Biology subjects

Gauthier, J.

Publications and source records attributed to Gauthier, J..

16 recordsLinked to original sources

bioRxiv2026

Cryptic diversification proceeds despite historical and contemporary hybridization in Patagonian ants

Understanding how independently evolving lineages arise despite ongoing gene flow remains a central question in evolutionary biology. Although genomic studies increasingly suggest that hybridization can accompany diversification, empirical evidence from ecologically dominant insect groups remains limited. Here, we present the first population-scale phylogenomic analysis of Patagonian ants, sampling Dorymyrmex across approximately 450,000 km2. Using genome-wide SNPs, coalescent phylogenetics, phylogenetic networks, demographic modelling, species delimitation, and genome scans, we reconstruct the evolutionary history of this widespread genus. We discovered extensive cryptic diversity with strong genomic differentiation and detected both recent and historical hybridization, demonstrating that substantial genomic divergence accumulated despite recurrent gene flow events. Genome scans further identify candidate loci associated with adaptation to Patagonias contrasting environments, suggesting that ecological divergence contributed to lineage diversification. Our results show that cryptic diversification can proceed despite recurrent gene flow, supporting hybridization as an integral component of the diversification process. More broadly, this study illustrates how genome-scale data can reveal hidden biodiversity and the evolutionary processes shaping it in ecologically important but genomically understudied taxa.

evolutionary biology↗

bioRxiv2026

Coordinated expansion of CD163⁺ monocytes and immature CD177⁺ neutrophils marks severe neurotoxicity after CD19 CAR T cell therapy

Immune effector cell-associated neurotoxicity syndrome (ICANS) is a major complication after CAR T cell therapy, but its underlying mechanisms remain poorly understood. We performed longitudinal immune profiling of paired whole blood and serum samples from patients with relapsed or refractory diffuse large B cell lymphoma (DLBCL) treated with CD19 CAR T cells. At peak neurotoxicity, high-dimensional mass cytometry and serum proteomics identified the expansion of CD163 monocytes and immature CD10lowCD101low neutrophils correlated with elevated serum ST2 and IL-2RA concentrations. Integrative immune module analysis identified these features among the strongest predictors of ICANS severity. Independent single-cell transcriptomic profiling validated the emergence of immunoregulatory CD163 monocytes and identified CD177 as a biomarker of ICANS-associated immature neutrophils. Together, these findings reveal a coordinated myeloid inflammatory network associated with ICANS and nominate candidate biomarkers and therapeutic targets for improving the safety of CAR T cell therapy. SignificanceWe demonstrate that immunoregulatory CD163+ monocytes and immature, activated CD177hiCD10lowCD101low neutrophils emerge in patients with moderate to severe ICANS at peak toxicity following CD19 CAR T cell therapy. These findings identify an uncharacterized myeloid network potentially contributing towards ICANS pathogenesis.

immunology↗

bioRxiv2026

Changing Pacific salmon nursery lake ecosystem dynamics over centuries to millennia: insights from sedimentary DNA metabarcoding

Pacific salmon are keystone species to North Pacific freshwater, coastal, and oceanic ecosystems, but many populations have declined or become more variable in recent decades due to anthropogenic impacts and climate change. Long-term records are needed to understand past changes, identify ecosystem stressors, and guide restoration. We used sedimentary DNA (sedDNA), an emerging paleoecological approach offering broader taxonomic information than traditional methods, to reconstruct ecosystem changes across five Pacific salmon nursery lakes in British Columbia (Canada). DNA metabarcoding targeting the 18S ribosomal RNA gene V7 region was used to track shifts in eukaryotic communities including algae and invertebrates over centuries to millennia. Most lakes showed notable algal community shifts over the past two centuries, with declining green algae and rising diatom relative abundances. Chrysophytes and dinoflagellates also increased over the past century in most lakes, likely driven by stronger thermal stratification, which favored these motile and mixotrophic algae that are capable of vertical migration and flexible nutrient acquisition. We contextualized the trajectories of each core through an ordination analysis based on 98 lakes distributed across British Columbia, which identified land-use changes and longer growing seasons as potential drivers. Network analyses of the sedDNA time series revealed decreasing modularity and increasing connection across lakes, suggesting a shift in resilience mechanisms from between-module buffering by compartmentalized specialists to within-guild insurance via functional overlap among generalists. Our findings demonstrate that sedDNA provides taxonomically rich, long-term insights into aquatic ecological dynamics, which are foundational for understanding and protecting Pacific salmon nursery habitats.

ecology↗

bioRxiv2026

Genetic erosion and projected habitat loss in the protected Alpine moth Actias isabellae galliaegloria (Lepidoptera: Saturniidae)

O_LIMontane and specialist insects are particularly vulnerable to habitat loss and climate change. The Spanish Moon Moth (Actias isabellae), a rare and protected species, hosts an isolated Alpine population (subspecies galliaegloria) whose conservation status remains unclear. C_LIO_LIWe combined Restriction-site Associated DNA sequencing (RADseq) and Ecological Niche Modelling (ENM) to assess its genetic diversity, population structure, and environmental vulnerability. C_LIO_LIGenomic analyses revealed extremely low genetic diversity and inbreeding in the Alpine subspecies, consistent with a historical bottleneck, reducing adaptive potential. C_LIO_LISpecies distribution models predict a major contraction of suitable habitat by 2050 due to rising temperatures and declines in its primary host, Scots pine (Pinus sylvestris). C_LIO_LIThese findings highlight the compounded risks posed by genetic impoverishment and habitat loss, emphasizing the urgent need for targeted conservation measures. C_LIO_LIOur study demonstrates the value of integrating genomic and ecological approaches to evaluate extinction risk and guide management strategies for montane specialist insects under rapid environmental change. C_LI

evolutionary biology↗

bioRxiv2025

The role of peripheral regions in shaping the phylogeography of the Bear s ear complex across the Alps

AimPeripheral regions of the Alps are often overlooked in molecular studies, yet they may play a major role in shaping the current distribution of species and genetic lineages. LocationEurope TaxonAngiosperms (Primulaceae: Primula) MethodsBy focusing on the bears ear (Primula auricula) complex as model species, we used genetic inferences for population genetic structure and performed genetic reconstructions, species delimitations and divergence time estimates in order to get a detailed view of its molecular evolution and current genetic structuring across the Alps sensu lato. ResultsThe Lombardian Alps and the southern eastern Alps are genetically distinct in the vicinity of the Adige valley. The northern and western Alps and their peripheries constitute a third clade and are separated by the siliceous central Alps. Within the latter, an additional cluster made of singular populations from the Devoluy and Vercors regions is retrieved, likely reflecting a strong founder effect rather than an ancient divergence. Main conclusionsThe biogeographic history P. auricula sensu lato pinpoints the importance of the peripheral regions in a phylogeographic context. Populations from northern peripheral regions exhibit long-lasting isolation and in situ survival during glaciations, followed by recolonization into the central Alpine massif.

genetics↗

bioRxiv2025

PqsE is conserved and functionally relevant in Pseudomonas aeruginosa

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen responsible for several acute and chronic infections. It produces a diverse array of virulence and survival determinants, many of which are tightly regulated by three interlinked quorum sensing (QS) systems named las, rhl and pqs. RhlR, the transcriptional regulator of the rhl system, activates multiple virulence genes upon binding to its cognate autoinducer signal. Meanwhile, the pqs system relies on 4-hydroxy-2-alkylquinolines (HAQs) as signaling molecules to induce the transcriptional regulator MvfR (PqsR). MvfR then activates the transcription of the pqsABCDE operon, encoding enzymes for HAQ biosynthesis. The final gene in this operon encodes PqsE, a multifunctional protein unique to P. aeruginosa. Beyond its thioesterase activity in HAQ biosynthesis, PqsE stabilizes RhlR, facilitating its regulation of target genes, some of which are implicated in virulence. Because of its role in pathogenicity, PqsE is regarded as a promising therapeutic target for combating P. aeruginosa infections. While the role of PqsE towards the RhlR regulon is increasingly understood in prototypical P. aeruginosa strains such as PA14 and PAO1, its broader relevance as an anti-virulence target remains underexplored. Here, we confirm that PqsE is functionally relevant across a panel of twelve genetically diverse P. aeruginosa strains using metabolite quantification and phenotypic assays. Significant strain-to-strain variations further highlight the importance of studying QS regulation among diverse isolates. Moreover, this study underscores PqsE as a key QS regulator with a conserved role in coordinating virulence determinant production and social behaviors across diverse P. aeruginosa populations. IMPORTANCEPseudomonas aeruginosa is a versatile opportunistic pathogen, naturally tolerant and readily acquiring resistance to multiple antibiotics. Consequently, the World Health Organization identified this bacterium as a high priority pathogen for researching and developing new antimicrobial strategies. P. aeruginosa utilizes quorum sensing, a cell-to-cell communication system, to regulate the expression of several of its virulence factors. Here, we confirm that the PqsE protein is conserved and that its function in quorum sensing, especially towards the RhlR regulator, is maintained across a panel of twelve genetically diverse P. aeruginosa strains. Since PqsE is conserved and unique to this bacterium, it could serve as an ideal target for anti-virulence therapies, offering new alternatives to combat antimicrobial resistance.

microbiology↗

bioRxiv2025

Conservation strategy insights for three protected Phengaris butterflies combining genetic and landscape analyses

Biodiversity loss is accelerating globally, with insects among the most affected taxa. Wetlands, crucial ecosystems providing essential services, have experienced significant decline due to agricultural intensification and habitat destruction. These changes threaten species that rely on wetland habitats, such as the Phengaris butterflies, which exhibit complex ecological dependencies on specific host plants and ant species. Their populations are structured into metapopulations, where connectivity between habitat patches plays a crucial role in species persistence. This study focuses on population genomics and landscape analysis of three Phengaris species (P. alcon, P. nausithous, P. teleius) in the Bugey Mountain Massif, France, with the aim of developing a conservation strategy. Using ddRAD sequencing, we analyzed genetic diversity, population structure, and gene flow across multiple localities, revealing distinct population clusters with varying degrees of connectivity. Despite some populations exhibiting high genetic diversity levels, others demonstrate low heterozygosity and signs of genetic isolation, emphasizing conservation concerns. Migration estimates and resistance mapping further identified key dispersal corridors and isolated patches requiring targeted interventions. Our findings support metapopulation conservation strategies that prioritize maintaining connectivity, enhancing degraded patches, and identifying new potential habitats. By combining genomic and landscape data, we propose an evidence-based approach to conservation planning, facilitating adaptive management for Phengaris species. This study provides a practical framework for habitat restoration and corridor management in fragmented ecosystems, ensuring long-term species resilience in rapidly changing landscapes.

evolutionary biology↗

bioRxiv2025

PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes

MotivationAntibiotic resistance is predicted to become the leading cause of human mortality by 2050. Despite this, no other major antibiotic class has been approved for medical use since 1987. Nevertheless, phage tail proteins offer a promising alternative, given their depolymerase activity toward outer membrane polysaccharides. Several pathogenic bacteria harbor prophages, thus making these prophages molecular target already known. ResultsWe therefore developed a wrapper for an existing machine learning-based phage depolymerase prediction tool (Depolymerase-Predictor), called PDP-Miner, which annotates phage tail proteins ab initio, detects depolymerase activity within this candidate protein subset, and then performs post-hoc validation by annotating protein domains thereby allowing the user to investigate for protein domains indicative of depolymerase activity. This tool allowed identification of 10 high confidence phage depolymerase gene candidates across all 1,294 Pseudomonas genomes available on the International Pseudomonas Consortium Database and could likely help detecting other candidates across other genome databases as well. Availability and ImplementationSource code is freely available for download at http:///www.github.com/jeffgauthier/pdpminer. Implemented in Bash, supported on native Linux or WSL and supports submitting subtasks to a SLURM workload queue. Requires Miniconda3 to install dependencies. This software is free and open source under the GNU General Public License v3.0. Contactjeff.gauthier.1@ulaval.ca; rclevesq@ibis.ulaval.ca Supplementary information[add Supp. Mat. URL here when available]

bioinformatics↗

bioRxiv2024

Major changes in gene expression between strains of diapausing and non-diapause spruce budworm despite little evidence of genetic divergence

To survive harsh winter conditions, many insects enter a state of dormancy called diapause which allows them to withstand extreme temperatures and lack of food. When diapause is induced, insects enter a state of arrested development and low metabolic rate. Because diapause and environmental conditions are closely linked, variation within and between species in diapause induction, depth, and duration is extremely common. Studies investigating the genetic underpinnings of diapause tend to focus on either different populations and/or environmental variation, which runs the risk of confounding the genetic signal either due to isolation-by-distance or variation in environmental conditions. We use the eastern spruce budworm (Choristoneura fumiferana) to circumvent these issues and investigate within-population variation in diapause. C. fumiferana usually diapauses as second instar larvae, but a small subset of individuals does not diapause and instead continues through development. This non-diapause phenotype can be selected to create a non-diapause strain. Here, we present a chromosome-level assembly of such a non-diapause strain, and compare it to an earlier published genome assembly of the diapause strain. We did not find evidence of major chromosome rearrangements, indicating that the genetic variation between strains is likely small and multi-genic. Gene expression comparisons between the strains indicate major gene expression changes, where genes associated with glycolysis and environmental signaling processing increase in expression in the diapause strain. Lastly, we found that gene expression diverges halfway through the first instar, and not before, indicating that the signal to induce diapause happens early in the first instar. Significance statementThe ability to enter diapause is a crucial adaptation for many insects to survive cold winters. The genetic underpinnings of the diapause phenotype has been the target of many investigations. However, many of these studies focus on variation in diapause on between geographic regions or changes in environmental conditions, which can lead to confounding factors. Here, we focus on within-population variation in diapause in the eastern spruce budworm, with two strains established from the same source population that vary in their ability to induce diapause. We present a chromosome level assembly of the non-diapause strain, and report that genetic changes between the diapause and the non-diapause line are likely small and involve multiple loci. Gene expression differences were extensive, and mostly associated with mechanisms to avoid freezing. This work sets the stage to further investigate how minimal genetic changes can lead to large-scale phenotypic changes as impactful as diapause.

genetics↗

bioRxiv2023

Dynamic gene expression analysis reveals distinct severity phases of immune and cellular dysregulation in COVID-19

BackgroundCOVID-19 patients experience dynamic changes in immune and cellular function over time with potential clinical implications. However, there is insufficient research investigating, on a gene expression level, the mechanisms that become activated or suppressed over time as patients deteriorate or recover, which can inform use of repurposed and novel drugs as therapies. ObjectiveTo investigate longitudinal changes in gene expression profiles throughout the COVID-19 disease timeline. MethodsThree-hundred whole blood samples from 128 adult patients were collected during hospitalization from COVID-19, with up to five samples per patient. Transcriptome sequencing (RNA-Seq), differential gene expression analysis and pathway enrichment was performed. Drug-gene set enrichment analysis was used to identify FDA-approved medications that could inhibit critical genes and proteins at each disease phase. Prognostic gene-expression signatures were generated using machine learning to distinguish 3 disease stages. ResultsSamples were longitudinally grouped by clinical criteria and gene expression into six disease phases: Mild, Moderate, Severe, Critical, Recovery, and Discharge. Distinct mechanisms with differing trajectories during COVID-19 hospitalization were apparent. Antiviral responses peaked early in COVID-19, while heme metabolism pathways became active much later during disease. Adaptive immune dysfunction, inflammation, and metabolic derangements were most pronounced during phases with higher disease severity, while hemostatic abnormalities were elevated early and persisted throughout the disease course. Drug-gene set enrichment analysis predicted repurposed medications for potential use, including platelet inhibitors in early disease, antidiabetic medications for patients with increased disease severity, and dasatinib throughout the disease course. Disease phases could be categorized using specific gene signatures for prognosis and treatment selection. Disease phases were also highly correlated to previously developed sepsis endotypes, indicating that severity and disease timing were significant contributors to heterogeneity observed in sepsis and COVID-19. ConclusionsHigher temporal resolution of longitudinal mechanisms in COVID-19 revealed multiple immune and cellular changes that were activated at different phases of COVID-19. Understanding how a patients gene expression profile changes over time can permit more accurate risk stratification of patients and provide time-dependent personalized treatments with repurposed medications. This creates an opportunity for timely intervention before patients transition to a more severe phase, potentially accelerating patients to recovery.

immunology↗

bioRxiv2022

The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species using morphology and DNA capture in type specimens

Recent developments in museomics enable genetic information to be recovered from previously unusable collection specimens and thus to answer complex taxonomic questions. Here we apply museomics to a taxonomic problem involving several species of Argyria Hubner (Pyraloidea, Crambinae), with previously unrecognized morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, we aimed to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridization capture protocol, we partially recovered the DNA barcode of the lectotype of Argyria lacteella (Fabricius, 1794) for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyria abronalis (Walker, 1859) holotype, thus confirming the synonymy of this name with A. lacteella, the holotype of A. lusella (Zeller, 1863), rev. syn., the holotype of A. multifacta Dyar, 1914, syn. n., newly synonymized with A. lacteella, and a specimen of Argyria diplomochalis Dyar, 1913, collected in 1992. A complementary sampling composed of nine specimens of A. lacteella, A. diplomochalis, A. centrifugens Dyar, 1914 and A. gonogramma Dyar, 1915, from North to South America, were integrated using classical COI amplification and Sanger sequencing. Argyria gonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A. lacteella. Following morphological study of its holotype, Argyria vestalis Butler, 1878, syn. n. is also synonymized with A. lacteella. The name A. pusillalis Hubner, 1818, is considered a nomen dubium associated with A. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A. lacteella, A. diplomochalis, A. centrifugens, and A. gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A. diplomochalis. Our work highlights the efficiency of the DNA hybrid capture enrichment method to retrieve DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.

zoology↗

bioRxiv2020

Evenness-richness scatter plots: a graphical, intuitive approach to alpha diversity analysis

Shannons diversity index is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent of both those parameters, there is theoretically an infinite number of richness / evenness value combinations translating into the same index score. By decoupling both components measured by Shannons index, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as PERMANOVA can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise.

bioinformatics↗

bioRxiv2020

Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

genomics↗

bioRxiv2017

DiscoSnp-RAD: de novo detection of small variants for population genomics

We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.\n\nLicenseGNU Affero general public license\n\nAvailabilityhttps://github.com/GATB/DiscoSnp\n\nContactjeremy.gauthier@inria.fr

bioinformatics↗

bioRxiv2017

Genomic divergence footprints in the bracovirus of Cotesia sesamiae identified by targeted re-sequencing approach

The African parasitoid wasp Cotesia sesamiae is structured in contrasted populations showing differences in host range and the recent discovery of a specialist related species, C. typhae, provide a good framework to study the mechanisms that link the parasitoid and their host range. To investigate the genomic bases of divergence between these populations, we used a targeted sequencing approach on 24 samples. We targeted a specific genomic region encoding the bracovirus, which is deeply involved in the interaction with the host. High sequencing coverage was obtained for all samples allowing the study of genetic variations between wasp populations and species. Combining population genetic estimations, the diversity ({pi}), the relative differentiation (FST) and the absolute differentiation (dxy), and branch-site dN/dS measures, we identified six divergent genes impacted by positive selection belonging to different gene families. These genes are potentially involved in host adaptation and in the specialization process. Fine scale analyses of the genetic variations also revealed deleterious mutations and large deletions on certain genes inducing pseudogenization and loss of function. These results highlight the crucial role of the bracovirus in the molecular interactions between the wasp and its hosts and in the evolutionary processes of specialization.

evolutionary biology↗

bioRxiv2017

Determinants of genetic structure of the Sub-Saharan parasitic wasp Cotesia sesamiae

Parasitoid life style represents one of the most diversified life history strategies on earth. There are however very few studies on the variables associated with intraspecific diversity of parasitoid insects, especially regarding the relationship with spatial, biotic and abiotic ecological factors. Cotesia sesamiae is a Sub-Saharan stenophagous parasitic wasp that parasitizes several African stemborer species with variable developmental success. The different host-specialized populations are infected with different strains of Wolbachia, an endosymbiotic bacterium widespread in arthropods that is known for impacting life history traits notably reproduction, and consequently species distribution. In this study, first we analyzed the genetic structure of C. sesamiae across Sub-Saharan Africa, using 8 microsatellite markers, and 3 clustering software. We identified five major population clusters across Sub-Saharan Africa, which probably originated in East African Rift region and expanded throughout Africa in relation to host genus and abiotic factors such as climatic classifications. Using laboratory lines, we estimated the incompatibility between the different strains of Wolbachia infecting C. sesamiae. We observed an incompatibility between Wolbachia strains was asymmetric; expressed in one direction only. Based on these results, we assessed the relationships between direction of gene flow and Wolbachia infections in the genetic clusters. We found that Wolbachia-induced reproductive incompatibility was less influential than host specialization in the genetic structure. Both Wolbachia and host were more influential than geography and current climatic conditions. These results are discussed in the context of African biogeography, and co-evolution between Wolbachia, virus parasitoid and host, in the perspective of improving biological control efficiency through a better knowledge of the biodiversity of biological control agents.

evolutionary biology↗