Biology subjects

Rey, O.

Publications and source records attributed to Rey, O..

11 recordsLinked to original sources

bioRxiv2026

Decoupling epigenetic variation from genetic variation reveals complementary dimensions of coral eco-evolutionary dynamics

Understanding how intraspecific diversity is structured is essential for predicting the eco-evolutionary trajectories of populations, especially under rapid environmental change. While such diversity has been extensively studied from a genetic perspective, much less is known about the distribution and ecological relevance of epigenetic variation within natural populations. To address this question, we focused on two species of reef-building corals belonging to distinct functional groups, Pocillopora acuta and Acropora hyacinthus, sampled across the South Pacific (New Caledonia, Fiji, French Polynesia). Using genome-wide Enzyme-Methyl sequencing, we jointly analyzed genetic (SNPs) and DNA methylation (CpGs) variation, while explicitly disentangling genetically associated from genetically independent epigenetic variation. Genetic and epigenetic structure showed contrasting spatial patterns, reflecting distinct temporal and ecological components of population dynamics. Genetic structure was strongest between archipelagos and followed an isolation-by-distance pattern consistent with long-term evolutionary processes. In contrast, epigenetic variation converged between colonies from different archipelagos. At finer spatial scales within archipelago, genetically independent epigenetic variation exhibited stronger structure than both genetic and genetically associated epigenetic variation, likely reflecting local environmental conditions. Together, our results show that genetic and epigenetic variation provide complementary insights into the eco-evolutionary processes shaping intraspecific diversity.

evolutionary biology↗

bioRxiv2026

Environmental RNA improves detection and surveillance of schistosomiasis transmission

Environmental diagnosis of schistosomiasis, a tropical disease affecting more than 250 million people globally, is still challenging, which limits efficient eradication plans. There is a crucial need for resolutive and highly sensitive environmental tools to improve disease control. However, a major obstacle is the inability of current methods, including environmental DNA (eDNA), to distinguish infectious parasite life stages. Here, we develop and validate an environmental RNA (eRNA) approach that enables the detection and absolute quantification of Schistosoma mansoni miracidia and cercariae directly from water samples. After identifying life stage-specific transcripts, we design specific ddPCR assays which are strongly specific to S. mansoni and to each life stage. Comparing with eDNA assays, laboratory experiments demonstrate that stage-specific eRNA assays accurately reflect the relative abundance of each life stage, detect nucleic acids released from organisms, exhibit detection limits tenfold lower than eDNA assays. Also, under laboratory conditions, RNA persists in water longer than DNA. Field validation at six endemic sites in Brazil confirms that eRNA outperforms eDNA and conventional snail surveys in detecting active presence of S. mansoni cercariae, which indicates schistosomiasis transmission risk to humans locally. By enabling active-stage discrimination in environmental monitoring and improving sensitivity (compared to eDNA), our study advances both fundamental understanding and applied surveillance of schistosomiasis transmission, supporting elimination initiatives in affected regions.

ecology↗

bioRxiv2025

Non-invasive eDNA reveals the ecological and genetic status of the Western Capercaillie (Tetrao urogallus aquitanicus) in the Eastern Pyrenees

The Anthropocene era is expected to bring about significant biodiversity and habitat loss for many species. These geographical changes, whether driven by climatic or anthropogenic factors, are likely to lead to considerable alterations in population size, structure, and genetic diversity. Monitoring natural populations is therefore essential to assess these impacts and enable informed conservation strategies for threatened species. The Western Capercaillie (Tetrao urogallus, L. 1758) has a widespread distribution in Boreal forests but fragmented in mountainous regions of the Palearctic, and is locally threatened by climate change, habitat destruction, and human disturbance. Our study focused on the eastern population of the subspecies T. u. aquitanicus, which is endemic to the Pyrenees mountains. The monitoring of this population has relied on direct methods and no genetic information had been generated so far. Here, we conducted a molecular study based on 229 non-invasive samples (faeces) to assess the ecological and genetic status of local population in the Catalan Nature Reserves of the Pyrenees-Orientales (Occitanie region, France). At the individual level, we assessed multi-locus genotypes, sexing, levels of inbreeding, stress level (Fecal Corticosterone Metabolites; FCMs) and diet. At the population level, we assessed sex ratio, genetic diversity and structure. We identified 62 individuals with a balanced sex ratio and estimated a census size of 79 individuals [95%CI = 68-92] in the study area. Genetic diversity was low and suggested significant inbreeding levels. FCM levels were lower in birds of areas considered as disturbed by humans and metabarcoding approach indicated a geographical structuring of diet composition at the reserve scale, with individuals exhibiting feeding behavior upon only one or few plant species. Our estimate of population census size was higher with figures assessed from lek counts, and the genetic approach provided additional insights on this population, establishing a baseline that will support conservation management plans.

ecology↗

bioRxiv2024

Transcriptomic plasticity in hybrid schistosomes can contribute to their zoonotic potential

Hybrids between Schistosoma haematobium and S. bovis are linked to both human and animal infections, highlighting the complex interspecies interactions that contribute to the spread of schistosomiasis. Additionally, S. bovis can infect multiple ruminant hosts, facilitating cross- species transmission and increasing the risk of zoonotic outbreaks. In this study, we investigated transcriptomic plasticity as a potential mechanism enabling hybrid schistosomes to adapt to alternative definitive hosts. We focused on two contexts: 1) introgressed S. haematobium x S. bovis hybrids, which demonstrated higher virulence in sheep compared to parental S. bovis, and 2) S. bovis infecting different host species. Our analysis uncovered 366 differentially expressed genes (DEGs), representing 4% of the total protein-coding genes, between introgressed hybrids and parental S. bovis in sheep. We also identified transcriptomic changes in S. bovis across different mammalian hosts (hamster and sheep), with around 30% of the total genes differentially expressed, demonstrating that S. bovis parasites display a high transcriptomic plasticity, allowing them to infect different definitive hosts. Shared enriched biological processes during introgression and host change include nuclear-transcribed mRNA catabolic processes, inner mitochondrial membrane organization, microtubule-based movement, response to endoplasmic reticulum stress, and sensory perception. These findings suggest that transcriptomic plasticity in S. bovis and hybrid worms enhance their ability to adapt and infect diverse host species, potentially increasing their zoonotic potential. This raises concerns for schistosomiasis epidemiology, as this plasticity could expand the parasites transmission capacity and complicate control efforts.

evolutionary biology↗

bioRxiv2024

Evidences that host genetic background more than the environment shapes the microbiota of the snail Bulinus truncatus, an intermediate host of Schistosoma species.

Microbiota are increasingly recognized as key players in regulating host biological functions, influencing both the ecology and evolution of organisms. However, the factors shaping microbiota diversity and structure in natural environments remain underexplored, especially the relative importance of host genetics versus environmental factors. In this study, we address this gap using the freshwater snail Bulinus truncatus, an intermediate host for some human and animal Schistosoma parasites, as a model species. We developed 31 new microsatellite markers to assess the population structure of B. truncatus across 9 sites in Senegal. We then applied metabarcoding to characterize the diversity and structure of individual snail bacterial microbiota and environmental communities associated with each sampling site using environmental DNA. We also used molecular diagnostics to determine trematode infection status of B. truncatus individuals. By integrating these data through multiple regression on distance matrices (MRM) analyses, we quantified the influence of B. truncatus population genetics, spatial distribution, environmental bacterial communities, and infection status on the snails microbiota structure. Our results show that the genetic structure of B. truncatus populations, and to a lower extent geographic distribution, are the main factors explaining the snails microbiota compositions. Neither the environmental bacterial communities nor trematode infection status significantly contributed to microbiota structure. A portion of the variance in microbiota composition remains unexplained, suggesting that additional ecological or intrinsic factors might be involved. These findings provide new insights into the drivers of microbiota structure in natural populations and highlight the complexity of host-microbiota-environment interactions. Key-words: Bulinus truncatus, Microbiota, Spatial structure, Population genetics, Trematodes, Multiple regressions on distance matrices

ecology↗

bioRxiv2024

Reconstructing the dynamics of past coral endosymbiotic algae communities using coral ancient DNA (coraDNA)

Most scleractinian corals are drastically threatened due to global changes but some colonies are intriguingly resistant to heat stress. Coral thermal tolerance partly relies on genomic determinism among the cnidarian compartment but also on the physiology of their associated symbiotic algae (Symbiodiniaceae). In fact, some corals can shift and/or shuffle their associated Symbiodiniaceae communities to temporally cope with heat stress. So far coral adjustments of their endosymbiotic algae were mainly observed at short-term evolutionary time scales and we lack a general vision of coral holobiont evolution at broader timescales. We here combined the use of ancient DNA from a coral core and a metabarcoding approach, to retrace past Symbiodiniaceae communities associated with a living colony of Porites lobata from New Caledonia over the last century. We were able to extract ancient DNA along the coral core at 19 time points dating back to the 1870s. Overall, we detected 13 OTUs, nine of which were affiliated to the Symbiodiniaceae Cladocopium clade, one to Azadinium spinosum (Dinophycae); one to the host P. lobata, the two other OTUs remained unidentified. One OTU was largely predominant and was ubiquitous over all samples. The number of OTUs was marginally correlated to the total number of sequences per sample but not to the age of the coraDNA sample. We found a generally stable core microbiota associated with P. lobata, although drastic change in community composition was observed in coraDNA samples corresponding to an extreme hot winter temperature event. More generally, this study paves the way for further investigations on the evolutionary dynamics of coral holobionts at the colony level over large temporal scales.

evolutionary biology↗

bioRxiv2023

Schistosoma haematobium and Schistosoma bovis first generation hybrids undergo large gene expressions remodeling consistent with species compatibility

When two species hybridize, the two parental genomes are brought together and some alleles might interact for the first time. To the date, the extent of the transcriptomic changes in first hybrid generations, along with their functional outcome constitute an important knowledge gap especially in non-model organisms. Here we explored the molecular and functional outcomes of hybridization in first-generation hybrid between the blood fluke parasites S. haematobium and S. bovis. To this aim we fist assembled a hybrid reference transcriptome allowing us to measure gene expression in both parental species and hybrids to further described and quantified the profiles of gene expression encountered in hybrids. We identified large-scale gene expression remodeling since up to 55% of genes were differentially expressed in hybrids compared to at least one of the parental species. We further showed that intermediate level of expression in hybrids compared to parental species was the most prevalent expression profile (38% of genes) in agreement with S. haematobium x S. bovis high genomic compatibility and limited divergence. Also, among the differentially expressed genes of each of the identified profiles (intermediate, under-, over-expressed, or matching the expression of one of the parental species), only a few biological processes were found enriched without patterns being consistent through crosses and sexes. Our findings suggest that hybrid heterosis could be due to change in expression of a large portion of random genes which affect various biological processes. Author SummaryWhen two species manage to produce a viable offspring, due to different parental genetic material, new allelic interactions might arise. We do not know much about how genes are expressed in such hybrids compared to their parental species and especially for non-model species. Here we gene expressions in first generation hybrids of two blood flukes parasites Schistosoma haematobium and S. bovis. We quantified and categorized gene differentially expressed in first generation hybrids. We showed that more than half the genes of the hybrids were differentially expressed compared to at least one of their parental species, hence showing major gene expression remodeling occurring during hybridization. However, the most common hybrid expression pattern was intermediate level of expression compared to parental species and various but no specific biological processes were associated with hybrids differentially expressed genes. We hypothesized that because S. haematobium and S. bovis remain very compatible, when hybridizing many non-specific genes can have their expression level remodeled hence impacting the overall molecular machinery of the offspring while still sustaining highly operational hybrids.

evolutionary biology↗

bioRxiv2020

Malacological survey in a bottle of water: A comparative study between manual sampling and environmental DNA metabarcoding approaches

AO_SCPLOWBSTRACTC_SCPLOWTo assess the effect of anthropogenic activities on ecosystems, it is of prime importance to develop new tools enabling a rapid characterisation of ecological communities. Freshwater ecosystems are particularly impacted and threatened by human activities and need thorough attention to preserve their biodiversity and the ecological services they provide. Studying such ecosystems is generally difficult because the associated organisms are hard to sample and to monitor. We present a ready to use environmental metabarcoding diagnostic tool to characterise and monitor the freshwater malacofauna from water samples. The efficiency of this new tool was compared to a classical malacological survey at 19 sampled sites from 10 distinct rivers distributed over Corsica Island (France). Our eDNA monitoring tool demonstrated a remarkable ability to reconstitute the local malacofauna compared to the malacological survey, with 97.1% of species detection confirmed by both methods. The present tool successfully detected the 11 freshwater snail species previously reported in Corsica by malacological survey but was limited at the genus level for some species. Moreover, our malacological survey allowed an update of the local distribution of a wide diversity of freshwater snails including invasive species (i.e. Potamopyrgus antipodarum and Physa acuta) as well as snail hosts of pathogens of medical and veterinary importance (i.e. Bulinus truncatus and Galba truncatula).

ecology↗

bioRxiv2019

Chromatin structure changes in Daphnia populations upon exposure to environmental cues - or - The discovery of Wolterecks \"Matrix\"

Phenotypic plasticity is an important feature of biological systems that is likely to play a major role in the future adaptation of organisms to the ongoing global changes. It may allow an organism to produce alternative phenotypes in responses to environmental cues. Modifications in the phenotype can be reversible but are sometimes enduring and can even span over generations. The notion of phenotypic plasticity was conceptualized in the early 20th century by Richard Woltereck. He introduced the idea that the combined relations of a phenotypic character and all environmental gradients that influence on it can be defined as \"norm of reaction\". Norms of reaction are specific to species and to lineages within species, and they are heritable. He postulated that reaction norms can progressively be shifted over generations depending on the environmental conditions. One of his biological models was the water-flee daphnia. Woltereck proposed that enduring phenotypic modifications and gene mutations could have similar adaptive effects, and he postulated that their molecular bases would be different. Mutations occurred in genes, while enduring modifications were based on something he called the Matrix. He suggested that this matrix (i) was associated with the chromosomes, (ii) that it was heritable, (iii) it changed during development of the organisms, and (iv) that changes of the matrix could be simple chemical substitutions of an unknown, but probably polymeric molecule. We reasoned that the chromatin has all postulated features of this matrix and revisited Wolterecks classical experiments with daphnia. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues. Our result indicates that chromatin structure changes consistently in daphnia upon this exposure confirming Wolterecks classical postulate.

evolutionary biology↗

bioRxiv2018

Gene expression plasticity and frontloading promote thermotolerance in Pocilloporid corals

Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response in Pocillopora coral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.

evolutionary biology↗

bioRxiv2018

Whole genome sequencing and morphological analysis of the human-infecting schistosome emerging in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites.

Schistosomes cause schistosomiasis, the worlds second most important parasitic disease after malaria. A peculiar feature of schistosomes is their ability to produce viable and fertile hybrids. Originally only present in the tropics, schistosomiasis is now also endemic in Europe. Based on two genetic markers the European species had been identified as a hybrid between the ruminant-infective Schistosoma bovis and the human-infective Schistosoma haematobium.\n\nHere we describe for the first time the genomic composition of the European schistosome hybrid (77% of S. haematobium and 23% of S. bovis origins), its morphometric parameters and its compatibility with the European vector snail and intermediate host Compatibility is a key parameter for the parasites life cycle progression. We also show that egg morphology (a classical diagnostic parameter) does not allow for differential diagnosis while genetic tests do so. Additionally, we performed genome assembly improvement and annotation of S. bovis, the parental species for which no satisfactory genome assembly was available.\n\nFor the first time since the discovery of hybrid schistosomes, these results reveal at the whole genomic level a complex admixture of parental genomes highlighting (i) the high permeability of schistosomes to other species alleles, and (ii) the importance of hybrid formation for pushing species boundaries not only conceptionally but also geographically.

genomics↗