Biology subjects

Jacquet, S.

Publications and source records attributed to Jacquet, S..

11 recordsLinked to original sources

bioRxiv2026

Fine-scale maternal structure and high nuclear connectivity in the French populations of the Geoffroy's Bat (Myotis emarginatus)

The Geoffroy's bat (Myotis emarginatus) is a sedentary species increasingly threatened by habitat alteration. Here, we assessed genetic diversity and population structure in 760 individuals from 18 French maternity colonies using 34 microsatellite markers and mitochondrial D-loop sequences. Mitochondrial data revealed subtle regional structure, consistent with female philopatry, and a broader phylogeographic split between Western Europe and the Greater Middle East, reflecting historical isolation. In contrast, microsatellites showed high nuclear diversity and minimal population structure across France, with weak isolation by distance and kin clustering, indicating extensive male-mediated gene flow. Moreover, demographic inference suggested population stability, consistent with both marker types. This nuclear homogeneity and demographic stability are strikingly similar to the patterns observed in Rhinolophus ferrumequinum populations sampled at the same colonies, suggesting that reproductive aggregation can maintain connectivity even in sedentary species. Overall, M. emarginatus functions as a largely connected population at the national scale, although localized maternal lineages suggest the presence of functional phylopatric units around key maternity sites that warrant protection. Future genome-wide studies could refine conservation strategies by integrating fine-scale female philopatry with male-mediated connectivity.

genetics↗

bioRxiv2026

DTX3L-PARP9 co-evolve as a single adaptive unit linking ubiquitination and ADP-ribosylation in antiviral immunity

Functional protein complexes are central to innate immunity, by integrating and diversifying signaling pathways of immune responses. Understanding how such complexes evolve is therefore key to elucidate the molecular basis of immune adaptation. Using a comparative genomics framework, we show that the DTX3L-PARP complex, which integrates ubiquitin-dependent and ADP-ribosylation pathways to regulate antiviral immunity, is an ancient and rapidly evolving functional module in vertebrates. We demonstrate that this complex has undergone recurrent adaptive evolution, with strong signatures of co-evolution between its components, consistent with early functional coupling and coordinated evolution as a single adaptive unit rather than independent proteins. Adaptive residues are enriched at protein-protein interaction surfaces within the RING-DTC domain of DTX3L, while PARP9 and PARP14 concentrate adaptive changes in regions involved in complex assembly and catalytic activities, consistent with hallmarks of pathogen-driven selection. These evolutionary signals remain detectable at short evolutionary timescales, including within species and sub-species, indicating ongoing adaptive evolution of the complex. These patterns support a model in which pathogens recurrently target the DTX3L-PARP axis to disrupt ubiquitin-ADP-ribose signaling, either by simultaneously interfering with catalytic domains or by destabilizing the complex interfaces. Altogether, our findings reveal the DTX3L-PARP9-PARP14 complex as a co-evolving adaptive module shaped by persistent host-virus arms races, highlighting how interconnected post-translational modification systems evolve in concert to sustain vertebrate antiviral immunity.

evolutionary biology↗

bioRxiv2025

Extensive adaptive changes in bat interferon pathway reveal specific molecular functions at the forefront of host - virus coevolution

The interferon (IFN) response is a fundamental component of the mammalian innate immune system, orchestrating a broad antiviral state through a network of interferon-stimulated genes (ISGs). In bats, which are natural reservoirs for diverse viruses, several ISGs exhibit lineage-specific evolutionary adaptations, reflecting unique immune strategies. While previous research has typically focused on individual ISGs or broad-scale genomic analyses, here, we conducted an evolutionary analysis of type I IFN-upregulated genes across diverse bat species to elucidate the forces shaping the full repertoire of their ISG responses. Our results reveal that key components of bats antiviral signaling, including viral dsRNA sensors, PARP-mediated ADP-ribosylation enzymes, and cytokine/chemokine signaling molecules, have been recurrent targets of strong positive selection. Notably, immune sensors such as TLR3, RIG-I, and MDA5 show adaptive changes in their RNA-binding domains, suggesting modified viral recognition. Members of the PARP family exhibit repeated selection in both macro and catalytic domains, consistent with intense host-virus conflict and immune modulation. Strikingly, chemokine genes--especially CXCL10 and CXCL16--and their receptors display some of the strongest and most concerted selection signatures, particularly in ligand-binding loops, consistent with arms-race coevolution potentially driven by viral mimicry. Several positively selected genes have pleiotropic functions in tissue repair, inflammation, and tumor control, suggesting that some of these adaptations may influence several physiological pathways. Altogether, our findings uncover a bat-specific antiviral architecture shaped by concerted adaptive evolution, highlighting a balance between viral control and immune tolerance, likely underlying bats exceptional resilience to disease. Author summaryBats exhibit a remarkable capacity to host a wide range of viral families, including viruses highly pathogenic to humans, while rarely displaying overt clinical symptoms. This resilience suggests unique immune adaptations to control infections while avoiding harmful inflammation. To investigate the genetic basis of this trait, we conducted a comparative evolutionary analysis of genes involved in the type I interferon (IFN) pathway, a core component of the mammalian antiviral response, across multiple bat species and other mammals. Our results reveal strong signatures of positive selection on key antiviral effectors in bats, including sensors of viral nucleic acids, ADP-ribosylating PARP enzymes, and components of chemokine signaling pathways. Notably, several chemokines and their receptors display accelerated evolution, pointing to a critical role in modulating immune responses. We further identify viral chemokine-binding proteins (vCKBPs) from poxviruses as one likely driver of natural selection, suggesting ongoing evolutionary arms races between host immune signaling and viral immune evasion. Overall, these findings fit with a model in which bats have evolved a balance with potent antiviral activity and controlled immune activation. Elucidating these mechanisms offers promising insights for developing novel approaches to managing inflammation and viral infections in humans.

evolutionary biology↗

bioRxiv2022

Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions

Several bat species act as asymptomatic reservoirs for many viruses that are instead highly pathogenic in other mammals. Here, we have characterized the functional diversification of the Protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats, in contrast to all studied mammals that possess a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. More importantly, we determined that duplicated PKRs of the Myotis species have undergone functional diversification allowing them to collectively escape from and enhance control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat specific immunity.

evolutionary biology↗

bioRxiv2022

Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19

The COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus that spilled from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional-genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus-host interfaces. Here, we performed high-throughput evolutionary analyses of 334 SARS- CoV-2 interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus-host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus-host arms-race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo important interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified functional adaptations involved in SARS- CoV-2 infection in bats and primates, critically enlightening modern genetic determinants of virus susceptibility and severity. Key findingsO_LIEvolutionary history of 334 SARS-CoV-2 interacting proteins (VIPs) in bats and primates identifying how the past has shaped modern viral reservoirs and humans - results publicly-available in an online resource. C_LIO_LIIdentification of 81 primate and 38 bat VIPs with signatures of adaptive evolution. The common ones among species delineate a core adaptive interactome, while the ones displaying distinct evolutionary trajectories enlighten host lineage-specific determinants. C_LIO_LIEvidence of primate specific adaptation of the entry factor TMPRSS2 pointing to its host- specific in vivo importance and predicting molecular interfaces. C_LIO_LIFYCO1 sites associated with severe COVID-19 in human (GWAS) display hallmarks of ancient adaptive evolution in primates, highlighting its importance in SARS-CoV-2 replication or pathogenesis and differences with the bat reservoir. C_LIO_LIIdentification of adaptive evolution in the bats multifunctional RIPK1 at residues that may differentially regulate inflammation. C_LI

evolutionary biology↗

bioRxiv2022

Genomic compatibility excels possible 'good genes' effects of sexual selection in lake char

Mating is rarely random in nature, but the effects of mate choice on offspring performance are still poorly understood. We sampled in total 47 wild lake char (Salvelinus umbla) during two breeding seasons and used their gametes to investigate the genetic consequences of different mating scenarios. In a first study, 1,464 embryos that resulted from sperm competition trials were raised singly in either a stress- or non-stress environment. Offspring growth turned out to be strongly reduced with increased genetic relatedness between the parents while male coloration (that reveal aspects of male health) was no significant predictor of offspring performance. In a second experiment one year later, block-wise full-factorial in vitro breeding was used to produce 3,094 embryos that were raised singly after sublethal exposures to a pathogen or water only. Offspring growth was again strongly reduced with increased genetic relatedness between the parents while male coloration was no significant predictor of offspring performance. We conclude that the genetic benefits of mate choice would be strongest if females avoided genetic similarity, while male breeding colors seem more relevant in intra-sexual selection. Impact SummaryMales and females usually compete for access to mating partners, and they usually choose their mates. Sexual selection is therefore a major force in evolution. It shapes sexual signals and mate preferences depending on the type of mating system. A comparatively simple mating system is when fertilization is external and neither males nor females care for their brood, as is the case in salmonid fish. A group of hypotheses then predicts that female mate preferences have evolved to maximize offspring growth and survival through indirect genetic benefits. There are two types of such indirect benefits. In models of good genes sexual selection, conspicuous signals reveal a males health and vigor because only males in good health can afford these costly traits. Females would then prefer males with strong signals. In compatible genes models, females would instead focus on signals that allow them to complement their own genotype to achieve high offspring viability. An example of the latter is inbreeding avoidance through odors that reveal kinship. We sampled wild lake char to compare the likely consequences of these two types of possible female preferences for offspring growth and survival. We experimentally crossed these fish in vitro and raised large numbers of offspring singly and for several months. Our first experiment revealed that offspring growth would be significantly increased if females would avoid mating with genetically more similar males, while preferring males with strong sexual ornaments (in this case: yellow skin colors) would not improve offspring performance. These results could be confirmed in a second experiment with a larger sample size. We conclude that the genetic benefit of mate choice is largest if females aim for compatible genes rather than focusing on the breeding colors that males display. These breeding colors are therefore likely to play a more important role in other contexts, e.g., in male-male competition.

evolutionary biology↗

bioRxiv2021

Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its anoxic chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean where early microbial life gave rise to Earths oxygenated atmosphere. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photo-synthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Anoxygenic phototrophic sulfur bacteria, Chromatium, dominated the chemocline along with Lentimicrobium, a newly observed genus of known fermenters. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios spanned an order of magnitude, peaking with high phytoplankton abundances and at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean. IMPORTANCEAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

microbiology↗

bioRxiv2021

Microbial loop of Proterozoic ocean analogue

Meromictic Lake Cadagno, an ancient ocean analogue, is known for its permanent stratification and persistent anoxygenic microbial bloom within the chemocline. Although the anaerobic microbial ecology of the lake has been extensively studied for at least 25 years, a comprehensive picture of the microbial food web linking the bacterial layer to phytoplankton and viruses, with explicit measures of primary and secondary production, is still missing. This study sought to better understand the abundances and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified zones of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested the presence of eukaryotic phytoplankton through the water column. Evidence supported high abundances of Ankyra judayi, a high-alpine adapted chlorophyte, in the oxic mixolimnion where oxygenic-primary production peaked. Through the no- and low-oxygen chemocline and monimolimnion, chlorophytes related to Closteriopsis acicularis, a known genus of meromictic lakes, and Parachlorella kessleri were observed. Chromatium, anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline suggesting primary producers depend on hetrotrophs for nutrient remineralization. As previously observed, sulfur reducing bacteria (SRBs), especially Desulfocapsa and Desulfobulbus, were present in the chemocline and anoxic monimolimnion. Virus-to-microbe ratios (VMR) peaked in the zone of phytoplankton, yet were at a minimum at the peak of Chromatium. These dynamic trends suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno and other permanently stratified systems. ImportanceAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

microbiology↗

bioRxiv2021

Die hard in Lake Bourget! The case of Planktothrix rubescens

Blooms of Planktothrix rubescens have been recorded for 15 years in Lake Bourget (France), from 1995 to 2009. Then, the presence of this filamentous and toxic cyanobacterium became anecdotic between 2010 and 2015 and it was clearly thought that such a proliferation was over. However, against all odds, blooms occurred again in 2016 and 2017 despite apparent very low phosphorus concentrations in surface waters of the lake. Aims of this study were thus to explain the reasons of this come back in order to propose scenarios likely to be helpful to stakeholders who need to know if such proliferations may occur again in the future. We show that phosphorus input, both from the main tributaries to the lake and possibly from the sediments, were likely the triggers of the new development of the cyanobacterium since a minimum autumn/winter inoculum of P. rubescens was detected the year before. Then, the bloom, that was observed deeper than previous years, was associated to a conjunction of factors already well-known to favour the development of this very competitive species (i.e. mild winter temperature, water column stability, available light at depth, surface water transparency, low predation, etc...). Although many factors and processes could account for the occurrence and bloom of the cyanobacterium, not observed, measured or taken into account here, a plausible scenario could be proposed and may be useful to deciders. One thing remains unclear: where do the cyanobacterium hides when it is not observed during the routine monitoring survey and thus from which place it could initiate its development (nearshore, in the pelagic zone, from the sediment?), unless it is simply not sampled and observed due to methodological bias.

ecology↗

bioRxiv2020

Rapid evolution of mammalian HERC6 and independent duplication of a chimeric HERC5/6 gene in rodents and bats suggest an overlooked role of HERCs in antiviral innate immunity

The antiviral innate immunity in mammals has evolved very rapidly in response to pathogen selective pressure. Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family including interferon-inducible antiviral effectors. Notably, HERC5 inhibits divergent viruses through the conjugation of ISG15 to diverse proteins-termed as ISGylation. Though HERC6 is the most closely-related protein of HERC5, it lacks the ISGylation function in humans. Interestingly, HERC6 is the main E3-ligase of ISG15 in mice, suggesting adaptive changes in HERC6 with implications in the innate immunity. Therefore, HERC5 and HERC6 have probably diversified through complex evolutionary history in mammals, and such characterization would require an extensive survey of mammalian evolution. Here, we performed mammalian-wide and lineage-specific phylogenetic and genomic analyses of HERC5 and HERC6. We used 83 orthologous sequences from bats, rodents, primates, artiodactyls and carnivores - the top five representative groups of mammalian evolution and the main hosts of viral diversity. We found that mammalian HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past genetic arms-races with viral pathogens. Importantly, we found accelerated evolution in the HERC6 spacer domain, suggesting that it might be a pathogen-mammal interface, targeting a viral protein and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat antiviral innate immunity. Altogether, we found major genetic innovations in mammalian HERC5 and HERC6. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.

evolutionary biology↗

bioRxiv2017

Bdellovibrio and like organisms bacterial predators are not equally distributed in peri-alpine lakes

Microbes drive a variety of ecosystem processes and services but still many of them remain largely unexplored because of our lack of knowledge on both diversity and functionality of some potentially key microbiological compartments. This is typically the case with and within the group of bacterial predators collectively known as Bdellovibrio and like organisms (BALOs). Here we report for the first time the abundance, distribution and diversity of the three main families of these natural and obligatory predators of gram negative bacteria in three peri-alpine lakes (e.g. lakes Annecy, Bourget and Geneva) at different depths (surface vs. 45 or 50 m) and along a few months (from August 2015 to January 2016). We show that, using PCR-DGGE and cloning-sequencing approaches, the diversity appeared relatively low and very specific to fresh waters or even of the lakes themselves. While the Peredibacteraceae family was represented mainly by a single species (i.e. Peredibacter starii), it could constitute up to 7% of the total bacterial cell abundances. Comparati vel y, the abundances of the two other families (referred to as Bdellovibrionaceae and Bacteriovaracaceae) were significantly lower. More interestingly, the distribution in the water column was very different between the three groups suggesting various life strategies/niches for each of them: Peredibactereacea dominated near surface while the Bdellovibrionaceae and the Bacteriovaracaceae were more abundant at depth. All in all, our results suggest that these bacterial predators are likely to play a significant role in mortality, carbon fluxes and prokaryotic community structure in lakes.

ecology↗