Biology subjects

Garcia, C.

Publications and source records attributed to Garcia, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Hippocampal-cingulate dynamics in the human brain link reinforcement-learning and memory

Reinforcement learning (RL) models describe how reward computations shape our choices, but whether the same computations also shape memory in the human brain is unclear. To address this question, we combined multi-areal intracranial recordings with computational modeling of reward and memory in neurosurgical patients. Patients played a gambling task in which decisions yielded monetary rewards tied to trial-unique images, followed immediately by a recognition test for those images. Model-derived positive reward prediction errors (RPEs) predicted later memory for each image. During feedback, multivariate high-frequency activity revealed the spatiotemporal evolution of RPE representations across distributed prefrontal cortex. During subsequent recognition, however, only anterior cingulate cortex (ACC) transiently reinstated RPE representations, and successful recognition specifically associated with hippocampal reinstatement of these ACC representations. Hippocampal-cingulate theta synchrony scaled with RPE during recognition, alongside hippocampal theta decoding of upcoming memory choices. Thus, the RL computations that guide decision-making also shape memory through hippocampal-cingulate circuit dynamics in the human brain.

neuroscience↗

bioRxiv2026

A Social Affordance Framework for Understanding Approach Decisions in Wild Crested Macaques (Macaca nigra)

Approaching conspecifics is a fundamental component of social interactions. Such decisions are typically investigated through the study of social relationships (e.g., kinship, dominance, affiliation) and their impact. In the framework, the role of social affordances, i.e., interaction opportunities arising from the immediate social environment, remains poorly understood. We investigated how context-dependent factors shape approach decisions in wild crested macaques (Macaca nigra) in North Sulawesi, Indonesia. From September 2024 to May 2025, we collected data on 27 adults (20 females, 7 males) using focal observations and an approach-specific protocol recording neighbours identities and behaviours at the initiation of close-proximity approaches (<1 body length). We first compared data collected during approaches with focal data, then conducted within-approach analyses contrasting approached partners and bystanders. We further tested the effects of behavioural state, subgroup size and composition, including infant presence. Bayesian models revealed that affiliative, neutral, and grooming behaviours were more frequent in approach contexts than in general observations. Within approaches, individuals avoided congeners already engaged in grooming and approached individuals in neutral or affiliative states (e.g., lip-smacking, embracing). Macaques globally approached more isolated individuals or dyads. When multiple subgroups were present (i.e., multiple choices), the likelihood of being approached increased with subgroup size and was higher in subgroups containing infants. These findings indicate that macaques use behavioural cues and local social density as affordance signals, adjusting approach decisions to maximize interaction opportunities and navigate complex social environments.

animal behavior and cognition↗

bioRxiv2026

Genomic footprints of selfing, introduction history, and long-distance dispersal in an invasive alien plant

Biological invasions are natural experiments for studying the evolutionary and ecological processes underlying colonization success and range expansion. Using genome-wide data -- generated via genotyping-by-sequencing (GBS) from 30 populations spanning Europe and South Africa-- we investigated the colonization history and successful spread of the invasive buttonweed Cotula coronopifolia, an annual plant introduced into Europe from South Africa about 300 years ago. Our analyses identified three major lineages in Europe distributed across the continent, often co-occurring without evidence of admixture. Phylogenomic dating revealed that these lineages diverged > 2,000 years ago --well before the earliest European records-- suggesting divergence within the native range and either multiple introductions or a single introduction with multiple lineages. Mating-system inference shows that reproduction occurs primarily via self-fertilization ([~]70% on average), although outcrossing predominates in some populations, revealing a facultative mating system. This high selfing rate has led to extremely low heterozygosity in most populations and a strong genetic structure. Genetic clustering also revealed admixed individuals resulting from rare inter-lineage outcrossing; comparisons of empirical and simulated data indicate that increased diversity after sporadic admixture events decays rapidly under subsequent selfing. Both the introduction history and long-distance dispersal facilitated by waterbirds likely explain the scattered distribution of lineages across Europe. Altogether, these results provide an empirical demonstration of Bakers "ideal weed" concept, highlighting the role of a flexible mating system in providing reproductive assurance during colonization and showing how predominant selfing shapes the genomic landscape of an invasive species. SIGNIFICANCE STATEMENTUnderstanding how reproductive strategies influence colonization and spread of alien species is central to invasion biology. By combining population genomics and phylogenomic inference, this study provides key insights into the colonization history and successful invasion of the self-fertilizing plant C. coronopifolia, introduced from South Africa to Europe in the 18th century. We show that the species invasion success relies on the introduction of multiple lineages and the predominance of selfing, which has drastically reduced genetic diversity yet contributed to reproductive assurance and spread across diverse habitats. Occasional outcrossing and long-distance dispersal by waterbirds or through horticultural transport have further shaped the species genetic landscape. These findings illustrate how self-compatibility and ecological generalism can overcome genetic constraints during range expansion and provide the basis for understanding the evolutionary dynamics of selfing plant invasions.

genomics↗

bioRxiv2026

Archaeogenomic and Bioinformatic Analysis of the Columbus Lineage: Evidence from the Counts of Gelves.

The geographical and familial origins of Christopher Columbus have remained a subject of intense historiographical debate for over five centuries. Despite numerous hypotheses, empirical genetic evidence capable of resolving his ancestral history or place of birth has been absent from the literature until now. This study presents the third stage of the first forensic genetic analysis performed on skeletal remains belonging to several direct descendants of Columbus, spanning the 16th to 18th centuries. By applying Massively Parallel Sequencing (MPS) to analyse autosomal, X- and Y- chromosome DNA markers, and integrating the results with multidisciplinary evidence from historical, genealogical, archaeological, and anthropological research implicated in this project, the identification of several individuals founded in the Crypt of Santa Maria de Gracia located in Gelves (Sevilla, Spain) has been achieved. The analysis of their biological relatedness enabled the reconstruction of kinship networks among the individuals interred in the crypt, which, when interpreted in the context of documented genealogical lineages, provides indirect but consistent evidence pointing toward the debated origin of the discoverer.

genetics↗

bioRxiv2026

Hypoxic stress granules trigger immunogenic dormancy in lung cancer

Induction of the MHC class I antigen processing and presentation pathway (C1APP) is a critical part of the IFN-{gamma} response necessary for effective cytotoxic immunity against tumors of epithelial origin1,2. Loss of this response is associated with worse disease outcomes and renders patients refractory to immunotherapies3-6. Without C1APP induction, tumor cells cannot optimally process and present immunopeptides from tumor-associated antigens (TAA) and neoantigens to effector cytotoxic T cells7-9. Here, we show that physiologic levels of hypoxia block induction of the immunoproteasome (IP) and other C1APP components in cancer cells, including human non-small cell lung cancer (NSCLC). In A549 cells, this leads to impaired presentation of more than 73% of detectable immunopeptides, including TAA and neoantigen-derived immunopeptides. This effect is independent of HIF-1 or HIF-2 signaling, protein degradation, autophagy, or stimulus type. Instead, hypoxia induces translational arrest of C1APP mRNAs prior to complete monosome loading, along with sequestration into hypoxia-associated stress granules. This phenomenon is reversible with the epitranscriptomic compound 5-azacytidine. Consistent with these findings, IP expression is excluded from hypoxic regions in most human NSCLC tumors. Together, these results link tumor hypoxia to a state of "immunogenic dormancy" and identify stress granules as a previously unrecognized mechanism of immune escape.

cancer biology↗

bioRxiv2026

Nicotine-driven hyperactivation of larval locomotion

Balance between excitatory and inhibitory activity is essential for nervous system function. Neuroactive substances like nicotine can disrupt this balance and hyperactivate dopaminergic circuits, with combined effects on behavior and neural activity. We use Drosophila larvae to examine nicotine-induced, linked behavioral changes over multiple time scales by integrating high-resolution locomotor analysis with genetic and pharmacological manipulations. Acute nicotine exposure produces concentration-dependent hyperactivity. Manipulations of the dopaminergic system establish dopamine as the main mediator for motor responses, and further exploration establishes the{gamma} lobe of the mushroom body as a key site for nicotine integration. Experiments with long-term and repetitive nicotine exposure suggest sustained circuit excitability. Finally, nicotine exposure history induces nicotine preference, highlighting experience-dependent plasticity contributing to addiction-like behaviors. These results help establish Drosophila larvae as a model organism to elucidate how neuroactive substances reconfigure neural circuits and behavior.

neuroscience↗

bioRxiv2026

5'Untranslated regions provide a versatile toolkit for tunable exogenous protein expression

Transient transfection is widely used for protein expression in heterologous systems, yet uncontrolled overexpression frequently introduces artifacts that confound functional analyses. Although stable cell lines can mitigate these issues, generating lines for multiple constructs or variants is often impractical. Common alternatives, such as DNA titration, altered transfection conditions, or promoter swapping, provide only coarse and inconsistent control of protein abundance. Here, we establish a panel of ten human 5 untranslated regions (5UTRs) as a modular strategy to tune protein expression during transient transfection. Across three soluble proteins and three membrane proteins, these 5UTRs produce a reproducible dynamic range of expression, including fine-grained control of eYFP and the large sensory ion channel TRPA1. Notably, one 5UTR consistently suppresses expression across all proteins tested and alleviates overexpression-associated artifacts, improving functional analysis of a hyperactive channel variant, substantially reducing background in proximity biotinylation assays, and enhancing the specificity of a stress granule marker. In contrast, most 5UTRs enhance expression of the TRPV1 and TRPM8 sensory receptors, improving protein yield in heterologous systems. Together, this work identifies 5UTRs as a compact, versatile, and broadly applicable tool to fine-tune protein abundance, enabling more physiologically relevant and assay-optimized expression in transient transfection experiments. Significance StatementO_LIProtein overexpression remains a pervasive limitation in transient transfection experiments, as commonly used strategies provide coarse, labor-intensive, and often unpredictable control over protein abundance, frequently leading to artifacts or loss of physiological relevance. C_LIO_LIA compact, modular 5UTR toolkit enables fine-grained and scalable control of protein abundance in transient transfection, providing a reproducible dynamic range across soluble and membrane proteins outperforming promoter swapping for continuous tuning of expression levels. C_LIO_LITunable expression improves experimental fidelity across diverse applications, allowing investigators to match protein abundance to specific assay needs, reducing overexpression artifacts, preserving physiological readouts, and enhancing yield when high expression is required. C_LI

biochemistry↗

bioRxiv2026

Genetic Compensation Restores Embryonic Viability in Fatty Acid Synthase Mutants

Fatty acid synthase (FASN) is a key rate-limited, dimeric multi-enzyme complex in the de novo lipogenesis pathway. Each FASN monomer contains seven catalytic domains, which coordinate the stepwise conversion of acetyl-CoA into fatty acids. While FASN has been extensively studied in cultured cells, particularly for its oncogenic role, its functions in the germline and early embryonic development remain elusive. A major challenge is that the FASN dysfunction typically causes embryonic lethality in animal models, which complicates detailed functional analysis and the identification of compensatory genetic interactors during development. To overcome this limitation and identify novel genetic suppressors of the FASN gene, we utilized a temperature-sensitive allele, fasn-1(g43ts) (A1424T), in the genetically tractable model Caenorhabditis elegans, to conduct unbiased forward genetic screens. We isolated 22 suppressor lines that significantly restored embryonic viability in the fasn-1(g43ts) mutant at the non-permissive temperature. Using a combination of MIP-MAP genomic mapping and a customized bioinformatic pipeline, we identified six missense mutations in the ptr-6 gene, which encodes a protein containing a patched domain associated with the Hedgehog signaling pathway. To validate this genetic suppression, we recreated one of the loss-of-function mutations, ptr-6 (W701*), in the fasn-1(g43ts) background using CRISPR/Cas9 gene editing. Notably, ptr-6(W701*) robustly rescued the embryonic lethality and permeability defects caused by fasn-1 loss-of-function. Taken together, our findings expand the genetic regulatory network of fatty acid synthase during early embryogenesis and highlight ptr-6 and Hedgehog signaling pathway as potential genetic modifiers of FASN-associated developmental and metabolic disorders.

genetics↗

bioRxiv2025

'Guess Who?': Forensic genetics and archaeology converge to identify Cristopher Columbus descendants.

The generation of DNA profiles from skeletal remains is a core challenge in forensic genetics, particularly for the identification of missing persons and the resolution of cold cases. Factors such as diagenesis, DNA fragmentation, and the presence of PCR inhibitors severely compromise traditional methodologies, limiting the potential for successful identification. Similarly, in many archaeological studies, the presence of multiple individuals within a single burial site presents a significant challenge for accurate identification. This study shows how the most innovative forensic genetic techniques can be integrated into archaeological research, enabling the identification of individuals through the establishment of familial relationships between remains recovered from an archaeological site. A large-scale SNP assay, Forenseq(R) Kintelligence HT, has been applied to a familial group dating back to the 16th-17th century, allowing robust kinship calculations and lineage studies, that, in a first stage, lead to the identification of four individuals spanning four generations within the same family.

genomics↗

bioRxiv2025

TMEM9 and SEC22B interact with ClC-5 to shape renal proximal tubule function and Dent's Disease type I pathogenesis

Cl-/H+ antiporter ClC-5 is a key regulator of renal proximal tubule function, primarily by controlling endosomal acidification. Loss-of-function mutations in ClC-5 cause Dents Disease type 1 (DD1), a rare renal tubulopathy that progresses to kidney failure with varying severity. To understand the specific mechanisms linking ClC-5 loss-of-function with DD1 phenotypic heterogeneity, three ClC-5 pathogenic mutations (I524K, E527D and V523{Delta}) were investigated using renal proximal tubule epithelial cell lines. We have identified distinct intracellular retention patterns of these ClC-5 mutants, all leading to altered endolysosomal pH and disrupted secretory pathway organization. Through an interactome analysis, we have uncovered several ClC-5 partners including TMEM9, which interacted with all ClC-5 forms. TMEM9 knockdown (KD) recapitulated key DD1 characteristics, like defective endocytosis and epithelial dedifferentiation, but paradoxically enhanced endosomal acidification. The secretory pathway was also altered in cells lacking TMEM9 (e.g. enlarged endosomes, and fragmented Golgi apparatus). A similar phenotype was observed in cells depleted of SEC22B; an R-SNARE that we have found to specifically interact with wild-type ClC-5, but not the mutants. Notably, its deletion impaired ClC-5 trafficking, causing its retention at the Golgi and endosomes. Altogether, our findings highlight the relevance of TMEM9 and SEC22B in ClC-5 function, suggesting them as DD1 pathophysiology modifiers.

cell biology↗

bioRxiv2025

Endothelial Adgrl2 expression and alternative splicing controls the cerebrovasculature

Central nervous system development requires parallel but interrelated processes of neural circuit assembly and vascularization. Intersecting between these two processes, the cell-adhesion G-protein coupled receptor Adgrl2 is expressed in select neuron populations where it has been found to localize and control the assembly of specific synaptic sites. Further, Adgrl2 is found to be expressed in select non-neuronal brain cells, where it is restricted to endothelial cells. Testing for Adgrl2 function in these cells, here we find that endothelial cell specific Adgrl2 deletion results in an impairment in cerebrovascular integrity. To understand how it might be possible for Adgrl2 to function independently in neuronal and endothelial contexts, we analyzed single-cell RNA sequencing datasets for differences in transcriptional identity between these cell classes. Doing so, we find that expression of Adgrl2 mRNA is subject to robust cell type-specific alternative splicing, resulting in distinct isoforms being produced in neurons compared to endothelial cells. Investigating the functional implication of this cell type-specific alternative splicing, we find that forced expression of the neuronal isoform of Adgrl2 in endothelial cells leads to alterations in cerebrovascular properties. Morphologically, endothelial cells with the non-native neuronal Adgrl2 isoform induce the formation of ectopic glutamatergic synaptic contacts onto endothelial cells, indicating alterations in the cell-cell recognition process. Functionally, in direct contrast to endothelial Adgrl2 deletion, this genetic expression switch instead enhances blood-brain barrier integrity. This overly restrictive cerebrovascular function results in dysregulation of blood to cerebrospinal fluid homeostasis, enlargement of brain ventricles, and a higher risk of hydrocephalus. As such, alternative splicing serves as a cell type specific mechanism that provides isoform specific Adgrl2 for discerning functions controlling neural circuit assembly and cerebrovascular homeostasis.

neuroscience↗

bioRxiv2025

Toll-like Receptor 4 Contributes to PCOS-like Metabolic and Reproductive Pathogenesis

Polycystic ovary syndrome (PCOS) is a reproductive disorder with heterogeneous symptoms and severity. Despite extensive research documenting chronic immune dysfunction as a hallmark of PCOS, the specific molecular mechanisms driving immune activation and its connection to the syndromes diverse symptoms remain poorly understood. Emerging evidence suggests that gut-derived bacterial endotoxins, particularly lipopolysaccharide (LPS), may breach the intestinal barriers in PCOS patients and trigger systemic inflammation through Toll-like receptor 4 (TLR4), a pattern recognition receptor of the innate immune system. This study investigated whether TLR4 serves as a critical mechanistic driver of PCOS pathogenesis by examining the effect of genetic TLR4 knockout (TLR4-/-) in a letrozole (LET)-induced mouse model of PCOS. Our results demonstrate that TLR4 deficiency reduces many PCOS-like symptoms, including elevated luteinizing hormone, anovulation, and metabolic dysfunction. TLR4 knockout also preserved estrous cycling and fertility, improved glucose tolerance, maintained gut barrier integrity, and reduced inflammatory markers in LET-treated females. These findings establish TLR4 as a key mediator orchestrating PCOSs multi-system pathology, positioning TLR4 as a critical convergence point rather than affecting individual symptoms in isolation. This novel work reveals that TLR4-mediated inflammation drives multiple PCOS pathologies, opening avenues for targeted anti-inflammatory treatments in women with this disorder. Significance StatementPolycystic ovary syndrome (PCOS) affects up to 15% of reproductive-age women worldwide. This study reveals that TLR4, an innate immune receptor, is key to the pathophysiology of PCOS-like symptoms in female mice. When TLR4 was genetically deleted, mice treated with letrozole to induce PCOS-like symptoms maintained normal weight, glucose regulation, estrous cycling, and fertility. The improvements coincided with preserved gut barrier breakdown and reduced inflammation. These findings identify TLR4 as a key mediator between gut health, immune activation, and PCOS pathophysiology, suggesting that targeting TLR4 could offer new therapeutic approaches for this common but poorly understood syndrome affecting millions of women.

immunology↗

bioRxiv2025

No baby boom of social mammals in European zoos resulting from COVID-19 lockdowns

Most zoo animals are exposed daily to human visitors, which could be a major disturbance on reproduction. Although few studies have examined the relationship between number of births and crowd size by comparing high and low visitor days, the effect of zoo visitors on animal reproduction over longer timescales has been overlooked. We assessed whether number of births in 34 social mammal species hosted in zoos from 23 European countries differed after prolonged periods of closure to the public (COVID-19 lockdowns) as compared with preceding years. An analysis restricted to the periods following the lockdowns and corresponding to any conception during closure (from 2020 to 2022), compared with the same periods in the two previous years (2018 and 2019), showed no effect of zoo closure on number of births, even when considering each species life history traits and whether they were managed under a breeding programme. We found no evidence that a complete and prolonged absence of visitors affected the ability to reproduce in social mammals housed across European zoos. By analysing birth variation in a large sample of mammalian species, this study contributes to a better knowledge of the natality of mammals in captive settings opened to the public.

zoology↗

bioRxiv2025

Refining type and timing of measured crop variables for the calibration of a new winter wheat cultivar in the STICS crop model

Crop models need to be regularly upgraded with parametrization for new cultivars but this requires calibration, which is a major challenge. With winter wheat cultivar Rubisko as a case study, we propose to apply a calibration protocol to estimate the parameters of this new cultivar with multi-trials experimental data. We tested the calibration protocol in different conditions including or not LAI and/or biomass experimental data and we found that the resulting LAI and biomass dynamics strongly diverge. Several key findings emerge from this study: (1) RUE parameters should be excluded from the calibration process, as their critical role in biomass dynamics causes the optimization algorithm to treat them as adjustment parameters, resulting in unrealistic values for multiple parameters; (2) either LAI or biomass variables alone are sufficient for calibration, enabling experimental efforts to focus on one variable rather than both; and (3) the use of a synthetic dataset has facilitated the identification of the optimal type and timing of data collection needed to parameterize a new variety in the model. Moreover, the proposed methodology offers extrapolatable solutions applicable to other contexts (e.g., different models or datasets) and provides guidance on acquiring the most effective dataset for optimal calibration. The unbalanced structure of our dataset also highlighted the need to mobilize other calibration criteria (weighted RMSE) and alternative solutions to bridge the gap between quantitative metrics and empirical visual assessments.

plant biology↗

bioRxiv2024

Glycosomal phosphoenolpyruvate carboxykinase CRISPR/Cas9-deletion and its role in Trypanosoma cruzi metacyclogenesis and infectivity in mammalian host

Trypanosoma cruzi, the causative agent of Chagas disease, possesses glycosomes - unique organelles that house key metabolic enzymes, several of which are promising therapeutic targets. Among them, phosphoenolpyruvate carboxykinase (PEPCK) plays a central role in succinic fermentation, the main pathway for NAD+ regeneration within the organelle. Using CRISPR/Cas9 editing, PEPCK gene was disrupted in T. cruzi, producing single- allele knockout epimastigotes (TcPEPCK-sKO) with reduced enzyme activity. This disruption impaired glucose consumption and mitochondrial respiration, particularly oxidative phosphorylation, reducing dependence on mitochondrial ATP production. To compensate, pyruvate phosphate dikinase was upregulated, increasing alanine production, possibly to maintain redox balance. Although TcPEPCK-sKO epimastigotes exhibited a minor reduction in growth, their differentiation (metacyclogenesis) and invasion were severely compromised. However, once inside the host cell, TcPEPCK-sKO amastigotes increased their replication, leading to enhanced trypomastigote production. The same was observed in in vivo infection, where TcPEPCK-sKO infection in IFN{gamma}-deficient mice caused uncontrolled parasitemia and severe pathology, highlighting the PEPCK critical role in host-pathogen interactions. However, an intact immune system effectively contained TcPEPCK-sKO infection. Taken together, our findings demonstrate that PEPCK is crucial for T. cruzi energy metabolism, enabling the parasite differentiation within the insect vector and controlling the infection of mammalian host cells.

microbiology↗

bioRxiv2024

Oncogenic GNAQ/11-induced remodeling of the IP3/Calcium signaling pathway protects Uveal Melanoma against Calcium-driven cell death

Despite being considered a rare tumor, uveal melanoma (UVM) is the most common adult intraocular malignancy. With a poor prognosis and limited treatment options, up to 50% of patients develop metastases, primarily in the liver. A range of mutations and chromosomal aberrations with significant prognostic value has been associated with UVM pathogenesis. The most frequently mutated genes are GNAQ and GNA11, which encode the subunits of Gq proteins and are described as driver mutations that activate multiple signaling cascades involved in cell growth and proliferation. Directly downstream of Gq/11 activation, PLC{beta} engagement leads to sustained production of DAG and IP3. While the DAG/PKC/RasGRP3/MAPK signaling branch has been identified as an essential component of UVM unregulated proliferation, the role of IP3-mediated signals has been largely overlooked. Here, we demonstrate that, whilst maintaining Ca{superscript 2} homeostasis, UVM cells have developed a decoupling mechanism between IP3 and ER Ca{superscript 2} release by altering IP3 receptor (IP3R) expression. This correlation was observed in human UVM tumors, where IP3Rs were found to be downregulated. Critically, when IP3R3 expression was restored, UVM cells exhibited an increased tendency to undergo spontaneous cell death and became more sensitive to pro-apoptotic modulators of IP3R-mediated Ca{superscript 2} signaling, such as staurosporine and the Bcl2-IP3R disrupter peptide BIRD2. Finally, inhibition of the Gq/11 signaling pathway revealed that IP3R expression is negatively regulated by GNAQ/11 oncogenic activation. Hence, we demonstrated that by remodeling IP3R expression, GNAQ/11 oncogenes protect UVM cells against IP3-triggered Ca{superscript 2} overload and cell death. Therefore, the GNAQ/11 pathway not only drives proliferation through DAG activity but also provides a protective mechanism to evade IP3/Ca{superscript 2}-mediated cell death. These dual functions could potentially be exploited in novel combinatorial therapeutic strategies to effectively block UVM cell proliferation while simultaneously sensitizing them to cell death.

cancer biology↗

bioRxiv2024

THE FIRST COMPREHENSIVE FORENSIC GENETIC STUDY OF A MEMBER OF CHRISTOPHER COLUMBUS' FAMILY: HIS GREAT-GREAT-GRANDSON

The present study has successfully obtained genetic information that allow the identification from direct descendants of Christopher Columbus, dating from 1526 to 1734. This represents the first achievement of this unique objective. The results obtained from the analysed samples, characterized by their significant antiquity, yield exceptional insights into forensic genetics and its newest protocols and methodologies applied to the study of ancient skeletal remains. This work presents the preliminary results of the whole family study using massive parallel sequencing, focusing on the autosomal Single Nucleotide Polymorphism (SNP) and Short Tandem Repeats (STR) markers, including their flanking region sequences, as well as ancestry informative markers (AIMS) of the great-great-grandson of the discoverer. The results of this project pave the way towards the application of new sequencing technologies for the study of genetic evolution, biogeographical origins and forensic identification of historical characters.

genomics↗

bioRxiv2024

The molecular arsenal of the key coastal bioturbator Hediste diversicolor faced with changing oceans

The importance of infaunal bioturbators for the functioning of marine ecosystems cannot be overstated. Inhabitants of estuarine and coastal habitats are expected to show resilience to fluctuations in seawater temperature and pH, which adds complexity to our understanding of the effects of global change drivers. Further, stress responses may be propagated through chemical cues within and across species, which may amplify the costs of life and alter species interactions. Research into the molecular mechanisms underlying this resilience has been limited by a lack of annotated genomes and associated molecular tools. In this study, we present the first chromosome-level, annotated draft genome of the marine ragworm Hediste diversicolor, specifically mapping genes important for chemical communication, sensing and pH homeostasis. Using these resources, we then evaluate the transcriptomic and behavioural responses of two distinct populations -- one field-sampled from Portugal (Ria Formosa) and one laboratory-acclimated and -bred from the United Kingdom (Humber) -- to changes in seawater pH, temperature, and odour cues from a low pH-stressed predator. Both populations displayed adaptive responses to future oceanic conditions, with targeted acid-base regulation in the Ria Formosa population experiment, and broader changes in metabolism and growth genes in the Humber population experiment. Chemical cues from stressed fish predators induced genes related to Schreckstoff biosynthesis in ragworms. Additionally, under future ocean conditions including increased temperature, the Humber population exhibited signs of cellular stress and damage. Our findings using the new annotated genome offer novel insights into the molecular arsenal of acid-base regulation which aids in predicting the impacts of an increasingly acidified and unstable ocean, and to transfer this knowledge to investigate these mechanisms in species with less tolerance.

genomics↗