Biology subjects

Charbonnel, N.

Publications and source records attributed to Charbonnel, N..

At least 19 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

Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland

Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks.

microbiology↗

bioRxiv2026

Broadleaved hedgerows as complementary habitats for small mammals in pine plantation landscapes

O_LIThe global decline of natural forests is accompanied by a rapid expansion of commercial tree plantations, which are expected to further increase to meet growing demand for wood products. However, planted forests generally support lower biodiversity than natural forests, particularly when monospecific and intensively managed. In this context, broadleaved hedgerows have been proposed as a nature-based solution to enhance biodiversity within conifer-dominated plantation landscapes. Such features may be especially beneficial for small mammals, including rodents and shrews, which are key contributors to forest ecosystem functioning. However, their effects on small mammal communities remain largely unquantified. C_LIO_LIHere, we assessed variation in small mammal communities among habitat types within a native pine plantation-dominated landscape in southwestern France. Using a multi-year, multi-season survey, we compared species richness and abundance among plantation edges, broadleaved hedgerows embedded within plantations and natural broadleaved forests. We further tested whether environmental descriptors of hedgerow sites influenced dominant species and whether seasonal and interannual demographic dynamics modified habitat-related patterns. C_LIO_LIPine plantation edges and broadleaved hedgerows supported lower small mammal species richness than natural broadleaved forests and were dominated by two habitat generalists, Apodemus sylvaticus and Crocidura russula. This pattern was driven by the near absence of the forest specialist Clethrionomys glareolus. Hedgerows did not increase species richness relative to plantations, but provided favourable habitat for A. sylvaticus, which was scarce in pine plantation, while supporting fewer C. russula. Variation in hedgerow structure and composition further influenced A. sylvaticus abundance, while seasonal and interannual rodent population dynamics modulated habitat-related differences. C_LIO_LIOur results indicate that intensively managed pine plantations act as environmental filters, excluding forest-associated small mammals. While broadleaved hedgerows benefited one species, their capacity to restore forest-specialist communities was limited without broader landscape-scale interventions. These findings highlight both the ecological benefits and constraints of edge-based habitat interventions and provide guidance for designing and evaluating biodiversity-oriented management in plantation landscapes. C_LI

ecology↗

bioRxiv2026

Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia

Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes disseminated infections remain poorly understood. To investigate this phenomenon, 22 strain pairs of Klebsiella spp. were sequentially isolated from rectal swabs and blood samples of ICU patients. All strains adhered to intestinal epithelial cells in vitro, but failed to invade or disrupt epithelial barrier integrity. Few phenotypic differences between strains of the same pair were observed regarding their biofilm-forming capacities and ampicillin resistance. Whole genome sequencing of five pairs showed diverse sequence types, the presence of numerous antibiotics resistance genes but few virulence genes. Pairwise comparison of genomic sequences of blood and fecal isolates evidenced a few single nucleotide polymorphisms and small insertions-deletions, mostly affecting genes involved in biosynthesis of surface structures (such as capsules, pili). Most genetic changes were driven by horizontal gene transfer events, with the notable acquisition of a plasmid that enhanced bacterial fitness by eliminating competitors. In addition, some blood isolates had reduced the number of antibiotic resistance genes, underscoring the high plasticity of the Klebsiella resistome. Finally, one bloodstream isolate carried a mutS mutation, conferring a hypermutator phenotype that could increase evolvability despite the fitness burden. Together, these findings indicate that within-host genetic adaptations, rather than the acquisition of virulence traits, can enhance the colonization, competitiveness and ultimately the ability of K. pneumoniae to cause invasive infections. ImportanceKlebsiella commonly colonizes the human gut, and this carriage can progress to infections, particularly in intensive care unit (ICU) patients. To better understand the in vivo evolution, genetically associated Klebsiella strains isolated from the feces and blood of ICU patients were analyzed. Although strains were able to adhere to intestinal cells, none could invade or damage the intestinal barrier. Genomic comparisons of pairs strains showed limited genetic differences, mostly mutations affecting surface structures. Frequent horizontal gene transfer events were observed, which could improve bacterial competitiveness and permits a remarkably flexible resistome. Overall, this study shows that within-host evolution, rather than the gain of virulence traits, can enhance the ability of Klebsiella to persist, outcompete other bacteria, and ultimately cause infections.

microbiology↗

bioRxiv2025

Host competence-abundance relationships drive the dilution effect across multiple small mammal-borne pathogens

The "dilution effect" hypothesis suggests that high host diversity can reduce the prevalence of certain zoonotic pathogens. Despite growing interest, its generality and practical relevance remain debated. In particular most previous studies have focused on large scale analyses or meta-analyses, limiting their potential use for zoonotic outbreak prevention. Here, we present an extensive field-based study of small mammals and their multiple pathogens to assess diversity-disease relationships at a local scale, revealing pathogen-specific patterns. While no significant association was detected between the prevalence of some pathogens and host diversity, others such as Orthopoxvirus and a strain of Mycoplasma haemomuris exhibited dilution effect patterns, whereas another Mycoplasma haemomuris strain and Mycoplasma coccoides displayed amplification effects. Crucially, we demonstrate that these contrasting outcomes are consistently explained by the host competence-abundance relationship. Our findings underscore the importance of host community composition and highlight the need to consider multiple pathogens when evaluating the ecological mechanisms underpinning the diversity-disease relationships.

ecology↗

bioRxiv2025

Urban bats change the menu: dietary plasticity across human-modified landscapes of a tropical island

In a rapidly urbanizing world, research on dietary habits of wildlife is essential to understand how plastic behaviors may guide evolutionary trajectories of endangered animal species. Bats are very sensitive to habitat destruction and land-use change, although some species have shown the capacity for adaptation to urban life. In this study, we tested to what extent urban insectivorous bats modify their feeding strategies in a recently human-modified tropical insular ecosystem. Using a DNA metabarcoding approach on fecal samples collected in seven roosts, we analyzed the dietary niche of free-tailed bats (Mormopterus francoismoutoui) endemic to Reunion Island. Our results revealed a wide dietary niche, including 174 arthropod species in 12 orders, among which lepidopterans were predominant. We identified several crop pests and disease vectors, highlighting the central role of this bat species for agroecology and epidemiology concerns. Our study also highlighted potential sex- and reproduction-related dietary strategies. Moreover, we found that agriculture areas, inferred from land cover surrounding bat roosts, were associated with higher relative abundance of Lepidoptera in the diet of bats. In contrast, bats roosting in urban areas increased their consumption of Blattodea. As Reunion free-tailed bats roost and thrive in human-modified landscapes, understanding the consequences of this dietary plasticity for bat health and fitness will be necessary for urban evolutionary research and conservation actions.

ecology↗

bioRxiv2024

Drivers of host-pathogen community assemblies in European forests and urban green spaces

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals - wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the "host-diversity begets parasite-diversity" hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector.

ecology↗

bioRxiv2023

Effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid and abrupt changes. One possible explanation for differential adaptative abilities between these species is that the microbiome may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under such anthropic perturbations, the microbiota composition of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness, potentially causing local extirpation. The links between the impact of urbanization on host communities and their gut microbiota have only been scarcely explored. In this study, we tested the hypothesis that the gut microbiota (GM) could play a role in host adaptation to urban environments. We addressed this question by studying several species of small terrestrial mammals sampled in forested areas along a forested gradient of urbanization (from rural forests to urban parks) during 2020 fall. The gut was collected and bacteria were described using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM. We analyzed these changes in terms of the presence and abundance of taxa and their putative functions to decipher the processes underlying these changes. We found that urbanization had marked impacts on small mammal communities and their GM, either directly or indirectly depending on small mammal species categories. The urban dweller species had a lower taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, which could indicate dysbiosis in these urban species. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite potential dysbiosis. Urbanization could also impact the diversity and taxonomic composition of GM in urban adapter species. However, their functional diversity and composition remained relatively stable. This observation can be explained by functional redundancy, where certain taxa express the same function. This could explain the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedback loops between the gut microbiota and the host species within communities, enabling rapid and flexible adaptation.

ecology↗

bioRxiv2023

Evolution and Genetic Characterization of Seoul Virus in Wild Rats Rattus Norvegicus from an urban park in Lyon, France 2020-2022

Seoul virus (SEOV) is an orthohantavirus primarily carried by rats that can cause hemorrhagic fever with renal syndrome (HFRS) in humans. Nowaday s, its incidence is likely underestimated. We developed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus population from a popular urban park within a large city ( Park of La Tete dOr, Lyon, France) between 2020 and 2022. We confirmed the circulation of SEOV in rats from the park (seroprevalence 17.2%). The SEOV strains detected showed high genetic similar ity with the strain previously described in 2013 in this area. We found low structuring of wild rat populations within Lyon city. This study confirms the circulation of SEOV in Lyon city, in a park where opportunities for SEOV transmission to humans are numerous. Given the high gene flow between rat populations in the park and the rest of the city, we recommend conducting city-wide SEOV surveillance.

microbiology↗

bioRxiv2022

Serological surveillance for wild rodent infection with SARS-CoV-2 in Europe

We report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.

microbiology↗

bioRxiv2022

Small scale geographical variation of three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations

BackgroundDespite its central role in host fitness, the gut microbiota may differ greatly between individuals. This variability is often mediated by environmental or host factors such as diet, genetics, and infections. Recently, a particular attention has been given to the interactions between gut bacteriota and helminths, as these latter could affect host susceptibility to other infections. Further studies are still required to better understand the three-way interactions between gut bacteriota, helminths and other parasites, especially because previous findings have been very variable, even for comparable host-parasite systems. MethodsIn our study, we used the V4 region of the 16S rRNA gene to assess the variability of gut bacteriota diversity and composition in wild populations of a small mammal, the bank vole Myodes glareolus. Four sites were sampled at a regional geographical scale (100 km) along a North-South transect in Eastern France. We applied analyses of community and microbial ecology to evaluate the interactions between the gut bacteriota, the gastro-intestinal helminths and the pathogenic bacteria detected in the spleen. ResultsWe identified important variations of the gut bacteriota composition and diversity among bank voles. They were mainly explained by sampling localities and reflected the North/South sampling transect. In addition, we detected two main enterotypes, that might correspond to contrasted diets. We found geographic variations of the Firmicutes/Bacteroidetes ratio, that correlated positively with body mass index. We found positive correlations between the specific richness of the gut bacteriota and of the helminth community, as well as between the composition of these two communities, even when accounting for the influence of geographical distance. The helminths Aonchotheca murissylvatici, Heligmosomum mixtum and the bacteria Bartonella sp were the main taxa associated with the whole gut bacteriota composition. Besides, changes in relative abundance of particular gut bacteriota taxa were specifically associated with other helminths (Mastophorus muris, Catenotaenia henttoneni, Paranoplocephala omphalodes and Trichuris arvicolae) or pathogenic bacteria. Especially, infections with Neoehrlichia mikurensis, Orientia sp, Rickettsia sp and P. omphalodes were associated with lower relative abundance of the family Erysipelotrichaceae (Firmicutes), while coinfections with higher number of bacterial infections were associated with lower relative abundance of a Bacteroidales family (Bacteroidetes). ConclusionsThese results emphasize complex interlinkages between gut bacteriota and infections in wild animal populations. They remain difficult to generalize due to the strong impact of environment on these interactions, even at regional geographical scales. Abiotic features, as well as small mammal community composition and within host parasite coinfections, should now be considered to better understand the spatial variations observed in the relationships between gut bacteriota, gastro-intestinal helminths and bacterial infections.

ecology↗

bioRxiv2020

How bank vole-PUUV interactions influence the eco-evolutionary processes driving nephropathia epidemica epidemiology: An experimental and genomic approach.

In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of haemorrhagic fever with renal syndrome (HFSR). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas, and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. We showed that the serological response and the presence of PUUV in excretory organs were more important in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs was higher than in other non-excretory organs for the NE endemic cross-infection, but not for the NE non-endemic cross-infection. Altogether, our results showed that genetically different PUUV strains, and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans, and in turn at least partly shape NE epidemiology in France.

evolutionary biology↗

bioRxiv2020

First isolation and genetic characterization of Puumala orthohantavirus strains from France

Puumala orthohantavirus (PUUV) causes a mild form of haemorrhagic fever with renal syndrome (HFRS) called nephropathia epidemica (NE), regularly diagnosed in Europe. France represents the western frontier of the expansion of NE in Europe with two distinct areas: an endemic area (north-eastern France) where PUUV circulates in rodent populations, with detection of many human NE cases, and a non-endemic area (south-western France) where the virus is not detected, with only a few human cases being reported. France is thus a relevant country in which to study the factors that influence the evolution of PUUV distribution. In this study, we describe for the first time the isolation of two PUUV strains from two distinct French geographical areas: Ardennes (endemic area) and Loiret (non-endemic area). To isolate PUUV efficiently, we selected wild bank voles (Myodes glareolus, the specific reservoir of PUUV) captured in these areas and that were seronegative for anti-PUUV IgG (ELISA), but showed a non-negligible viral RNA load in their lung tissue (qRT-PCR). With this study design, we were able to cultivate and maintain these two strains in Vero E6 cells and also propagate both strains in immunologically neutral bank voles efficiently and rapidly. Complete coding sequences of the S and M segments were determined by Sanger sequencing from RNA extracted from positive bank voles (naturally and experimentally infected) and from supernatants of Vero E6 cell extracts. For the M segment, nucleotide sequences were 100% identical for both strains. For the S segment, the amino-acid sequences from each strain revealed one mismatch between sequences obtained from tissue and from cell supernatants, revealing distinct "bank vole" and a "cell" molecular profile. High-throughput sequencing confirmed Sanger results, and provided a better assessment of the impact of isolation methods on intra-host viral diversity.

microbiology↗

bioRxiv2020

eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio-temporal plasticity

Dietary plasticity is an important issue for conservation biology as it may be essential for species to cope with environmental changes. However, this process still remains scarcely addressed in the literature, potentially because diet studies have long been constrained by methodological limits. The advent of molecular approaches now makes it possible to get a precise picture of diet and its plasticity, even for endangered and elusive species. Here we focused on the greater horseshoe bat (Rhinolophus ferrumequinum) in Western France, where this insectivorous species has been classified as Vulnerable on the Regional Red List in 2016. We applied an eDNA metabarcoding approach on 1986 fecal samples collected in six maternity colonies at three sampling dates. We described its diet and investigated whether the landscape surrounding colonies and the different phases of the maternity cycle influenced the diversity and the composition of this diet. We showed that R. ferrumequinum feed on a highly more diverse spectrum of prey than expected from previous studies, therefore highlighting how eDNA metabarcoding can help improving diet knowledge of a flying elusive endangered species. Our approach also revealed that R. ferrumequinum diet is composed of two distinct features: the core diet consisting in a few preferred taxa shared by all the colonies (25% of the occurrences) and the secondary diet consisting in numerous rare prey that were highly different between colonies and sampling dates (75% of the occurrences). Energetic needs and constraints associated with the greater horseshoe bat life-cycle, as well as insect phenology and landscape features, strongly influenced the diversity and composition of both the core and whole diets. Further research should now explore the relationships between R. ferrumequinum dietary plasticity and fitness, to better assess the impact of core prey decline on R. ferrumequinum populations viability.

ecology↗

bioRxiv2020

Pathogen community composition and co-infection patterns in a wild community of rodents

Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.

ecology↗

bioRxiv2019

In silico and empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

This last decade, environmental DNA metabarcoding approaches have been developed and improved to minimize biological and technical biases; some challenges, however, remain, as the design of primers. Here we have performed a comprehensive assessment of ten COI and two 16S primer sets. We have combined in silico, in vivo-mock community of 33 arthropod taxa from 16 orders and guano analyses to identify primer sets that should maximize arthropod detection and taxonomic identification, whilst identifying bat species and minimizing labour time and cost. We have focused on two insectivorous bat species living in mixed-colonies, the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroys bat (Myotis emarginatus). We have found that the level of primer degeneracy is the main factor influencing arthropod detection for in silico and mock community analyses, while the amplicon length is critical for the detection of arthropods from degraded DNA samples. Our results confirm the importance of performing predator detection and taxonomic identification, simultaneously with arthropod sequencing, as faeces samples can be contaminated by different insectivorous species. Moreover, amplifying bat DNA does not affect the primers capacity to detect arthropods. We therefore recommend the systematic simultaneous identification of predator and prey. Finally, we evidenced that one third of the prey occurrences are unreliable and probably not of primary interest in diet studies, which might decrease the relevance of combining several primer sets instead of using one efficient primer set. In conclusion, this study provides general criteria enabling the selection of primers whilst considering different scientific and methodological constraints.

molecular biology↗

bioRxiv2019

Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history of R. ferrumequinum colonies in the Western European part of its distribution. We found high levels of genetic diversity and large population size on the European mainland and lower estimates in England and Northern France. Analyses of clustering and isolation by distance showed a barrier effect of the Channel and potentially of the Mediterranean Sea on R. ferrumequinum bat dispersal. Conversely, we could not reveal any gene flow disruption from both sides of the Western Pyrenees. These results provide important information to improve the delineation of R. ferrumequinum management units in its western range. We suggest that a large management unit corresponding to the European mainland population must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and Northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.

evolutionary biology↗

bioRxiv2018

Fluctuating pathogen-mediated selection drives the maintenance of innate immune gene polymorphism in a widespread wild ungulate

Toll-like Receptors (TLR) play a central role in recognition and host frontline defence against a wide range of pathogens. A number of recent studies have shown that TLR genes (Tlrs) often exhibit a large polymorphism in natural populations. Yet, there is little knowledge on how this polymorphism is maintained and how it influences disease susceptibility in the wild. In a previous work, we showed that some Tlrs exhibit similarly high levels of genetic diversity than Mhc and contemporary signatures of balancing selection in roe deer (Capreolus capreolus), an abundant and widespread ungulate in Europe. Here, we tested whether Mhc-Drb or Tlr (Tlr2, Tlr4 and Tlr5) diversity is driven by pathogen-mediated selection. We examined the relationships between their genotype (heterozygosity status and presence of specific alleles) and infections with Toxoplasma and Chlamydia, two intracellular pathogens known to cause reproductive failure in ungulates. We showed that Toxoplasma and Chlamydia exposures vary significantly across year and landscape structure with few co-infection events detected, and that the two pathogens act antagonistically on Tlr2 polymorphism. By contrast, we found no evidence of association with Mhc-Drb and a limited support for Tlr heterozygosity advantage. Our study confirmed the importance of looking beyond Mhc genes in wildlife immunogenetic studies. It also emphasized the necessity to consider multiple pathogen challenges and their spatiotemporal variation to improve our understanding of vertebrate defence evolution against pathogens.

evolutionary biology↗