Biology subjects

Gauthier, P.

Publications and source records attributed to Gauthier, P..

8 recordsLinked to original sources

bioRxiv2026

Intensive pine plantation management shapes infectious agent communities in the generalist rodent Apodemus sylvaticus, with consequences for zoonotic hazard

Land use change is widely recognized as a major driver of emerging zoonotic diseases. Yet, while forest plantations are expanding worldwide, their consequences on the circulation of infectious agents in wildlife remain poorly understood. We investigated how native pine plantations and broadleaved habitats shape rodent-associated infectious hazard in the generalist wood mouse (Apodemus sylvaticus), in southwestern France. Using a multi-season survey, we screened 424 wood mice for a broad range of infectious taxa and compared infection probability and infected-host abundance among pine plantation edges, broadleaved hedgerows embedded within pine plantations and broadleaved forests. Using a combination of linear mixed model and joint species distribution modelling, we tested whether infectious hazard differed between pine plantations and broadleaved forests, whether broadleaved hedgerows shifted these patterns towards those observed in broadleaved forests, and how these habitat-related patterns varied across seasons. We detected 22 potentially infectious taxa, including nine recognized zoonotic bacteria. Season strongly influenced infectious patterns, while habitat effects were taxa and season dependent. In spring, pine plantation edges increased infection probability for Bartonella grahamii and Neoerhlichia mikurensis compared to broadleaved forest, but their strong negative effect on wood mouse abundance resulted in consistently lower infected-host abundance for most infectious taxa. Broadleaved hedgerows showed distinct and season-dependent patterns with infectious profiles resembling those of pine edges in spring, but with higher infectious hazard than both other habitats for several taxa in autumn. Our results highlight that habitat effects on infectious hazard cannot be inferred from infection probability alone. Pine plantations may reduce rodent-associated zoonotic hazard through their strong negative effect on host abundance, despite increasing infection probability for some agents. Forest diversification and restoration initiatives, such as broadleaved hedgerows here, may have unforeseen epidemiological consequences, underscoring the need to integrate disease ecology into forest management and restoration to anticipate variation in zoonotic risks, while maximizing ecological benefits.

ecology↗

bioRxiv2026

Genomic signatures of selection and putative adaptive introgression during the African expansion of the house mouse

How species adapt to novel environments following biological invasion remains a central question in evolutionary biology. The recent human-mediated expansion of the western house mouse (Mus musculus domesticus) across Africa provides an opportunity to investigate the genomic basis of these rapid evolutionary responses. Using whole-genome data from 218 wild mice sampled across Europe and Africa, we combined complementary genome-wide differentiation, genotype-environment association, haplotype-based selection, and localized introgression analyses to investigate genomic signatures of selection and assess the contribution of interspecific gene flow from the native congener Mus spretus to these patterns. Genome-wide differentiation analyses identified candidate regions enriched for immune and epithelial-barrier functions, chemosensory perception, and neural or developmental pathways. Genotype-environment association analyses recovered fewer candidates linked mainly to precipitation, whereas haplotype-based scans highlighted recent selective signals involving sensory, immune, and neural functions. Across analyses, candidate regions were dominated by non-coding variation, supporting a predominantly regulatory and likely polygenic genomic architecture. Although excess allele sharing with M. spretus varied among populations, overlap between introgression and selection candidates was limited but greater than expected by chance. Several overlapping regions were also present in European populations, indicating that introgressed variants likely predated African colonization. Overall, our results suggest that the genomic signatures accompanying the African expansion of house mice were driven mainly by selection on M. m. domesticus variation, whereas introgressed M. spretus alleles contributed to a smaller subset of candidate loci and may have played a role in adaptation in African populations.

evolutionary biology↗

bioRxiv2025

Ecological and Genetic Determinants of Essential Oil Diversity in Mediterranean Thymus

The Mediterranean Basin is a hotspot of plant diversity, with many species producing aromatic essential oils (EOs) that mediate ecological interactions and stress responses. Within Lamiaceae, the genus Thymus shows remarkable chemical variability, yet high intraspecific EO variation often limits its taxonomic resolution. We investigated EO composition, genetic structure, and environmental influences across 39 populations of Thymus sect. Mastichina in the Iberian Peninsula, using GC-MS alongside soil and climatic data to assess drivers of chemical variation and refine taxonomic characterization. We identified 14 major EO compounds, dominated by oxygenated monoterpenes. Most populations exhibited 1,8-cineole-rich chemotypes, yet seven populations showed linalool dominance, and multiple chemotypes often co-occurred within the same populations, revealing high intrapopulation chemical diversity. Minor compounds, including camphor, borneol, and camphene, varied among genetic clusters and were significantly correlated with temperature and precipitation gradients. Differences in EO composition were also detected between ploidy levels and genetic groups, although the major compounds (1,8-cineole and linalool) remained relatively consistent, indicating both conserved and locally adaptive chemical traits. These findings suggest that EO diversity in Thymus sect. Mastichina arises from a complex interplay of environmental conditions, genetic background, and ploidy. Integrating chemical, genetic, and ecological data provides a robust framework for understanding the evolutionary and ecological drivers of EO variation in Mediterranean aromatic plants, with implications for taxonomy, conservation, and the study of adaptive chemical traits.

evolutionary biology↗

bioRxiv2025

Genetic structure of Rattus rattus populations in an endemic plague focus in Madagascar: implications for rodent surveillance and management

BackgroundPlague remains a major public health concern in Madagascar. In the Central Highlands, where the disease is still endemic, the black rat (Rattus rattus) is the main reservoir of the causative agent Yersinia pestis. Understanding its population dynamics and structure is therefore crucial to inform control strategies, as dispersal may greatly limit the effectiveness of local interventions during outbreaks. In such a context, this study aims at investigating the genetic diversity and temporal structure of R. rattus populations at a fine geographical scale. Methodology/Principal findingsSampling was conducted in six villages of the Ankazobe district, both inside houses and outside villages. A total of 480 individuals, captured in March - May 2019 and 2020, were genotyped at 17 microsatellite loci. Our results show that genetic diversity levels were relatively homogeneous among villages and years. However, subpopulations living outside villages displayed significantly higher genetic diversity and lower genetic differentiation levels than those from inside houses, indicating larger effective population sizes outside villages in the cultivated habitats. These findings suggest more restricted movement among rat subpopulations from the houses, and greater connectivity among subpopulations living outside villages. However, overall genetic differentiation was rather low, suggesting extensive dispersal of rats at the scale of the district, facilitating rapid recolonization after local control efforts. ConclusionAn integrated approach combining flea control within houses together with measures to reduce human-rodent contact would thus appear more appropriate than rodent control only to limit plague transmission.

ecology↗

bioRxiv2023

Toxoplasma gondii and Trypanosoma lewisi infection in urban small mammals from Cotonou, Benin, with special emphasis on co-infection patterns

A growing number of studies has highlighted the importance of co-infections in eco-evolutionary processes underlying host-parasite interactions and the resulting epidemiology of zoonotic agents. Small mammals, and particularly rodents, are known to be important reservoirs of many zoonotic pathogens, such as Toxoplasma gondii and Trypanosoma lewisi that are responsible for toxoplasmosis and atypical trypanosomiasis in human, respectively. Laboratory experiments on rodent models have shown that primary infection with T. lewisi increases the host susceptibility to other co-infectious parasites, including T. gondii, following an alteration of the immune system. However, data on potential interactions between these parasites in wild small mammals remain scarce. In this study, we estimate the T. lewisi prevalence in 553 small mammals from four localities of Cotonou city, Benin. They were then combined with T. gondii data previously collected on the same individuals in order to investigate the influence of T. lewisi on T. gondii infection, and vice-versa, using cooccurrence tests and Generalized Linear Mixed Models. Despite quite high overall prevalence (32.5% and 15.2% for T. gondii and T. lewisi, respectively), we observed a clear and significant segregation between the two parasites. This may be explained by (i) differences in the species-specific susceptibility of small mammal host species to infection by these two parasites, with R. rattus and M. natalensis being the main reservoirs of T. lewisi while C. olivieri and M. m. domesticus are the main hosts for T. gondii; and/or by (ii) a possibly high mortality in co-infected animal in the wild. Although dedicated experimental studies are required to confirm this pattern, as they stand, our data fail to support that infection of small mammals by one of these two parasites favours widespread infection by the second one in nature.

ecology↗

bioRxiv2023

Ongoing convergent evolution of a selfing syndrome threatens plant-pollinator interactions

O_LIPlant-pollinator interactions evolved early in the angiosperm radiation. Ongoing environmental changes are however leading to pollinator declines that may cause pollen limitation to plants and change the evolutionary pressures shaping plant mating systems. C_LIO_LIWe used resurrection ecology methodology to contrast ancestors and contemporary descendants in four natural populations of the field pansy (Viola arvensis) in the Paris region (France), a depauperate pollinator environment. We combine population genetics analysis, phenotypic measurements and behavioural tests on a common garden experiment. C_LIO_LIPopulation genetics analysis reveals 27% increase in realized selfing rates in the field during this period. We documented trait evolution towards smaller and less conspicuous corollas, reduced nectar production and reduced attractiveness to bumblebees, with these trait shifts convergent across the four studied populations. C_LIO_LIWe demonstrate the rapid evolution of a selfing syndrome in the four studied plant populations, associated with a weakening of the interactions with pollinators over the last three decades. This study demonstrates that plant mating systems can evolve rapidly in natural populations in the face of ongoing environmental changes. The rapid evolution towards a selfing syndrome may in turn further accelerate pollinator declines, in an eco-evolutionary feedback loop with broader implications to natural ecosystems. C_LI

evolutionary biology↗

bioRxiv2020

Using karyotyping and achene morphology to accurately identify Sonchus oleraceus (Asteraceae) in the context of its biological control

In weed biocontrol, accurate identification of the target weed is essential to select effective and host-specific biocontrol agents. This study focuses on the biocontrol of an invasive weed species in Australia, native from Europe, the common sowthistle, Sonchus oleraceus L. (Asteraceae). During field surveys, the distinction between S. oleraceus and a morphologically related species (S. asper L.) was difficult because of specimens bearing intermediate morphological features. These observations raised questions about the reliability the morphological characters used for distinguishing between these species and the identity of the intermediate phenotypes. First, cytological analyses coupled with morphological comparisons were carried out on specimens collected in Europe and Australia. Results showed that specimens morphologically described as S. oleraceus and S. asper possessed, in accordance with literature 32 and 18 chromosomes, respectively. Specimens with intermediate morphotypes had 32 chromosomes, showing that they belong to S. oleraceus species. The variability of characters used for diagnosis is discussed and for a particular feature, achene ornamentation, an inquiry among 30 people was carried out to determine how this character might be relevant for distinguishing the two species herein considered. The successful identification rate was 92.2% (SE {+/-} 0.77) showing the practical interest of this feature for diagnosis.

plant biology↗

bioRxiv2019

Impact of historical and current features of the cityscape on the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

AO_SCPLOWBSTRACTC_SCPLOWPopulation genetic approaches may be used to investigate dispersal patterns of species living in highly urbanized environment in order to improve management strategies for biodiversity conservation or pest control. However, in such environment, population genetic structure may reflect both current features of the cityscape and urbanization history. This can be especially relevant when focusing on exotic commensal rodents that have been introduced in numerous primary colonial European settlements. Accounting for spatial and temporal cityscape heterogeneity to determine how past and recent demographic events may interplay to shape current population genetic structure of synanthropic rodents may provide useful insights to manage their populations. In this study, we addressed these issues by focusing on the house mouse, Mus musculus domesticus, in Dakar, Senegal, where the species may have been introduced as soon as Europeans settled in the middle of the nineteenth century. We examined genetic variation at one mitochondrial locus and 15 nuclear microsatellite markers from individuals sampled in 14 sampling sites representing different stages of urbanization history and different socio-economic environments in Dakar. We used various approaches, including model-based genetic clustering and model-free smoothing of pairwise genetic estimates. We further linked observed spatial genetic patterns to historical and current features of Dakar cityscape using random forest and Bayesian conditional autoregressive models. Results are consistent with an introduction of the house mouse at colonial time and the current genetic structure exhibits a gradient-like pattern reflecting the historical process of spatially continuous expansion of the city from the first European settlement. The genetic patterns further suggest that population dynamics of the house mouse is also driven by the spatial heterogeneity of the current cityscape, including socio-economics features, that translate in habitat quality. Our results highlight the potential importance of accounting for past demographic events to understand spatial genetic patterns of nonnative invasive commensal rodents in highly urbanized environment.

ecology↗