquitoes are ectotherms, temperature strongly governs biological rates and physiology; however, mosquitoes also experience other environmental factors that may interact with temperature to shape the thermal performance of traits driving population dynamics. Here, we use a factorial life-table experiment spanning five relative humidities (30-90%) and seven temperatures (16-38{whitebullet}C) to show that humidity modifies the thermal performance of key fitness traits in adult Anopheles stephensi, an invasive urban malaria vector. When integrated into a demographic model, humidity markedly reshapes projections of population fitness relative to temperatureonly models, suppressing growth and contracting year-round suitability in hot, arid regions while enhancing fitness in more humid or high-elevation climates characteristic of South Asia and Africa. Together, these results highlight the need to integrate multiple environmental drivers into projections of climatic suitability, as temperature-only approaches may mischaracterize both the magnitude and spatial structure of mosquito population fitness. More broadly, our findings demonstrate how moisture availability reshapes thermal niches, population fitness, and climate-driven projections of vector distributions.

ecology↗

bioRxiv2025

Multi-omics integration reveals sex-based differences in the circulating extracellular vesicle lipidome and miRNome of alcohol use disorder patients

Integrated multi-omics and extracellular vesicle (EV) analysis are emerging as powerful, complementary strategies for biomarker discovery. These approaches offer promising tools to enhance early detection, diagnosis, and treatment of alcohol use disorder (AUD). Here we applied an integrated miRNomic and lipidomic approach to analyze plasma EVs from AUD patients and controls of both sexes to gain a comprehensive understanding of the underlying molecular mechanisms. We identified an AUD signature with predictive potential for diagnostic applications. Individual features (e.g., hsa-miR-99b-3p, hsa-miR-556-5p, Cer_NDS-d39:1, and PI18:0_18:2) represented important components; however, the strength of this signature lay in the combined profile rather than isolated markers. We also revealed an AUD-sex signature that provided insight into how biological responses to alcohol differ between females and males (including features such as hsa-miR-1301-3p and PC39:4), which also underscored the power of multi-omic integration. The individual miRNome approach also revealed an opposite functional alteration by sex in various alcohol related systems, such as pathways associated with immunity, oxidative stress, and autophagy. An open-access Shiny web application (https://carpercle.shinyapps.io/SexEVEthOmics/) accompanies this study, providing interactive access to the complete dataset and additional analyses for customized exploration. Together, our findings underscore the added value of multi-omics integration in identifying clinically relevant molecular signatures of disease; this sex-informed approach offers a promising path toward more personalized diagnostic tools and therapeutic strategies in AUD.

bioinformatics↗

bioRxiv2025

Evolutionary trade-offs between functional and immune selection shape multigene families in pathogens

Major surface antigens in many pathogens are encoded by rapidly diversifying multigene families, generating fitness variation through antigenic and functional differences. These variations align with the niche and absolute fitness axes of Modern Coexistence Theory (MCT). Yet, how such gene families evolve along these axes under competition for hosts and across transmission gradients remains poorly understood, as prior MCT studies have not explicitly accounted for evolutionary dynamics in high dimensions. We use a stochastic computational model of Plasmodium falciparum transmission to examine how transmission intensity and selection shape var multigene family evolution and composition within parasite genomes. Results show that selection alone cannot maintain the observed stable ratio of two gene groups within parasite genomes, indicating that group-based classifications do not clearly reflect transmission strategy or virulence. When a trade-off exists between diversification rates and absolute fitness, strong immune selection under high transmission favors fast-recombining genes while attenuating functional selection on R0-associated traits. In general, stronger immune selection increases the invasion probability of novel antigens and the niche differentiation among parasite genomes, while reducing the variance in gene-level transmissibility and expression duration, and therefore R0. This outcome, combining enhanced niche differentiation and reduced absolute fitness variation, departs from MCT predictions.

evolutionary biology↗

bioRxiv2025

Deciphering lipidomics landscape of urine extracellular vesicles in alcohol use disorder patients

Urine extracellular vesicles (EVs) have garnered increasing interest in recent years as, in combination with their lipid content, they represent a potential source of non-invasive biomarkers. Alcohol use disorder (AUD) is one of the most common psychiatric disorders and a significant contributor to morbimortality. Thus, there is growing interest in assessing previous alcohol consumption and evaluating the severity of liver or brain injury, particularly via non-invasive methods. Here, we employed a novel approach based on urine EVs and a highly sensitive lipidomics strategy to characterize lipid species in male AUD patients, as well as to evaluate the differential functional roles and enzymatic activity networks of urine EV lipids. Our results show, for the first time, that the lipidomic profiling of urine EVs in AUD males is characterized by an enrichment of fatty acyls and glycerophospholipids, with FA 22:0 emerging as a potential biomarker. Notably, increased acyl chain saturation and elevated long-chain fatty acids (22-24 carbons) suggest links to AUD-associated inflammation, cancer, and metabolic dysfunction. These findings support an improved understanding of the urine EV lipidome, which could contribute to the identification of novel lipid targets and the discovery of non-invasive biomarkers in AUD.

pathology↗

bioRxiv2025

Beyond temperature: Relative humidity systematically shifts the temperature dependence of population growth in a malariavector

Understanding ectotherm responses to environmental change is central to coping with many of humanitys current and future challenges in public health, biodiversity conservation, and food security. Complex relationships between abiotic and biotic factors can influence ectotherm abundance and distribution patterns by introducing stage-specific variation in fitness trait responses. Variation in temperature, rainfall, competition, and habitat have all been considered in previous attempts to understand how environmental factors can interact and vary in their relative influence on species maximal population growth rates, rm. However, the combined effects of temperature and humidity on this fundamental metric are poorly understood. We show that variation in relative humidity can influence juvenile trait responses and rms temperature dependence in Anopheles stephensi, an important malaria vector. Our climate suitability maps show that the interactive effects of temperature x humidity on juvenile traits have important implications for predicting how environmental change will influence arthropod-mediated systems.

ecology↗

bioRxiv2025

Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe-Virus Coevolutionary System

Microbial host populations evolve traits conferring specific resistance to viral predators via various defense mechanisms, while viruses reciprocally evolve traits to evade these defenses. Such co-evolutionary dynamics often involve diversification promoted by negative frequency-dependent selection. However, microbial traits conferring competitive asymmetries can induce directional selection, opposing diversification. Despite extensive research on microbe-virus co-evolution, the combined effect of both host trait types and associated selection remains unclear. Using a CRISPR-mediated co-evolutionary system, we examine how the co-occurrence of both trait types impacts viral evolution and persistence, previously shown to be transient and non-stationary in computational models. A stochastic model incorporating host competitive asymmetries via variation of intrinsic growth rates reveals that competitively-advantaged host clades generate the majority of immune diversity. Greater asymmetries extend viral extinction times, accelerate viral adaptation locally in time, and augment long-term local adaptation. These findings align with previous experiments, and provide further insights into long-term co-evolutionary dynamics.

evolutionary biology↗

bioRxiv2025

Negative frequency-dependent selection contributes to modular structure of effector repertoires in Pseudomonas syringae

The evolutionary fate of multi-strain pathogens is shaped by host-pathogen ecological interactions. In bacterial pathogens of plants, enhanced strain characterization and advances in our understanding of molecular mechanisms underlying defense pathways open the door for revisiting the role of negative frequency-dependent selection (NFDS) in strain structure, including its interplay with genetic exchange. NFDS arising from specific defense is one potential mechanism for generating, maintaining, and structuring pathogen diversity. In plants, specific protection against microbial pathogens involves Resistance proteins (R-proteins) that recognize virulence factors (effectors) secreted by pathogens, typically to subvert the initial line of host defense. Here we formulate a stochastic computational co-evolution model that explicitly incorporates variable length R-gene and effector repertoires, and migration from their regional pools. We use this model to understand potential mechanisms shaping effector repertoire structure and associated strain coexistence in the generalist plant pathogen P. syringae. The demonstration of a modular structure in our numerical simulations motivates the analysis of genome sequences from 76 strains collected in the Midwestern US and 1104 strains from global sources. We find that effector repertories both locally and globally exhibit a modular structure, with higher similarity within than between clusters. The observed modules are consistent with the core genome phylogeny and are unexplained by plant host species, location of isolation, and genetic linkage between effectors. An extension of the model is needed to take into account the evidence for genetic exchange and the phylogenetic congruence of effector modules. We initialize the system with a phylogenetically congruent modular structure and include recombination rates decreasing as a function of phylogenetic distance. We show that NFDS can counter-balance the effects of mixing due to recombination and in so doing, contributes to the maintenance of strain structure. These findings indicate that the observed similarity clusters may constitute, in part, emergent niches arising from eco-evolutionary dynamics that contribute to strain coexistence.

ecology↗

bioRxiv2024

Unveiling the role of miRNAs from MSC-EVs in neuroinflammation and behavioral impairments induced by chronic alcohol consumption

Extracellular vesicles derived from mesenchymal stromal cells (MSC-EVs) have emerged as a promising form of regenerative and immunomodulatory therapy; indeed, micro (mi)RNAs contained within MSC-EVs modulate target gene expression and impact disease-associated pathways. Chronic alcohol consumption results in neuroinflammation, brain damage, and impaired cognition; in this study, we asked whether the repeated intravenous administration of MSC-EVs could ameliorate neuroinflammation and behavioral impairment induced by chronic alcohol consumption in mice. MSC-EVs diminished the increased binding of a micro-positron emission tomography tracer (18F-FDG) when analyzing whole-brain 3D images and brain coronal sections of ethanol-treated mice. MSC-EV administration protected against ethanol-induced proinflammatory gene upregulation, cognitive dysfunction, and addictive-like behavior. miRNA sequencing data from MSC-EVs helped to reveal the elevated expression of EV-derived miR-483-5p and miR-140-3p in the brains of ethanol-treated mice following MSC-EV administration. In addition, MSC-EVs modulated the expression of pro-inflammatory-related miRNA target genes (e.g., Socs3, Tnf, Mtor, Atf6) in the brains of ethanol-treated mice. These results suggest that MSC-EVs could function as a neuroprotective therapy to ameliorate the neuroinflammation, cognitive dysfunction, and addictive-like behavior associated with chronic alcohol consumption.

neuroscience↗

bioRxiv2024

Unravelling the impact of TLR4 and sex on chronic alcohol consumption-induced lipidome dysregulation in extracellular vesicles

The lipids that form extracellular vesicles (EVs) play critical structural and regulatory roles, and cutting-edge bioinformatics strategies have shown the ability to decipher lipid metabolism and related molecular mechanisms. We previously demonstrated that alcohol abuse induces an inflammatory immune response through Toll-like receptor 4 (TLR4), leading to structural and cognitive dysfunction. This study evaluated how TLR4 and sex as a variable (male/female) impact the lipidome of plasma-resident EVs after chronic alcohol exposure. Using a mouse model of chronic ethanol exposure in wild-type and TLR4-deficient mice, enrichment networks generated by LINEX2 highlighted significant ethanol-induced changes in the EV lipid substrate-product of enzyme reactions associated with glycerophospholipid metabolism. We also demonstrated ethanol-induced differences in Lipid Ontology enrichment analysis in EVs, focusing on terms related to lipid bilayer properties. A lipid abundance analysis revealed higher amounts of significant lipid subclasses in all experimental comparisons associated with inflammatory responses and EV biogenesis/secretion. These findings suggest that interrogating EV lipid abundance with a sensitive lipidomic-based strategy can provide deep insight into the molecular mechanisms underlying biological processes associated with sex, alcohol consumption, and TLR4 immune responses and open new avenues for biomarker identification and therapeutic development.

neuroscience↗

bioRxiv2023

Emerging role of mesenchymal stem cell-derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence

NOD-like receptors are innate immunity sensors that provide an early and effective response to pathogenic or injury conditions. However, abnormalities in these receptors may cause excessive inflammation. Our studies have reported that an activation of the NLRP3-inflammasome complex in ethanol-treated astrocytes and in chronic alcohol-fed mice could be associated with neuroinflammation and brain damage. Considering the therapeutic role of the molecules contained in the extracellular vesicles (EVs) derived by mesenchymal stem cells (MSC-EVs), the present study aims to evaluate whether the intravenous administration of MSC-EVs from adipose tissue, through inhibiting the NLRP3 inflammasome activation, is capable of reducing hippocampal neuroinflammation in adolescent mice treated with binge drinking. We demonstrate that MSC-EVs ameliorate the activation of the hippocampal NLRP3 inflammasome complex and other NLRs inflammasomes (e.g., NLRP1, NLRC4 and AIM2), as well as the alterations of inflammatory genes (IL-1{beta}, IL-18, iNOS, NF-{kappa}B, MCP-1 and CX3CL1) and miRNAs (miR-21a-5p, miR-146a-5p and miR-141-5p) induced by binge-like ethanol treatment in adolescent mice. Bioinformatic analysis further revealed the involvement of miR-21a-5p and miR-146a-5p with inflammatory target genes and NOD-like receptor signaling pathways. Taken together, these findings provide, for the first time, evidence of the therapeutic potential of MSC-derived EVs to restore the hippocampal neuroinflammatory response through the NLRP3 inflammasome activation induced by binge drinking in adolescence.

neuroscience↗

bioRxiv2023

Novel role of Periploca laevigata extracts as anti-diabetic and anti-inflammatory function in pancreatic β cells exposed to hyperglycaemia

Type 2 Diabetes (T2D) is a major health problem worldwide. This metabolic disease is associated with high blood glucose levels due to insufficient insulin production by the pancreas, leading to an inflammatory immune response. Considering the beneficial roles of medicinal plants to control the diabetic complications of T2D, as well as the therapeutic roles of the extracts from Periploca laevigata (PL), this study evaluates the anti-diabetic and anti-inflammatory properties of PL extracts in the pancreatic {beta} cell line INS-1E under hyperglycaemic. Our findings demonstrated, for the first time, that whereas PL extracts tends to upregulate the insulin gene expression, PL extract from leaves increase significantly the gene expression of GLUT-2 and the transcription factor PDX-1 in glucose-treated INS-1E cells. Notably, some PL extracts are also capable to decrease significantly the gene expression of iNOS and to increase the IL-10 gene expression in glucose-treated INS-1E cells. However, the PL extracts show a tendency to decrease the gene expression of NF-kB and MCP-1 in glucose-treated INS-1E cells. In conclusion, our findings suggest that the treatment with PL extracts could benefit the pancreatic {beta} cell function and alleviate the pancreatic inflammation, thereby representing potential advantages of the glucose metabolism in the T2D.

physiology↗

bioRxiv2023

A paradoxical population structure of var DBLα types in Africa

The var multigene family encodes the P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology of P. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBL-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBL types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm, cUps, we performed an in silico exploration of DBL conservation through time and space in Africa. In all three ups groups, the population structure of DBL types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBL types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBL types within each isolate DBL repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBL types in Africa.

genetics↗

bioRxiv2023

Oleoylethanolamide effects on stress-induced alcohol consumption: a lipid at crossroads between stress, reward and neuroinflammation

The endocannabinoid system is involved in multiple drug-related behavior as well as in the stress response. The transient increase in endogenous cannabinoids as well as endocannabinoid-like molecules contributes to healthy adaptation to stress exposure. In this study, we tested the effect of systemic OEA treatment (10mg/kg) before or after social defeat (SD) on alcohol self-administration (SA). Mice were divided into non-stressed (EXP) and stressed mice (SD) and randomly assigned to a treatment condition (CTRL, OEA or 10OEA). Mice in the EXP/SD-OEA group received four doses before each SD encounter while mice in the EXP/SD-10OEA mice received 10 daily doses after stress exposure. Three weeks after SD, mice were trained to alcohol 20% (vol/vol) SA. Upon extinction, a cue-induced reinstatement test was performed. Our results showed that only multiple-dose chronic OEA treatment (SD-10OEA group) was effective in preventing the stress-induced increase in alcohol consumption observed in defeated mice. We did not observe any effects of OEA on relapse-like behavior. Altogether, these data suggest that exogenously increasing OEA levels counteracts the adverse effects of stress on alcohol drinking.

animal behavior and cognition↗

bioRxiv2023

Region-specific gene expression changes associated to oleoylethanolamide-induced attenuation of alcohol self-administration

Oleoylethanolamide (OEA) is a lipid with anti-inflammatory activity that modulates multiple reward-related behaviors. Previous studies have shown that OEA treatment reduces alcohol self-administration (SA) while inhibiting alcohol-induced inflammatory signaling. Nevertheless, the specific mechanisms that OEA is targeting to achieve these effects have not been widely explored. Here, we tested the effects of OEA treatment during alcohol SA, extinction or previous to cue-induced reinstatement of alcohol seeking. In addition, we measured gene expression changes in the striatum and hippocampus of relevant receptors for alcohol consumption (DrD1, DrD2, CNR1, OPRM1) as well as immune-related proteins (IL-6, IL-1{beta}, TLR4) and the brain-derived neurotrophic factor (BDNF). Our results confirmed that when administered contingently, systemic OEA administration reduced alcohol SA and attenuated cue-induced reinstatement. Interestingly, we also observed that OEA treatment reduced the number of sessions needed for extinction of alcohol seeking. Biochemical analyses showed region-specific OEA dopaminergic and cannabinoid receptor gene expression alterations. Also, OEA treatment modulated the long-term immune response and increased BDNF expression. These results suggest that boosting OEA levels may be an effective strategy for reducing alcohol SA and preventing relapse.

neuroscience↗

bioRxiv2023

Lipid network of plasma extracellular vesicles reveals sex-based differences in the lipidomic profile from patients with alcohol use disorder

Alcohol use disorder (AUD) is one of the most common psychiatric disorders, and the consumption of this substance is considered one of the main causes of preventable deaths worldwide. Lipids play a crucial functional role in cell membranes, however little is known about the role of lipids containing extracellular vesicles (EVs), as regulatory molecules and biomarkers. In this study, a highly sensitive lipidomic strategy is employed to characterize plasma EV lipid species from individuals with AUD, to evaluate differential functional roles and enzymatic activity networks to improve the knowledge of lipid metabolism in the alcohol consumption. Plasma EV lipids from female and male patients with AUD and healthy individuals were analyzed to obtain lipid differential abundance, as well as biological interpretation of LINEX2 lipidomics data, evaluating enzymatic dysregulation through an enrichment algorithm. Our results showed for the first time that females with AUD exhibit greater substrate-product changes in LPC and PC lipids, as well as phospholipases and acyltransferases activity, potentially linked to cancer progression and neuroinflammation. Conversely, males with AUD showed dysregulation in Cer and SM lipid, involving sphingomyelinases, sphingomyelin phosphodiesterase, and sphingomyelin synthase, which could be related with hepatotoxicity. Notably, females with AUD showed LION-terms associated with "positive intrinsic curvature", while males exhibited "negative intrinsic curvature, contributing to vesicle fusion processes. These methodological developments allow a better understanding of lipid metabolism and its regulatory mechanisms, which contributes not only to identify novel lipid targets, but also the discovery of sex-specific clinical biomarkers in the AUD.

pathology↗

bioRxiv2022

Evaluating restriction enzyme selection for genome reduction in conservation genomics

Conservation genomic studies in non-model organisms generally rely on genome reduction techniques based on restriction enzymes to identify population structure as well as candidate loci for local adaptation. These reduced libraries ensure a high density of SNP loci and high coverage for accurate genotyping. Despite the fraction of the genome that is sequenced is expected to be randomly located, the reduction of the genome might depend on the recognition site of the restriction enzyme used. Here, we evaluate the distribution and functional composition of loci obtained after Genotyping-by-sequencing (GBS) genome reduction with two widely used restriction enzymes (EcoT22I and ApeKI). To do so, we compared data from two endemic fish species (Symphodus ocellatus and Symphodus tinca, EcoT22I enzyme) and two ecosystem engineer sea urchins (Paracentrotus lividus and Arbacia lixula, ApeKI enzyme). In brief, we mapped the sequenced loci to the phylogenetically closest reference genome available (Labrus bergylta for fish and Strongylocentrotus purpuratus for sea urchins), classified them as exonic, intronic, and intergenic, and studied their functionality by using GO terms. We detected an enrichment towards exonic or intergenic regions depending on the restriction enzyme used, and we did not detect differences between total loci and candidate loci for adaptation. Despite most GO terms being shared between species, the analysis of their abundance showed differences between taxonomic groups, which may be attributed to differences of the targeted loci. Our results highlight the importance of restriction enzyme selection and the need for high-quality annotated genomes in conservation genomic studies.

genomics↗