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1. Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Author: Marie Bouilloud, Maxime Galan, Julien Pradel, Anne Loiseau, Julien Ferrero, Romain Gallet, Benjamin Roche, and Nathalie Charbonnel
Subjects: Community, Dysbiosis, Bacterial gut microbiota, Rodents, Urban ecology, Wildlife, Veterinary medicine, SF600-1100, Microbiology, QR1-502
Abstract: Abstract Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial 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, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.
Published: 2024
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2. Evolution and genetic characterization of Seoul virus in wild rats Rattus norvegicus from an urban park in Lyon, France 2020-2022.

Author: Hussein Alburkat, Teemu Smura, Marie Bouilloud, Julien Pradel, Gwendoline Anfray, Karine Berthier, Lara Dutra, Anne Loiseau, Thanakorn Niamsap, Viktor Olander, Diana Sepulveda, Vinaya Venkat, Nathalie Charbonnel, Guillaume Castel, and Tarja Sironen
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: BackgroundSeoul virus (SEOV) is an orthohantavirus primarily carried by rats. In humans, it may cause hemorrhagic fever with renal syndrome (HFRS). Its incidence is likely underestimated and given the expansion of urban areas, a better knowledge of SEOV circulation in rat populations is called for. Beyond the need to improve human case detection, we need to deepen our comprehension of the ecological, epidemiological, and evolutionary processes involved in the transmission of SEOV.Methodology / principal findingsWe performed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus in a popular urban park within a large city (Lyon, France) to provide essential information to design surveillance strategies regarding SEOV. We sampled rats within the urban park of 'La Tête d'Or' in Lyon city from 2020 to 2022. We combined rat population genetics, immunofluorescence assays, SEOV high-throughput sequencing (S, M, and L segments), and phylogenetic analyses. We found low structuring of wild rat populations within Lyon city. Only one sampling site within the park (building created in 2021) showed high genetic differentiation and deserves further attention. We confirmed the circulation of SEOV in rats from the park with high seroprevalence (17.2%) and high genetic similarity with the strain previously described in 2011 in Lyon city.Conclusion/significanceThis study confirms the continuous circulation of SEOV in a popular urban park where the risk for SEOV transmission to humans is present. Implementing a surveillance of this virus could provide an efficient early warning system and help prepare risk-based interventions. As we reveal high gene flow between rat populations from the park and the rest of the city, we advocate for SEOV surveillance to be conducted at the scale of the entire city.
Published: 2024
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3. Small terrestrial mammals (Rodentia and Soricomorpha) along a gradient of forest anthropisation (reserves, managed forests, urban parks) in France

Author: Julien Pradel, Marie Bouilloud, Anne Loiseau, Sylvain Piry, Maxime Galan, Emmanuelle Artige, Guillaume Castel, Julien Ferrero, Romain Gallet, Geoffrey Thuel, Nathalie Vieira, and Nathalie Charbonnel
Subjects: rodents, shrews, community, biodiversity, forests, Biology (General), QH301-705.5
Abstract: Understanding the relationships between wildlife biodiversity and zoonotic infectious diseases in a changing climate is a challenging issue that scientists must address to support further policy actions. We aim at tackling this challenge by focusing on small mammal-borne diseases in temperate forests and large urban green spaces. Small mammals are important reservoirs of zoonotic agents, with a high transmission potential for humans and domestic animals. Forests and large urban green spaces are ecosystems where efforts are undertaken to preserve biodiversity. They are put forward for their contribution to human well-being in addition to other ecosystem services (e.g. provisioning and regulating services). Moreover, forests and large urban green spaces are environments where small mammals are abundant and human/domestic-wildlife interactions are plausible to occur. These environments are, therefore, focal points for conservation management and public health issues.The European Biodiversa BioRodDis project (https://www6.inrae.fr/biodiversa-bioroddis) aims at better understanding the relationships between small terrestrial mammal biodiversity and health in the context of global change and, in particular, of forest anthropisation and urbanisation. Here, we present the data gathered in France. The dataset will enable us to describe the diversity of small terrestrial mammal communities in forested areas corresponding to different levels of anthropisation and to evaluate the variability of this diversity over time, between seasons and years.The dataset contains occurrences of small terrestrial mammals (Rodentia and Soricomorpha) trapped in forested areas in eastern France (administrative Departments: Rhône, Ain, Jura). The sampling sites correspond to different degrees of anthropisation. Forests included in biological reserves are the least anthropised sites. Then, public forests and urban parks experience increasing levels of anthropisation. Data were collected during spring and autumn 2020 (three to four sampling sites), 2021 (six sampling sites) and 2022 (four sampling sites). These variations in the number of sites between years were due to lockdown restrictions in 2020 or to the legal authorisation to trap around biological reserves granted in 2021 only. The capture of animals was carried out in various types of forests (pine, deciduous, mixed) and in different habitats within urban parks (wooded areas, buildings, hay storage yards, riverside vegetation, restaurants, playground for kids, botanical garden, landfills). Animals were captured using live traps that were set on the ground for one to 11 nights. During this study period, 1593 small mammals were trapped and identified. They belong to 15 species, amongst which were nine species of rodents (Muridae, Cricetidae, Gliridae) and six species of shrews (Soricidae). They were weighted (gram) and measured (cm): head-body length, tail length and hind-foot length. Sexual characteristics were also recorded.
Published: 2022
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4. Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

Author: Laure Olazcuaga, Julien Foucaud, Candice Deschamps, Anne Loiseau, Jean‐Loup Claret, Romain Vedovato, Robin Guilhot, Cyril Sévely, Mathieu Gautier, Ruth A. Hufbauer, Nicolas O. Rode, and Arnaud Estoup
Subjects: Adaptive phenotypic plasticity, Drosophila suzukii, genetic effects, host fruits, local adaptation, reciprocal common garden experiment, Evolution, QH359-425
Abstract: Abstract Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, whereas highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used Drosophila suzukii as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural D. suzukii populations collected from cherry, strawberry, and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.
Published: 2022
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5. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Author: Orianne Tournayre, Jean‐Baptiste Pons, Maxime Leuchtmann, Raphael Leblois, Sylvain Piry, Ondine Filippi‐Codaccioni, Anne Loiseau, Jeanne Duhayer, Inazio Garin, Fiona Mathews, Sébastien Puechmaille, Nathalie Charbonnel, and Dominique Pontier
Subjects: Chiroptera, connectivity, conservation, demographic inference, microsatellites, population genetics, Ecology, QH540-549.5
Abstract: Abstract 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 part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining 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 the near future.
Published: 2019
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6. A new suite of twenty-two polymorphic microsatellite loci in the parasitic wasp, Habrobracon hebetor (Hymenoptera: Braconidae): Promising molecular tools for studying the population genetics of several beneficial braconid species

Author: Madougou GARBA, Anne LOISEAU, Laure BENOIT, and Nathalie GAUTHIER
Subjects: hymenoptera, braconidae, habrobracon hebetor, bracon spp., biological control, parasitic wasp, microsatellite, population genetics, gene flow, Zoology, QL1-991
Abstract: Combining a biotin-enrichment protocol and 454GS-FLX titanium pyrosequencing technology, we characterised 22 polymorphic microsatellite loci from the parasitic wasp, Habrobracon hebetor (Say) (Hymenoptera: Braconidae), a cosmopolitan species commonly used in biological control against a wide range of both major lepidopterous pests of stored products and field crops in different parts of the world. Three multiplex PCR sets were optimised and characterised across 46 H. hebetor specimens from two samples collected from millet fields in Niger. Two to 11 alleles were found per locus and observed heterozygosity ranged from 0.289 to 0.826. Polymorphism was detected in both samples with a similar level of observed heterozygosity (0.482 vs. 0.502) and number of alleles (4.1 vs. 3.6). Deviation from Hardy-Weinberg equilibrium was detected at the same five loci in both samples and five or seven more loci in each sample but was not associated with heterozygote deficiencies. Even though evidence for linkage disequilibrium was found between a few alleles, these new loci segregated independently. The variability of the 22 loci will enable estimates of genetic diversity and structure patterns, as well as gene flow between H. hebetor populations at different spatial scales. Cross-species amplifications were successful among the six Bracon spp. tested and nine loci will be particularly appropriate for population genetic studies in B. brevicornis.
Published: 2016
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7. Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica

Author: Séverine Murri, Sarah Madrières, Caroline Tatard, Sylvain Piry, Laure Benoit, Anne Loiseau, Julien Pradel, Emmanuelle Artige, Philippe Audiot, Nicolas Leménager, Sandra Lacôte, Johann Vulin, Nathalie Charbonnel, Philippe Marianneau, and Guillaume Castel
Subjects: Myodes glareolus, Puumala virus, diversity, molecular evolution, nephropathia epidemica, France, Medicine
Abstract: Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.
Published: 2020
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8. How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology—An Experimental and Genomic Approach

Author: Sarah Madrières, Caroline Tatard, Séverine Murri, Johann Vulin, Maxime Galan, Sylvain Piry, Coralie Pulido, Anne Loiseau, Emmanuelle Artige, Laure Benoit, Nicolas Leménager, Latifa Lakhdar, Nathalie Charbonnel, Philippe Marianneau, and Guillaume Castel
Subjects: Puumala virus, Myodes glareolus, France, experimental cross-infections, within-host viral diversity, transmission, Medicine
Abstract: In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). 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. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, 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.
Published: 2020
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9. New set of microsatellite markers for the spotted-wing Drosophila suzukii (Diptera: Drosophilidae): A promising molecular tool for inferring the invasion history of this major insect pest

Author: Antoine FRAIMOUT, Anne LOISEAU, Donald K. PRICE, Anne XUÉREB, MARTIN Jean-François, Renaud VITALIS, Simon FELLOUS, Vincent DEBAT, and Arnaud ESTOUP
Subjects: diptera, drosophilidae, drosophila suzukii, population genetics, microsatellite, invasion routes, invasive species, genetic structure, Zoology, QL1-991
Abstract: Historical and observational data for invasive species are often sparse and incomplete, so molecular genetic markers are increasingly used and have proved to be efficient tools to make inferences about invasion histories. Here, we report the development of 28 polymorphic microsatellite markers in the invasive spotted-wing drosophila, Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae) designed from recent genomics resources, and their cross-amplification in closely related Drosophila species of the suzukii subgroup. The markers, located on autosomal chromosomes, were characterized in two distinct invasive populations from France and Hawaii (USA), and in four sister species of the suzukii subgroup. They all showed substantial polymorphism as well as revealing strong genetic differentiation between the two genotyped populations. These markers represent a promising molecular tool for population genetic studies on D. suzukii, more especially in order to reconstruct the pathways and demographic processes of the world-wide invasion in this major insect pest.
Published: 2015
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10. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

Author: Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Helene Vignes, and Jean-François Cosson
Subjects: bacteria, emerging infectious diseases, high-throughput sequencing, metabarcoding, molecular epidemiology, next-generation sequencing, Microbiology, QR1-502
Abstract: ABSTRACT The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculusdomesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.
Published: 2016
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11. Urban Market Gardening and Rodent-Borne Pathogenic Leptospira in Arid Zones: A Case Study in Niamey, Niger.

Author: Gauthier Dobigny, Madougou Garba, Caroline Tatard, Anne Loiseau, Max Galan, Ibrahima Kadaouré, Jean-Pierre Rossi, Mathieu Picardeau, and Eric Bertherat
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: Leptospirosis essentially affects human following contact with rodent urine-contaminated water. As such, it was mainly found associated with rice culture, recreational activities and flooding. This is also the reason why it has mainly been investigated in temperate as well as warm and humid regions, while arid zones have been only very occasionally monitored for this disease. In particular, data for West African countries are extremely scarce. Here, we took advantage of an extensive survey of urban rodents in Niamey, Niger, in order to look for rodent-borne pathogenic Leptospira species presence and distribution across the city. To do so, we used high throughput bacterial 16S-based metabarcoding, lipL32 gene-targeting RT-PCR, rrs gene sequencing and VNTR typing as well as GIS-based multivariate spatial analysis. Our results show that leptospires seem absent from the core city where usual Leptospira reservoir rodent species (namely R. rattus and M. natalensis) are yet abundant. On the contrary, L. kirschneri was detected in Arvicanthis niloticus and Cricetomys gambianus, two rodent species that are restricted to irrigated cultures within the city. Moreover, the VNTR profiles showed that rodent-borne leptospires in Niamey belong to previously undescribed serovars. Altogether, our study points towards the importance of market gardening in maintain and circulation of leptospirosis within Sahelian cities. In Africa, irrigated urban agriculture constitutes a pivotal source of food supply, especially in the context of the ongoing extensive urbanization of the continent. With this in mind, we speculate that leptospirosis may represent a zoonotic disease of concern also in arid regions that would deserve to be more rigorously surveyed, especially in urban agricultural settings.
Published: 2015
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12. Characterization of polymorphic microsatellite loci in the neotropical plant-ant Allomerus decemarticulatus (Formicidae: Myrmicinae) and multiplexing with other microsatellites from the ant subfamily Myrmicinae

Author: Pierre-Jean G. MALÉ, Anne LOISEAU, Arnaud ESTOUP, Angélique QUILICHINI, and Jérôme ORIVEL
Subjects: hymenoptera, formicidae, myrmicinae, allomerus, ant-plant mutualism, microsatellites, plant-ant, Zoology, QL1-991
Abstract: Five polymorphic microsatellite loci of the arboreal ant Allomerus decemarticulatus (Myrmicinae) were isolated and characterized. The amplification and polymorphism of seven additional microsatellite loci, previously developed for the ant species A. octoarticulatus and Wasmannia auropunctata, were also tested and the amplification conditions necessary for genotyping the complete set of 12 multiplexed markers in A. decemarticulatus determined. The number of alleles per locus ranged from three to 15 and observed heterozygosity varied from 0.09 to 0.95. Cross-species amplification of these loci was also successfully achieved in additional species of the same ant subfamily, Myrmicinae. This set of microsatellite markers will be used in studies on the mating system and population genetic structure of Myrmicinae in general and A. decemarticulatus in particular.
Published: 2010
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13. Distribution of endosymbiotic reproductive manipulators reflects invasion process and not reproductive system polymorphism in the little fire ant Wasmannia auropunctata.

Author: Olivier Rey, Arnaud Estoup, Benoit Facon, Anne Loiseau, Alexandre Aebi, Olivier Duron, Fabrice Vavre, and Julien Foucaud
Subjects: Medicine, Science
Abstract: Endosymbiotic reproductive manipulators may have drastic effects on the ecological and evolutionary dynamics of their hosts. The prevalence of these endosymbionts reflects both their ability to manipulate their hosts and the history of the host populations. The little fire ant Wasmannia auropunctata displays a polymorphism in both its reproductive system (sexual versus clonal populations) and the invasive status of its populations (associated to a habitat shift). We first screened for the presence of a diverse array of reproductive parasites in sexual and clonal populations of W. auropunctata, as a means to investigate the role of endosymbionts in reproductive phenotypes. Wolbachia was the only symbiont found and we then focused on its worldwide distribution and diversity in natural populations of W. auropunctata. Using a multilocus scheme, we further characterized the Wolbachia strains present in these populations. We found that almost all the native sexual populations and only a few clonal populations are infected by Wolbachia. The presence of similar Wolbachia strains in both sexual and clonal populations indicates that they are probably not the cause of the reproductive system polymorphism. The observed pattern seems rather associated to the invasion process of W. auropunctata. In particular, the observed loss of Wolbachia in clonal populations, that recurrently emerged from sexual populations, likely resulted from natural heat treatment and/or relaxed selection during the shift in habitat associated to the invasion process.
Published: 2013
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14. Increase in male reproductive success and female reproductive investment in invasive populations of the harlequin ladybird Harmonia axyridis.

Author: Guillaume J M Laugier, Gilles Le Moguédec, Ashraf Tayeh, Anne Loiseau, Naoya Osawa, Arnaud Estoup, and Benoît Facon
Subjects: Medicine, Science
Abstract: Reproductive strategy affects population dynamics and genetic parameters that can, in turn, affect evolutionary processes during the course of biological invasion. Life-history traits associated with reproductive strategy are therefore potentially good candidates for rapid evolutionary shifts during invasions. In a series of mating trials, we examined mixed groups of four males from invasive and native populations of the harlequin ladybird Harmonia axyridis mating freely during 48 hours with one female of either type. We recorded the identity of the first male to copulate and after the 48 h-period, we examined female fecundity and share of paternity, using molecular markers. We found that invasive populations have a different profile of male and female reproductive output. Males from invasive populations are more likely to mate first and gain a higher proportion of offspring with both invasive and native females. Females from invasive populations reproduce sooner, lay more eggs, and have offspring sired by a larger number of fathers than females from native populations. We found no evidence of direct inbreeding avoidance behaviour in both invasive and native females. This study highlights the importance of investigating evolutionary changes in reproductive strategy and associated traits during biological invasions.
Published: 2013
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15. Plague circulation and population genetics of the reservoir Rattus rattus: the influence of topographic relief on the distribution of the disease within the Madagascan focus.

Author: Carine Brouat, Soanandrasana Rahelinirina, Anne Loiseau, Lila Rahalison, Minoariso Rajerison, Dominique Laffly, Pascal Handschumacher, and Jean-Marc Duplantier
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: BACKGROUND:Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. METHODOLOGY/PRINCIPAL FINDINGS:We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. CONCLUSIONS/SIGNIFICANCE:Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.
Published: 2013
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16. Contrasted patterns of selection on MHC-linked microsatellites in natural populations of the Malagasy plague reservoir.

Author: Charlotte Tollenaere, Svilena Ivanova, Jean-Marc Duplantier, Anne Loiseau, Lila Rahalison, Soanandrasana Rahelinirina, and Carine Brouat
Subjects: Medicine, Science
Abstract: Plague (Yersinia pestis infection) is a highly virulent rodent disease that persists in many natural ecosystems. The black rat (Rattus rattus) is the main host involved in the plague focus of the central highlands of Madagascar. Black rat populations from this area are highly resistant to plague, whereas those from areas in which the disease is absent (low altitude zones of Madagascar) are susceptible. Various lines of evidence suggest a role for the Major Histocompatibility Complex (MHC) in plague resistance. We therefore used the MHC region as a candidate for detecting signatures of plague-mediated selection in Malagasy black rats, by comparing population genetic structures for five MHC-linked microsatellites and neutral markers in two sampling designs. We first compared four pairs of populations, each pair including one population from the plague focus and one from the disease-free zone. Plague-mediated selection was expected to result in greater genetic differentiation between the two zones than expected under neutrality and this was observed for one MHC-class I-linked locus (D20Img2). For this marker as well as for four other MHC-linked loci, a geographic pattern of genetic structure was found at local scale within the plague focus. This pattern would be expected if plague selection pressures were spatially variable. Finally, another MHC-class I-linked locus (D20Rat21) showed evidences of balancing selection, but it seems more likely that this selection would be related to unknown pathogens more widely distributed in Madagascar than plague.
Published: 2012
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17. Evolution and Genetic Characterization of Seoul Virus in Wild RatsRattus Norvegicusfrom an urban park in Lyon, France 2020-2022

Author: Hussein Alburkat, Teemu Smura, Marie Bouilloud, Julien Pradel, Gwendoline Anfray, Karine Berthier, Lara Dutra, Anne Loiseau, Thanakorn Niamsap, Viktor Olander, Diana Sepulveda, Vinaya Venkat, Nathalie Charbonnel, Guillaume Castel, and Tarja Sironen
Abstract: 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 inRattus norvegicuspopulation from a popular urban park within a large city (‘Park of La Tête d’Or’, 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.
Published: 2023
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18. Biological invasions in international seaports: a case study of exotic rodents in Cotonou

Author: Sylvestre Badou, Karmadine Hima, Clément Agbangla, Philippe Gauthier, Antoine A. Missihoun, Gualbert Houéménou, Anne Loiseau, Carine Brouat, Gauthier Dobigny, Ecole Polytechnique d'Abomey Calavi (EPAC), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université Abdou Moumouni [Niamey], Unité Peste - Plague Unit [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Sylvestre Badou was granted a Doctoral Research Fellowship (ARTS) by IRD (2019–2022). Data used in this work were produced through the genotyping and sequencing facilities of Labex CeMEB mutualized GenSeq platform (Mediterranean Center for Environment and Biodiversity, Genotyping-Sequencing Platform). This work is part of the PASPort/PPSE project funded by ACP, IRD and ENABEL., and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: Urban Studies, Rodent management, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, Population genetics, Movement, Urban, Invasive rodents Population genetics Movement Urban Rodent management, Invasive rodents
Abstract: Black rat (Rattus rattus), brown rat (Rattus norvegicus), and house mouse (Mus musculus) are known to be among the most common anthropophilic rodent species in cities worldwide. These species are responsible for the destruction of domestic and industrial materials, considerable damage to food stocks as well as zoonotic pathogens circulation and transmission to humans and animals. These invasive species have disseminated in all continents following human-mediated exchanges, especially maritime transports. In particular, seaports appear as privileged rats and mice’s entry points into new regions, thus making them international regulations’ priorities for rodent surveillance and management. Yet, studies on seaport rodents are rare; in particular, investigations on their genetic structure are almost inexistent, thus precluding science-guided interventions. In order to fill such a gap, our study focused on the population genetics of R. rattus, R. norvegicus and M. musculus in the Autonomous Port of Cotonou, Benin. Nine different sites were surveyed for three years. In total, 366 R. rattus, 188 R. norvegicus and 244 M. musculus were genotyped using 18 microsatellites, 16 microsatellites and 17 microsatellites, respectively. Our results show very well-structured genetic clusters in all three species as well as limited impacts of rodent control campaigns. Using comparisons with genotypes from other European, Asian and African countries, we suggest for the first time that settlement of newly introduced individuals may be a rare event. Implications in terms of management units and control and monitoring are discussed.
Published: 2023
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19. Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: insights from Acanthodactylus erythrurus (Reptilia: Lacertidae)

Author: Paul Doniol-Valcroze, Loïs Rancilhac, José Carlos Brito, Aurélien Miralles, Philippe Geniez, Laure Benoit, Anne Loiseau, Raphaël Leblois, Christophe Dufresnes, and Pierre-André Crochet
Abstract: Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotspot which still hosts a large fraction of unrecognised biodiversity, notably in small vertebrates. Species delimitations have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification in this context can be obscured by incomplete lineage sorting, introgression or isolation by distance. Recently, integrative approaches coupling various sets of characters or analyses of contact zones aiming at estimating reproductive isolation (RI) have been advocated instead. Analyses of introgression patterns in contact zone with genomic data represent a powerful way to confirm the existence of independent lineages and estimate the strength of their RI at the same time. The Spiny-footed Lizard Acanthodactylus erythrurus (Schinz, 1833) is widespread in the Iberian Peninsula and the Maghreb and exhibits a large amount of genetic diversity, although the precise number and distribution of its genetic lineages remain poorly understood. We applied a RADseq approach to obtain a genome wide SNPs dataset on a contact zone in central Morocco between the previously described Rif and Middle-Atlas lineages. We show that these two lineages exhibit strong RI across this contact zone, as shown by the limited amount and restricted spatial extant of gene flow. We interpret these results as evidence for species-level divergence of these two lineages. Our study confirms the usefulness of RADseq approaches applied on contact zones for cryptic diversity studies and therefore to resolve Linnaean and Wallacean shortfalls.
Published: 2022
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20. Prise en charge de la malnutrition aiguë modérée à Madagascar, s’appuyant sur la méthodologie des Nutricartes®

Author: Anne Loiseau and Emilie Maucoeur
Subjects: Pharmacology (medical)
Published: 2020
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21. Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)

Author: Marion Borderon, Philippe Gauthier, Arame Ndiaye, Karine Berthier, Carine Brouat, Mamadou Kane, Laurent Granjon, Claire Stragier, Sylvain Piry, Youssoupha Niang, Aliou Sow, Mamoudou Diallo, Anne Loiseau, Institut de Recherche pour le Développement (IRD [Réunion]), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Vienna [Vienna], Unité de Pathologie Végétale (PV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Developpement (IRD) funding, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, microsatellite, Rodent, cityscape, socio-economic urban habitat, Population genetics, 010603 evolutionary biology, 01 natural sciences, House mouse, West africa, 03 medical and health sciences, Sénégal, Urbanization, biology.animal, Genetic variation, D-loop, invasion biology, 030304 developmental biology, 0303 health sciences, Mus musculus domesticus, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], population genetics, landscape genetics, 15. Life on land, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Geography, Evolutionary biology, Genetic structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Cityscape, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Population 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.
Published: 2022
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22. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Author: Raphaël Leblois, Jean-Baptiste Pons, Ondine Filippi-Codaccioni, Anne Loiseau, Dominique Pontier, Jeanne Duhayer, Fiona Mathews, Maxime Leuchtmann, Sylvain Piry, Sébastien J. Puechmaille, Nathalie Charbonnel, Inazio Garin, Orianne Tournayre, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Lyon, Nature environment, Partenaires INRAE, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of Sussex, GCMP, CREN, Toulouse, France, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), LABEX CEMEB : ANR-11-IDEX-0007, LABEX ECOFECT : ANR-11-LABX-0048 European Union (EU), DREAL Nouvelle-Aquitaine, Region Auvergne-Rhone-Alpes, Region Bourgogne-Franche-Comte, Region Hauts-de-France, Region Nouvelle-Aquitaine, ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: 0106 biological sciences, Demographic history, Population, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Chiroptera, lcsh:QH540-549.5, Biologie animale, IUCN Red List, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, connectivity, conservation, demographic inference, population genetics, 030304 developmental biology, Nature and Landscape Conservation, Isolation by distance, Animal biology, 0303 health sciences, education.field_of_study, Near-threatened species, Habitat fragmentation, Ecology, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Rhinolophus ferrumequinum, 15. Life on land, biology.organism_classification, Geography, Threatened species, Biological dispersal, lcsh:Ecology
Abstract: 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 EuropeanIUCN Red List of Threatened Animalsand 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 ofR. ferrumequinumcolonies 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 onR. ferrumequinumbat 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 ofR. ferrumequinummanagement 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.
Published: 2019
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23. Oviposition Preference and Larval Performance of Drosophila suzukii (Diptera: Drosophilidae), Spotted-Wing Drosophila: Effects of Fruit Identity and Composition

Author: Anne Loiseau, Ruth A. Hufbauer, Nicolas O. Rode, Arnaud Estoup, Julien Foucaud, Virginie Ravigné, Aurélien Ausset, Mathieu Gautier, Nicolas Leménager, Laure Olazcuaga, Benoit Facon, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Colorado State University [Fort Collins] (CSU), Region Occitanie, INRA Scientific Department SPE (AAP-SPE), French National Research Agency (ANR) : ANR-16-CE02-0015-01, National Science Foundation (NSF) : DEB-0949619, USDA Agriculture and Food Research Initiative award : 2014-67013-21594, United States Department of Agriculture (USDA) : 1012868, French Agropolis Fondation (LabEx Agro-Montpellier) : CfP 2015-02, French National Research Agency (ANR), LabEx CEMEB, CeMEB LabEx/University of Montpellier : ANR-10-LABX-04-01, European Union (EU), and Conseil Regional de la Reunion
Subjects: 0106 biological sciences, Integrated pest management, compound, Oviposition, Biology, Fragaria, 01 natural sciences, 03 medical and health sciences, Drosophilidae, Animals, chemical composition, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Drosophila suzukii, Drosophila, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Larva, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, food and beverages, biology.organism_classification, Preference, Blowing a raspberry, 010602 entomology, Horticulture, mother knows best hypothesis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fruit, Insect Science, host use, Female, PEST analysis
Abstract: A better understanding of the factors affecting host plant use by spotted-wing drosophila (Drosophila suzukii) could aid in the development of efficient management tools and practices to control this pest. Here, proxies of both preference (maternal oviposition behavior) and performance (adult emergence) were evaluated for 12 different fruits in the form of purees. The effect of the chemical composition of the fruits on preference and performance traits was then estimated. We synthesized the literature to interpret our findings in the light of previous studies that measured oviposition preference and larval performance of D. suzukii. We show that fruit identity influences different parts of the life cycle, including oviposition preference under both choice and no-choice conditions, emergence rate, development time, and number of emerging adults. Blackcurrant was always among the most preferred fruit we used, while grape and tomato were the least preferred fruits. Larvae performed better in cranberry, raspberry, strawberry, and cherry than in the other fruits tested. We found that fruit chemical compounds can explain part of the effect of fruit on D. suzukii traits. In particular, oviposition preference under choice conditions was strongly influenced by fruit phosphorus content. In general, the consensus across studies is that raspberry, blackberry, and strawberry are among the best hosts while blackcurrant, grape and rose hips are poor hosts. Our results generally confirm this view but also suggest that oviposition preferences do not necessarily match larval performances. We discuss opportunities to use our results to develop new approaches for pest management.
Published: 2019
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24. Author response for 'Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments'

Author: Nicolas Leménager, Nicolas O. Rode, Virginie Ravigné, Laure Olazcuaga, Ruth A. Hufbauer, Julien Foucaud, Anne Loiseau, Mathieu Gautier, Candice Deschamps, Arnaud Estoup, and Benoit Facon
Subjects: Evolutionary biology, Biology, Adaptation, Drosophila suzukii, biology.organism_classification
Published: 2021
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25. How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis

Author: Arnaud Estoup, Aurélien Ausset, Nicolas Leménager, Bastien Poutout, Anne Loiseau, Pauline Gneux, Arthur Weyna, Laure Olazcuaga, Lian-Sheng Zang, Virginie Ravigné, Julien Foucaud, Benoit Facon, Elise Bonnet, Ruth A. Hufbauer, Vincent Dreuilhe, Su Wang, Ashraf Tayeh, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Colorado State University [Fort Collins] (CSU), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Academy of Agriculture and Forestry Sciences, Jilin Agricultural University (JAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0303 health sciences, Experimental evolution, biology, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Context (language use), Phenotypic trait, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phenotype, Harmonia axyridis, 03 medical and health sciences, Evolutionary biology, Trait, Reproduction, Selection (genetic algorithm), 030304 developmental biology, media_common, Espèce envahissante
Abstract: Ce rapport est disponible dans : BioRxiv. This article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology; Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evolve in concert and contribute to the success of invasive populations as an ‘invasion syndrome’. The invasive Harlequin ladybird Harmonia axyridis displays such an invasion syndrome with, for instance, females from invasive populations being larger and heavier than individuals from native populations, allocating more resources to reproduction, and spreading reproduction over a longer lifespan. Invasion syndromes could emerge due to selection acting jointly and directly on a multitude of traits, or due to selection on one or a few key traits that drive correlated indirect responses in other traits. Here, we investigated the degree to which the H. axyridis invasion syndrome would emerge in response to artificial selection on either female body mass or on age at first reproduction, two traits involved in their invasion syndrome. To further explore the interaction between environmental context and evolutionary change in molding the phenotypic response, we phenotyped the individuals from the selection experiments in two environments, one with abundant food resources and one with limited resources. The two artificial selection experiments show that the number of traits showing a correlated response depends upon the trait undergoing direct selection. Artificial selection on female body mass resulted in few correlated responses and hence poorly reproduced the invasion syndrome. In contrast, artificial selection on age at first reproduction resulted in more widespread phenotypic changes, which nevertheless corresponded only partly to the invasion syndrome. The artificial selection experiments also revealed a large impact of diet on the traits, with effects dependent on the trait considered and the selection regime. Overall, our results indicate that direct selection on multiple traits was likely necessary in the evolution of the H. axyridis invasion syndrome. Furthermore, they show the strength of using artificial selection to identify the traits that are correlated in different selective contexts, which represents a crucial first step in understanding the evolution of complex phenotypic patterns, including invasion syndromes.
Published: 2021

26. How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology— An Experimental and Genomic Approach

Author: Laure Benoit, Sylvain Piry, Johann Vulin, Séverine Murri, Nicolas Leménager, Maxime Galan, Guillaume Castel, Philippe Marianneau, Nathalie Charbonnel, Caroline Tatard, Anne Loiseau, Emmanuelle Artige, Sarah Madrieres, Coralie Pulido, Latifa Lakhdar, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Sarah Madrières was funded by an INRA-EFPA/ANSES fellowship., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: Microbiology (medical), medicine.medical_specialty, Eco evolutionary, [SDV]Life Sciences [q-bio], Zoology, lcsh:Medicine, Puumala virus, Article, law.invention, Serology, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, Myodes glareolus, Epidemiology, Nephropathia epidemica, medicine, Immunology and Allergy, Mild form, Molecular Biology, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, biology, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BA]Life Sciences [q-bio]/Animal biology, MESH: Puumala virus, lcsh:R, transmission, biology.organism_classification, medicine.disease, 3. Good health, Bank vole, Infectious Diseases, Transmission (mechanics), Sympatric speciation, within-host viral diversity, France, experimental cross-infections
Abstract: International audience; In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). 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. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, 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.
Published: 2020
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27. Rapid evolution of local adaptation to different host fruits in wild D. suzukii populations

Author: Laure Olazcuaga, Julien Foucaud, Candice Deschamps, Anne Loiseau, Mathieu Gautier, Hufbauer, Ruth A., Arnaud Estoup, Nicolas Rode, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Colorado State University [Fort Collins] (CSU), Instituto Gulbenkian de Ciência, Oeiras, Portugal, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Rode, Nicolas
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

28. Patterns and drivers of genetic diversity and structure in the biological control parasitoid Habrobracon hebetor in Niger

Author: Laure Benoit, Nathalie Gauthier, Madougou Garba, Caroline Tatard, Anne Loiseau, Direction Générale de la Protection des Végétaux, Ministère de l'Agriculture du Niger, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and This study was partly funded by the West Africa Agricultural Productivity Program (WAAP/PPAAO) in Niger and the Institut de Recherche pour le Developpement (IRD), France, through a collaborative programme between the 'Direction Generale de la Protection des Vegetaux', Niamey and the IRD.
Subjects: 0106 biological sciences, millet, Population genetics, biological control, 010603 evolutionary biology, 01 natural sciences, microsatellites, Gene flow, Parasitoid, Bracon, Génétique des populations, complementary sex determination, mitochondrial genes, Mating, parasitoid, Genetic diversity, biology, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, food and beverages, population genetics, Parasitoïde, General Medicine, Mating system, biology.organism_classification, H10 - Ravageurs des plantes, Lutte biologique, 010602 entomology, Insect Science, Biological dispersal, PEST analysis, Agronomy and Crop Science, Insecte nuisible
Abstract: When a promising natural enemy of a key pest exists locally, it is a common practice in biological control (BC) to rear and release it for supplementary control in the targeted agroecosystem even though significant knowledge gaps concerning pre/post release may still exist. Incorporating genetic information into BC research fills some of these gaps.Habrobracon hebetor, a parasitoid of many economically important moths that infest stored and field crops worldwide is commonly used, particularly against the millet head miner (MHM), a key pest of millet in Sahelian countries. To advance our knowledge on howH. hebetorthat occurs naturally in open-field cropping systems and grain stores as well as being mass-produced and released for MHM control, performs in millet agroecosystems in Niger we evaluated its population genetics using two mitochondrial and 21 microsatellite markers. The field samples were genetically more diverse and displayed heterozygote excess. Very few field samples had faced significant recent demographic bottlenecks. The mating system (i.e. nonrandom mating with complementary sex determination) of this species may be the major driver of these findings rather than bottlenecks caused by the small number of individuals released and the scarcity of hosts during the longlasting dry season in Niger.H. hebetorpopulation structure was represented by several small patches and genetically distinct individuals. Gene flow occurred at local and regional scales through human-mediated and natural short-distance dispersal. These findings highlight the importance of the mating system in the genetic diversity and structure ofH. hebetorpopulations, and contribute to our understanding of its reported efficacy against MHM in pearl millet fields.
Published: 2019
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29. A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

Author: Mathieu Gautier, Marc Kenis, Mathilde Paris, Arnaud Estoup, Nicolas Borowiec, Heiko Vogel, Heidrun Vogt, Lauren M Diepenbrock, Anne Loiseau, Benoit Facon, Benjamin Prud'homme, Donald K. Price, Christelle Guédot, Jinping Zhang, Xiao Chen, Antoine Fraimout, Hugues Parrinello, Laure Olazcuaga, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), University of Wisconsin-Madison, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Chinese Academy of Agricultural Sciences (CAAS), Yunnan Agricultural University, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius Kühn-Institut (JKI), University of Nevada [Las Vegas] (WGU Nevada), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, BayPass, [SDV]Life Sciences [q-bio], Genome, Insect, Population, Adaptation, Biological, Genome Scan, Genome-wide association study, Single-nucleotide polymorphism, Biology, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene Frequency, Drosophila suzukii, Genetics, Animals, GWAS, Biological invasions, education, Molecular Biology, Allele frequency, Drosophila, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Pool-Seq 1, Models, Genetic, Pool-Seq, AcademicSubjects/SCI01130, 15. Life on land, biology.organism_classification, Evolutionary biology, Drosophila melanogaster, Introduced Species
Abstract: Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophilaDrosophila suzukiiduring the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we calledC2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genesRhoGEF64Candcpo, the latter contributing to natural variation in several life-history traits (including diapause) inDrosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes ofD. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
Published: 2019
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30. Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments

Author: Mathieu Gautier, Benoit Facon, Arnaud Estoup, Nicolas O. Rode, Laure Olazcuaga, Anne Loiseau, Ruth A. Hufbauer, Virginie Ravigné, Julien Foucaud, Nicolas Leménager, and Candice Deschamps
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Experimental evolution, Fitness landscape, Population, Replicate, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Evolutionary biology, Adaptation, education, Drosophila suzukii, 030304 developmental biology, Maladaptation, Local adaptation
Abstract: The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.
Published: 2019
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31. Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal

Author: Stéphanie Rialle, Anne Loiseau, Christophe Diagne, Maxime Galan, Dany Severac, Caroline Tatard, Carine Brouat, Hughes Parinello, Nathalie Charbonnel, Ambroise Dalecky, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the ANR ENEMI project (ANR-11-JSV7-0006), and by the French Embassy in Senegal, which provided the funding for PhD scholarships., ANR-11-JSV7-0006,ENEMI,Conséquences évolutives des ennemis naturels dans des invasions biologiques majeures : le rôle des parasites dans le succès de l'invasion de deux rongeurs commensaux(2011), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Aix Marseille Université (AMU), Institut de Recherche pour le Développement (IRD [Réunion]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, lcsh:Medicine, Rodentia, Evolutionary ecology, 010603 evolutionary biology, 01 natural sciences, House mouse, Article, Transcriptome, Evolution, Molecular, 03 medical and health sciences, Mice, Immune system, Immunity, Animals, Colonization, lcsh:Science, Gene, 030304 developmental biology, 0303 health sciences, biology, Invasive species, Sequence Analysis, RNA, [SDV.BA]Life Sciences [q-bio]/Animal biology, Gene Expression Profiling, lcsh:R, Phenotypic trait, Biodiversity, biology.organism_classification, Senegal, Rats, Africa, Western, Genetics, Population, Black rat, Evolutionary biology, lcsh:Q, Molecular ecology, Introduced Species
Abstract: This preprint has been reviewed and recommended by Peer Community in Ecology.; International audience; Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.
Published: 2019
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32. Use of Multi-Intake Temporal Dominance of Sensations (TDS) to Evaluate the Influence of Cheese on Wine Perception

Author: Pascal Schlich, Anne Loiseau, Michel Visalli, and Mara Virginia Galmarini
Subjects: 0301 basic medicine, Wine, Taste, 030109 nutrition & dietetics, biology, 04 agricultural and veterinary sciences, Sweetness, biology.organism_classification, 040401 food science, 03 medical and health sciences, 0404 agricultural biotechnology, Dominance (ethology), Multivariate analysis of variance, Food science, Wine tasting, Analysis of variance, Aroma, Food Science, Mathematics
Abstract: Though the gastronomic sector recommends certain wine-cheese associations, there is little sensory evidence on how cheese influences the perception of wine. It was the aim of this study to dynamically characterize 4 wines as they would be perceived when consumed with and without cheese. The tasting protocol was based on multi-intake temporal dominance of sensations (TDS) coupled with hedonic rating. In the 1st session, 31 French wine and cheese consumers evaluated the wines (Pacherenc, Sancerre, Bourgogne, and Madiran) over 3 consecutive sips. In the following sessions, they performed the same task, but eating small portions of cheese (Epoisses, Comte, Roquefort, Crottin de Chavignol) between sips. All cheeses were tasted with all wines over 4 sessions. TDS data were mainly analyzed in terms of each attribute's duration of dominance by analysis of variance, multivariate analysis of variance, and canonical variate analysis. Results showed that cheese consumption had an impact (P < 0.1) on dominance duration of attributes and on preference for most wines. For example, in Madiran, all cheeses reduced dominance duration (P < 0.01) of astringency and sourness and increased duration of red fruit aroma. Although the number of consumers was small to make extended general conclusions on wine's preference, significant changes were observed before and after cheese intake.
Published: 2016
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33. The genomic basis of colour pattern polymorphism in the harlequin ladybird

Author: Benjamin Prud'homme, Aurelien Ausset, Arnaud Estoup, Hélène Bergès, Cécile Donnadieu, Julien Foucaud, Junichi Yamaguchi, Heiko Vogel, Danny Severac, Jacques Lagnel, Céline Lopez-Roques, Lian-Sheng Zang, B Gschloessl, Etienne Loire, Anne Loiseau, Benoit Facon, Lori Lawson-Handley, Maxime Manno, Karim Gharbi, Mathieu Gautier, Hugues Parrinello, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Ressources Génomiques Végétales (CNRGV), Edinburgh Genomics, University of Edinburgh, Norwich Research Park, Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Jilin Agricultural University (JAU), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ProdInra, Migration, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)
Subjects: 0106 biological sciences, 0303 health sciences, biology, Locus (genetics), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phenotype, Harmonia axyridis, Population genomics, 03 medical and health sciences, Taxon, Evolutionary biology, Coccinellidae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Allele, Gene, 030304 developmental biology
Abstract: Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research1–6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybirdHarmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the genepanniercontrols melanic pattern polymorphism inH. axyridis. We show thatpannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation inpannierleads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns inH. axyridis. Recombination betweenpannieralleles may be reduced by a highly divergent sequence of ca. 170 kb in thecis-regulatory regions ofpannierwith a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations throughcis-regulatory allelic variation of a single gene.
Published: 2018
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34. Wine and Cheese: Two Products or One Association? A New Method for Assessing Wine-Cheese Pairing

Author: Mara Virginia Galmarini, Michel Visalli, Pascal Schlich, Lucie Dufau, Anne Loiseau, Galmarini, Mara V., Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université Bourgogne Franche-Comté [COMUE] (UBFC), Consejo Nacional de Investigaciones Científicas y Técnicas, Pontificia Universidad Católica Argentina (UCA), AgroParisTech, This research was also partly financed by the Burgundy Council, project PARI 2014-VIGNE et VIN No. 29000857, together with the collaboration of the following partners: Comite Interprofessionnel de Gestion du Comte (CIGC), Centre Technique des Fromages Comtois (CTFC), Syndicat de defense de l'Epoisses, Syndicat du Crottin de Chavignol, Institut Francais de la Vigne et du Vin (IFV) 0-SICAREX and Bureau Interprofessionnel des Vins de Bourgogne (BIVB)., and European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
Subjects: 0301 basic medicine, Otras Ingenierías y Tecnologías, sensory evaluation, CONSUMERS, consommateur, lcsh:TX341-641, dynamic liking, fromage, INGENIERÍAS Y TECNOLOGÍAS, PANEL SENSORIAL, consumers, Alimentos y Bebidas, 03 medical and health sciences, 0404 agricultural biotechnology, appariement, intensité du goût, vin, Food and Nutrition, Food science, TEMPORAL DOMINANCE OF SENSATIONS, SENSORY EVALUATION, lcsh:RC620-627, temporal dominance of sensations, wine-cheese pairing, DYNAMIC LIKING, Flavor, QUESO, Mathematics, purl.org/becyt/ford/2.11 [https], 2. Zero hunger, Wine, 030109 nutrition & dietetics, dominance temporelle des sensations, WINE-CHEESE PAIRING, association, 04 agricultural and veterinary sciences, 040401 food science, lcsh:Nutritional diseases. Deficiency diseases, purl.org/becyt/ford/2 [https], Alimentation et Nutrition, ANALISIS ORGANOLEPTICO, VINOS, lcsh:Nutrition. Foods and food supply, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Fil: Galmarini, Mara Virginia. Centre des Sciences du Goût et de l’Alimentation. Université de Bourgogne; Francia Fil: Galmarini, Mara Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Galmarini, Mara Virginia. Pontificia Universidad Católica Argentina. Facultad de Ingeniería y Ciencias Agrarias; Argentina Fil: Dufau, Lucie. Centre des Sciences du Goût et de l’Alimentation. Université de Bourgogne; Francia Fil: Dufau, Lucie. AgroParisTech; Francia Fil: Loiseau, Anne Laure. Centre des Sciences du Goût et de l’Alimentation. Université de Bourgogne; Francia Fil: Visalli, Michel. Centre des Sciences du Goût et de l’Alimentation. Université de Bourgogne; Francia Fil: Schlich, Pascal. Centre des Sciences du Goût et de l’Alimentation. Université de Bourgogne; Francia Abstract: The aim of this study was to identify which attributes impacted the dynamic liking of cheese and wine individually, as well as when consumed together. Three wines (one white, Pouilly Loché; and two red, Maranges and Beaujolais) and three cheeses (Comté, Époisses, Chaource) were individually evaluated by a group of 60 consumers using mono-intake Temporal Dominance of Sensations (TDS) with simultaneous hedonic ratings. The same data acquisition screen was used for all products showing a unique list of 14 descriptors (covering cheese and wine perception) and a hedonic scale for dynamical rating of liking. The dynamic hedonic data were associated with the TDS profiles obtaining Temporal Drivers of Liking (TDL). Furthermore, the nine associations that resulted from combining each wine with each cheese were evaluated by multi-bite and multi-sip TDS. Individually, Chaource had practically no TDL; for Comté, mushroom flavor was a positive TDL, and in Époisses, salty was a negative TDL. As for wines, negative TDL were only found in the red wines: bitter, sour and astringent. Positive TDL for wines were: fruity, spicy and woody. Changes in the dynamic perception had a bigger impact on liking of wine compared to cheese. For the associations, the negative TDL were only three and mostly wine related: sour (for seven out of nine combinations), bitter (six out of nine) and astringent (five out of nine). Positive TDL were more varied (a total of 10 descriptors) and were related either to wine or cheese. As opposed to what was found in cheese alone, salty was a positive TDL in two of the combinations. It was observed that the dynamic sensory perception had a more important impact on liking in wine-cheese combinations than when consumed separately. TDS and TDL have a big potential in the study of food pairing, which should be further exploited.
Published: 2018
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35. Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

Author: Audrey Rohfritsch, Anne Loiseau, Mathieu Gautier, Carole Kerdelhué, Christian Burban, Maxime Galan, Karim Gharbi, Julien Foucaud, Renaud Vitalis, Raphaël Leblois, Manuela Branco, Laure Sauné, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Universidade de Lisboa (ULISBOA), Centro de Estudos Florestais, Technical University of Lisbon-Instituto Superior de Agronomia, University of Edinburgh, Edinburgh Genomics, This work was supported by a grant from the French National Research Agency (ANR-10-JCJC-1705—GENOPHENO) and by the Institut National de la Recherche Agronomique (GAPP project, INRA AIP BioRessources 2012). Part of this work was carried out with the resources of the INRA MIGALE (http://migale.jouy.inra.fr) and GENOTOUL bioinformatics platforms. We also relied on the HPC of the CBGP and of the Montpellier Bioinformatics Biodiversity (MBB) platform of the LabEx CeMEB (Laboratoire d'Excellence Centre Méditerranéen de l'Environnement et de la Biodiversité), and we benefitted from the technical assistance of A. Dehne-Garcia. Edinburgh Genomics is funded in part by grants from the UK Natural Environment Research Council (R8/H10/56) and Medical Research Council (G0900740). The work in Portugal was partially funded by the FCT national project UID/AGR/00239/2013., ANR-10-JCJC-1705,GenoPheno,Génomique de la phénologie chez la processionnaire du pin, Thaumetopoea pityocampa(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Universidade de Lisboa = University of Lisbon (ULISBOA), Technical University of Lisbon-Instituto Superior de Agronomia [Lisboa] (ISA), and Universidade de Lisboa = University of Lisbon (ULISBOA)-Universidade de Lisboa = University of Lisbon (ULISBOA)
Subjects: Gene Flow, 0106 biological sciences, 0301 basic medicine, Time Factors, population genomics, Demographic history, Lineage (evolution), [SDV]Life Sciences [q-bio], Genome, Insect, Population, detection of selection, Moths, Biology, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, phenology, Gene flow, Population genomics, 03 medical and health sciences, Gene Frequency, Genetic drift, Genetics, Animals, education, Phylogeny, Ecology, Evolution, Behavior and Systematics, Demography, Principal Component Analysis, education.field_of_study, Ecology, Population size, Genetic Variation, RAD-sequencing, demographic inference, pine processionary moth, Adaptation, Physiological, Genetics, Population, 030104 developmental biology, Evolutionary biology, Sympatric speciation, [SDE]Environmental Sciences, Seasons
Abstract: Understanding the processes of adaptive divergence, which may ultimately lead to speciation, is a major question in evolutionary biology. Allochronic differentiation refers to a particular situation where gene flow is primarily impeded by temporal isolation between early and late reproducers. This process has been suggested to occur in a large array of organisms, even though it is still overlooked in the literature. We here focused on a well-documented case of incipient allochronic speciation in the winter pine processionary moth Thaumetopoea pityocampa. This species typically reproduces in summer and larval development occurs throughout autumn and winter. A unique, phenologically shifted population (SP) was discovered in 1997 in Portugal. It was proved to be strongly differentiated from the sympatric "winter population" (WP), but its evolutionary history could only now be explored. We took advantage of the recent assembly of a draft genome and of the development of pan-genomic RAD-seq markers to decipher the demographic history of the differentiating populations and develop genome scans of adaptive differentiation. We showed that the SP diverged relatively recently, i.e. few hundred years ago, and went through two successive bottlenecks followed by population size expansions, while the sympatric WP is currently experiencing a population decline. We identified outlier SNPs that were mapped onto the genome, but none were associated with the phenological shift or with subsequent adaptations. The strong genetic drift that occurred along the SP lineage certainly challenged our capacity to reveal functionally important loci. This article is protected by copyright. All rights reserved.
Published: 2018
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36. Unbalanced polyandry in wild-caught ladybirds Harmonia axyridis (Coleoptera: Coccinellidae)

Author: Oldřich Nedvěd, Guillaume J. M. Laugier, Anne Loiseau, Mona Awad, Faculty of Science, University of South Bohemia, Institute of Entomology, Czech Academy of Sciences [Prague] (CAS), Université du Caire, Partenaires INRAE, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), and The study was supported by grant no. QH82047 from the Ministry of Agriculture of the Czech Republic and by a grant from the Agropolis Fondation (RTRA—Montpellier, BIOFIS project).
Subjects: 0106 biological sciences, Entomology, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Zoology, Paternity, Introduced species, 010603 evolutionary biology, 01 natural sciences, Mating, Overwintering, media_common, biology, Ecology, Reproduction, biology.organism_classification, Mating system, Promiscuity, Propagule size, Harmonia axyridis, 010602 entomology, Fertilization, Insect Science, Coccinellidae
Abstract: International audience; We investigated the mating and fertilization patterns in one Czech local population of the invasive aphidophagous ladybird Harmonia axyridis (Pallas), sampling the same mixed generations before and after overwintering. Our study using eight microsatellite loci provides the first direct evidence that females of H. axyridis are highly polyandrous in the wild and that they not only mate multiple times but also use the sperm from multiple males to fertilize their eggs. Three types of values (minimum number of fathers, estimated number of fathers and effective number of fathers contributing to progeny of one mother) were about two times higher in the spring sample (2.9, 5.2, 3.1), in the peak of their reproduction period, than in the preceding autumn sample (1.6, 2.8, 1.6). The contribution of individual fathers to the number of progeny was highly unbalanced, with a few dominating fathers and many fathers with low number of progeny.
Published: 2015
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37. Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times

Author: Mamadou Kane, Sylvain Piry, Raphaël Leblois, Anne Loiseau, Youssoupha Niang, Cédric Lippens, Karine Berthier, Mamoudou Diallo, Jean-Marc Duplantier, Arnaud Estoup, M.K. Hima, Carine Brouat, Caroline Tatard, Aliou Sow, Khalilou Bâ, Ambroise Dalecky, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Funding provided by the Institut de Recherche pour le Developpement (IRD)., ANR-11-JSV7-0006,ENEMI,Conséquences évolutives des ennemis naturels dans des invasions biologiques majeures : le rôle des parasites dans le succès de l'invasion de deux rongeurs commensaux(2011), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche pour le développement (IRD [Sénégal]), and Unité de Pathologie Végétale (PV)
Subjects: 0106 biological sciences, 0301 basic medicine, Demographic history, MESH: Bayes Theorem, Population genetics, MESH: Genetics, Population, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, House mouse, 03 medical and health sciences, Mice, MESH: Senegal, Genetic variation, Genetics, Animals, MESH: Animals, MESH: Genetic Variation, MESH: Models, Genetic, MESH: Mice, Genetics (clinical), [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Models, Genetic, Ecology, MESH: Animal Distribution, MESH: DNA, Mitochondrial, Genetic Variation, Bayes Theorem, biology.organism_classification, Senegal, Phylogeography, 030104 developmental biology, Genetics, Population, MESH: Phylogeography, Genetic structure, Biological dispersal, Original Article, MESH: Microsatellite Repeats, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution, Founder effect, Microsatellite Repeats, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 12 pages; International audience; Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.
Published: 2017
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38. Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region

Author: Anne Loiseau, Laure Benoit, Séverine Murri, Jean-Baptiste Pons, Coralie Pulido, Adelaide Dubois, Latifa Lakhdar, Guillaume Castel, Nathalie Charbonnel, Philippe Marianneau, Maxime Galan, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université de Lyon (COMUE), INRA-EFPA/ANSES fellowship, European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, experimental infections, Rodent, ecoimmunology, Gene Expression, Myodes glareolus, Population genetics, Antibodies, Viral, L73 - Maladies des animaux, Puumala virus, Serology, Zoonoses, Nephropathia epidemica, Non endemic, Puumala hantavirus, 2. Zero hunger, 0303 health sciences, Vegetal Biology, biology, Arvicolinae, rodent, 000 - Autres thèmes, 3. Good health, Bank vole, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, Zoology, 03 medical and health sciences, biology.animal, medicine, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Natural reservoir, population genetics, Disease Reservoirs, 030304 developmental biology, 030306 microbiology, biology.organism_classification, medicine.disease, Virology, Antiviral gene, 030104 developmental biology, Immunoglobulin G, Biological dispersal, Animal Science and Zoology, Parasitology, Biologie végétale
Abstract: Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole,Myodes glareolus. Despite the continuous distribution of the reservoir in Europe, PUUV occurence is highly fragmented. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions using serological and virological surveys. We used bank vole population genetics to demonstrate the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to establish, circulate and persist in the NE-free region. Immune responsiveness was phenotyped both in the wild and during experimental infections, using serological, virological and immune related gene expression assays. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. In natural populations, antiviral gene expression (TnfandMx2genes) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE endemic region. Altogether, our results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, what might limit PUUV circulation and persistence, and in turn, the risk of NE.Graphical abstract
Published: 2017
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39. Biological invasions in rodent communities: from ecological interactions to zoonotic bacterial infection issues

Author: Khalilou Bâ, Nathalie Charbonnel, d’Ambrosio J, Christophe Diagne, Maxime Galan, Carine Brouat, Caroline Tatard, Aliou Sow, Mamadou Kane, Jean-François Cosson, Youssoupha Niang, Ambroise Dalecky, Odile Fossati-Gaschignard, Mbacké Sembène, Anne Loiseau, Mamoudou Diallo, and Lucie Tamisier
Subjects: 0106 biological sciences, 2. Zero hunger, Zoonotic Bacterial Infection, biology, Rodent, Ecology, Ecology (disciplines), 030231 tropical medicine, Biodiversity, Community structure, Parasitism, Zoology, 15. Life on land, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, House mouse, 03 medical and health sciences, 0302 clinical medicine, Black rat, 13. Climate action, biology.animal
Abstract: Several hypotheses (such as ‘enemy release’, ‘novel weapon’, ‘spillback’ and ‘dilution/density effect’) suggest changes in host-parasite ecological interactions during biological invasion events. Such changes can impact both invasion process outcome and the dynamics of exotic and/or endemic zoonotic diseases. To evaluate these predictions, we investigated the ongoing invasions of the house mouse Mus musculus domesticus, and the black rat, Rattus rattus, in Senegal (West Africa). We focused on zoonotic bacterial communities depicted using 16S rRNA amplicon sequencing approach in both invasive and native rodents sampled along two well-defined invasion routes. Overall, this study provided new ecological evidence connecting parasitism and rodent invasion process, with diverse potential roles of zoonotic bacteria in the invasion success. Our results also highlighted the main factors that lie behind bacterial community structure in commensal rodents. Further experimental studies as well as comparative spatio-temporal surveys are necessary to decipher the actual role of zoonotic bacteria in these invasions. Our data also gave new support for the difficulty to predict the direction in which the relationship between biodiversity changes and disease risk could go. These results should be used as a basis for public health prevention services to design reservoir monitoring strategies based on multiple pathogen surveillance.
Published: 2017
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40. Experimental infections of wild bank voles (Myodes glareolus) from nephropatia epidemica endemic and non-endemic regions revealed slight differences in Puumala virological course and immunological responses

Author: Philippe Marianneau, Jean-Baptiste Pons, Adelaide Dubois, Anne Loiseau, Coralie Pulido, Séverine Murri, Laure Benoit, Maxime Galan, Latifa Lakhdar, Guillaume Castel, Nathalie Charbonnel, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de Virologie, Institut de Recherches Biomédicales des Armées, Plateforme d’expérimentation animale (PFEA), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme Expérimentation Animale, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: 0301 basic medicine, Cancer Research, Nephropathia epidemica, [SDV]Life Sciences [q-bio], Immunology, Myodes glareolus, Biology, Antibodies, Viral, Puumala virus, Wild bank vole, 03 medical and health sciences, Human disease, Virology, medicine, Animals, Humans, Viral rna, Non endemic, Disease Reservoirs, Virulence, Arvicolinae, biology.organism_classification, medicine.disease, Bank vole, 030104 developmental biology, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, Immunoglobulin G, Experimental infections, RNA, Viral, Disease Susceptibility, France, Regional differences
Abstract: A. Dubois et N. Charbonnel : contributions égales au travail; In Europe, the occurrence of nephropathia epidemica (NE), a human disease caused by Puumala virus (PUUV), exhibits considerable geographical heterogeneity despite the continuous distribution of its reservoir, the bank vole Myodes glareolus. To better understand the causes of this heterogeneity, wild voles sampled in two adjacent NE endemic and non-endemic regions of France were infected experimentally with PUUV. The responses of bank voles to PUUV infection, based on the levels of anti-PUUV IgG and viral RNA, were compared. Slight regional differences were highlighted despite the high inter-individual variability. Voles from the NE non-endemic region showed greater immune responsiveness to PUUV infection, but lower levels of RNA in their organs than voles from the endemic region. These results suggest the existence of regional variations in the sensitivity of bank voles that could contribute to the apparent absence of PUUV circulation among voles and the absence of NE in the non endemic region.
Published: 2017
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41. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

Author: Nathalie Charbonnel, Anne Loiseau, Alexandre Dehne-Garcia, Emilie Bard, Muriel Vayssier-Taussat, Carine Brouat, Jean-François Cosson, Lucie Tamisier, Maria Razzauti, Maria Bernard, Maxime Galan, Caroline Tatard, Hélène Vignes, Galan, Maxime, Cosson, Jean-Francois, Bik, Holly, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), New York University [New York] (NYU), NYU System (NYU), Agence Nationale de la Recherche (ANR) (ENEMI ANR-11-JSV7-0006, Institut National de la Recherche Agronomique (INRA) (MEM Patho-ID)., European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Unité de recherche d'Épidémiologie Animale (UEA), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie
Subjects: 0301 basic medicine, Streptobacillus, Physiology, Biodiversité et Ecologie, lcsh:QR1-502, L73 - Maladies des animaux, medicine.disease_cause, molecular epidemiology, Biochemistry, lcsh:Microbiology, Clinical Science and Epidemiology, bacteria, emerging infectious diseases, high-throughput sequencing, metabarcoding, rodents, West Africa, zoonoses, Ehrlichia, Orientia, QR1-502, 3. Good health, Computer Science Applications, Modeling and Simulation, L72 - Organismes nuisibles des animaux, Research Article, zoonose, Bartonella, 030106 microbiology, relation homme-faune, Zoology, Context (language use), Biology, Séquence d'ARN, Agent pathogène, Microbiology, Biodiversity and Ecology, 03 medical and health sciences, Borrelia, Genetics, medicine, Surveillance épidémiologique, Molecular Biology, Transmission des maladies, Ecology, Evolution, Behavior and Systematics, Bactérie pathogène, Rattus, Mycoplasma, L10 - Génétique et amélioration des animaux, biology.organism_classification, Virology, 030104 developmental biology, Enquête pathologique, Maladie infectieuse, Mastomys, next-generation sequencing, Rongeur, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses., The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.
Published: 2016
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42. 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection

Author: Carine Brouat, Emilie Bard, Nathalie Charbonnel, Lucie Tamisier, Jean-François Cosson, Hélène Vignes, Muriel Vayssier-Taussat, Maria Bernard, Maxime Galan, Maria Razzauti, Alexandre Dehne-Garcia, Caroline Tatard, and Anne Loiseau
Subjects: 0303 health sciences, medicine.medical_specialty, 030306 microbiology, business.industry, Transmission (medicine), Wildlife, Biology, 16S ribosomal RNA, medicine.disease, biology.organism_classification, Biotechnology, 03 medical and health sciences, Pandemic, Epidemiology, medicine, Coinfection, Amplicon sequencing, business, Bacteria, 030304 developmental biology
Abstract: SummaryHuman impact on natural habitats is increasing the complexity of human-wildlife interfaces and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents collected from 24 villages in Senegal, including 208Mus musculus domesticus, 189Rattus rattus, 93Mastomys natalensisand 221Mastomys erythroleucus.Seven major genera of pathogenic bacteria were detected in their spleens:Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, StreptobacillusandOrientia. The last five of these genera have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable for continuous pathogen surveillance in the context of disease monitoring programs.
Published: 2016
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43. Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger

Author: Raphaël Leblois, Sama Gagaré, Ambroise Dalecky, Anne Loiseau, Sylvain Piry, Philippe Gauthier, Gauthier Dobigny, Karine Berthier, Madougou Garba, Carine Brouat, Miguel Navascués, Caroline Tatard, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Université Abdou Moumouni [Niamey], Direction Générale de la Protection des Végétaux, Ministère de l'Agriculture du Niger, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre Régional AGRHYMET (CRA), Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), partnership agreement (number 301027/00) between IRD and the Republic of Niger, SRC-IRD research bursary for international mobility (2011–2012), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Station de Pathologie Végétale (AVI-PATHO)
Subjects: 0106 biological sciences, 0301 basic medicine, Current distribution, [SDE.MCG]Environmental Sciences/Global Changes, Population, Population genetics, 010603 evolutionary biology, 01 natural sciences, Rattus rattus, Interview data, 03 medical and health sciences, trade-mediated invasion, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, biology, Ecology, Propagule pressure, Genetic data, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, 030104 developmental biology, Black rat, Africa, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, urban habitat
Abstract: International audience; Human population migrations, as well as long-distance trade activities, have been responsible for the spread of many invasive organisms. The black rat, Rattus rattus, has colonized most of the world following ship-mediated trade. Owing to its tight association with human infrastructures, this species has been able to survive in unfavourable environments, such as Sahelian Africa. In this work, we combined interview-based and population genetic surveys to investigate the processes underlying the ongoing invasion of southwestern Niger by black rats, with special emphasis on the capital city, Niamey. Our trapping and interview data are quite congruent, and all together point towards a patchy, but rather widespread, current distribution of R. rattus. Genetic data strongly suggest that road network development for truck-based commercial flow from/to international harbours located in neighbouring countries (Benin, Togo, and Nigeria) facilitates the passive dispersal of black rats over a long distance through unfavourable landscapes. Another potentially, more ancient, invasion route may be associated with boat transport along the Niger River. Human-mediated dispersal thus probably allows the foundation of persisting populations within highly anthropized areas while population dynamics may be more unstable in remote areas and mostly depends on propagule pressure.
Published: 2016
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44. A new suite of twenty-two polymorphic microsatellite loci in the parasitic wasp, Habrobracon hebetor (Hymenoptera: Braconidae): Promising molecular tools for studying the population genetics of several beneficial braconid species

Author: Laure Benoit, Nathalie Gauthier, Madougou Garba, Anne Loiseau, Direct Gen Protect Vegetaux, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), West Africa Agricultural Productivity Program (WAAP/PPAAO) in Niger and the Institut de Recherche pour le Développement (IRD), France through a collaborative programme between 'La Direction Générale de Protection des Végétaux', Niamey and the IRD., Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Direction Générale de la Protection des Végétaux
Subjects: 0106 biological sciences, 0301 basic medicine, Linkage disequilibrium, microsatellite, [SDV]Life Sciences [q-bio], Population, Population genetics, Habrobracon hebetor, biological control, Locus (genetics), Biology, parasitic wasp, 01 natural sciences, Gene flow, Loss of heterozygosity, 03 medical and health sciences, Braconidae, education, Genetics, Genetic diversity, education.field_of_study, Bracon spp, population genetics, H10 - Ravageurs des plantes, Hymenoptera, J11 - Manutention, transport, stockage et conservation des produits d'origine végétale, 010602 entomology, 030104 developmental biology, QL1-991, Insect Science, Microsatellite, gene flow, Zoology
Abstract: Combining a biotin-enrichment protocol and 454GS-FLX titanium pyrosequencing technology, we characterised 22 polymorphic microsatellite loci from the parasitic wasp, Habrobracon hebetor (Say) (Hymenoptera: Braconidae), a cosmopolitan species commonly used in biological control against a wide range of both major lepidopterous pests of stored products and field crops in different parts of the world. Three multiplex PCR sets were optimised and characterised across 46 H. hebetor specimens from two samples collected from millet fields in Niger. Two to 11 alleles were found per locus and observed heterozygosity ranged from 0.289 to 0.826. Polymorphism was detected in both samples with a similar level of observed heterozygosity (0.482 vs. 0.502) and number of alleles (4.1 vs. 3.6). Deviation from Hardy-Weinberg equilibrium was detected at the same five loci in both samples and five or seven more loci in each sample but was not associated with heterozygote deficiencies. Even though evidence for linkage disequilibrium was found between a few alleles, these new loci segregated independently. The variability of the 22 loci will enable estimates of genetic diversity and structure patterns, as well as gene flow between H. hebetor populations at different spatial scales. Cross-species amplifications were successful among the six Bracon spp. tested and nine loci will be particularly appropriate for population genetic studies in B. brevicornis.
Published: 2016
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45. Urban population genetics of the invasive black rats in Franceville, Gabon

Author: Mathieu Bourgarel, Eric M. Leroy, Jean Marc Duplantier, Anne Loiseau, Carine Brouat, J.B. Mangombi, O.L. Banga, Centre International de Recherches Médicales de Franceville (CIRMF), UPR AGIR, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Animal et gestion intégrée des risques (Cirad-Bios-UPR 22 AGIRs), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Animal et gestion intégrée des risques (UPR AGIRs), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], urban areas, Large population, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, Invasive species, Rattus rattus, microsatellites, invasive species, 03 medical and health sciences, Human health, population genetic structure, dispersal, Ecology, Evolution, Behavior and Systematics, Isolation by distance, Ecology, Rattus, biology.organism_classification, stomatognathic diseases, 030104 developmental biology, Black rat, Genetic structure, Biological dispersal, Animal Science and Zoology, L20 - Écologie animale, zoonotic diseases, L72 - Organismes nuisibles des animaux
Abstract: The invasive black rat Rattus rattus has established commensal populations in most cities of the world. Known as a reservoir of numerous zoonotic diseases, this species is considered as an urban pest and may have major consequences on human health. However, little is known about the genetic structure of urban populations, although it could help to design the scale of appropriate control strategies (at the city or at the district level). In this study, we characterize the genetic structure of R. rattus within Franceville (Republic of Gabon), an African tropical city that has undergone a recent growth, like many other cities of the developing countries. Sampling was conducted in six different districts of the city, chosen to represent variable levels of connectivity and building aggregation. Genetic structure was assessed using 16 microsatellite markers. Our results suggest the occurrence of a large population of R. rattus that is continuously distributed at the scale of the city, with no impact of urban characteristics or putative barriers on genetic differentiation. Isolation by distance analyses show that effective dispersal of R. rattus is, however, spatially limited to a few hundred meters. Regarding management strategies, our results suggest that rodent control should be envisaged at the scale of the city. (Resume d'auteur)
Published: 2016
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46. Can things get worse when an invasive species hybridizes? The harlequin ladybirdHarmonia axyridisin France as a case study

Author: Laurent Crespin, Arnaud Estoup, Anne Loiseau, Eric Lombaert, Alexandra Magro, and Benoit Facon
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, biology, Population, Zoology, Population genetics, Reproductive isolation, Quantitative genetics, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Invasive species, Harmonia axyridis, Life history theory, 03 medical and health sciences, Genetic variation, Genetics, General Agricultural and Biological Sciences, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: So far, only a few studies have explicitly investigated the consequences of admixture for the adaptative potential of invasive populations. We addressed this question in the invasive ladybird Harmonia axyridis. After decades of use as a biological control agent against aphids in Europe and North America, H. axyridis recently became invasive in four continents and has now spread widely in Europe. Despite this invasion, a flightless strain is still sold as a biological control agent in Europe. However, crosses between flightless and invasive individuals yield individuals able to fly, as the flightless phenotype is caused by a single recessive mutation. We investigated the potential consequences of admixture between invasive and flightless biological control individuals on the invasion in France. We used three complementary approaches: (i) population genetics, (ii) a mate-choice experiment, and (iii) a quantitative genetics experiment. The invasive French population and the biological control strain showed substantial genetic differentiation, but there are no reproductive barriers between the two. Hybrids displayed a shorter development time, a larger size and a higher genetic variance for survival in starvation conditions than invasive individuals. We discuss the potential consequences of our results with respect to the invasion of H. axyridis in Europe.
Published: 2010
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47. Worldwide invasion by the little fire ant: routes of introduction and eco-evolutionary pathways

Author: Merav Vonshak, Jan Oettler, Anne Loiseau, Jean Luc Mercier, Arnaud Estoup, Hervé Jourdan, Alexander S. Mikheyev, Jean-Bruno Mikissa, Djoël Konghouleux, Maurice Tindo, Jérôme Orivel, Terry McGlynn, Dominique Fresneau, Jacques H. C. Delabie, and Julien Foucaud
Subjects: 0106 biological sciences, 0303 health sciences, Fire ant, biology, Eco evolutionary, Ecology, Range (biology), Human evolutionary genetics, 15. Life on land, Wasmannia, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Invasive species, 03 medical and health sciences, Habitat, Genetics, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Biological invasions are generally thought to occur after human aided migration to a new range. However, human activities prior to migration may also play a role. We studied here the evolutionary genetics of introduced populations of the invasive ant Wasmannia auropunctata at a worldwide scale. Using microsatellite markers, we reconstructed the main routes of introduction of the species. We found three main routes of introduction, each of them strongly associated to human history and trading routes. We also demonstrate the overwhelming occurrence of male and female clonality in introduced populations of W. auropunctata, and suggest that this particular reproduction system is under selection in human-modified habitats. Together with previous researches focused on native populations, our results suggest that invasive clonal populations may have evolved within human modified habitats in the native range, and spread further from there. The evolutionarily most parsimonious scenario for the emergence of invasive populations of the little fire ant might thus be a two-step process. The W. auropunctata case illustrates the central role of humans in biological change, not only due to changes in migration patterns, but also in selective pressures over species.
Published: 2010
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48. Reproductive system, social organization, human disturbance and ecological dominance in native populations of the little fire ant, Wasmannia auropunctata

Author: Arnaud Estoup, Julien Le Breton, Jérôme Orivel, Julien Foucaud, Philippe Cerdan, Jacques H. C. Delabie, Denis Fournier, and Anne Loiseau
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Ecology, Population, Niche, Interspecific competition, 15. Life on land, Biology, Wasmannia, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, Invasive species, 03 medical and health sciences, Habitat, Genetics, Dominance (ecology), education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non-dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non-dominant native populations in natural and human-modified habitats. Microsatellite and mtDNA data indicated that dominant and non-dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human-modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species' ecological features and the adaptive potential of clonal reproductive systems.
Published: 2009
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49. Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

Author: Carine Brouat, Emilie Lecompte, Elisabeth Fichet-Calvet, Gauthier Dobigny, Khalilou Bâ, Sylvain Piry, Jean-Marc Duplantier, Laurent Granjon, Jean-François Cosson, Karine Mouline, Anne Loiseau, Caroline Tatard, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD), Institut de recherche pour le développement (IRD [Sénégal]), and Muséum national d'Histoire naturelle (MNHN)
Subjects: AFRICA, 0106 biological sciences, SAVANNA, [SDV]Life Sciences [q-bio], Biogeography, Population, Context (language use), phylogeography, 010603 evolutionary biology, 01 natural sciences, PHYLOGEOGRAPHY, 03 medical and health sciences, MTDNA, parasitic diseases, Vicariance, Mastomys erythroleucus, sub-Sahara, education, QUATERNARY HISTORY, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MASTOMYS ERYTHROLEUCUS, 0303 health sciences, education.field_of_study, Ecology, biology, mtDNA, Quaternary history, rodent, 15. Life on land, biology.organism_classification, SUB-SAHARA, savanna, RODENT, Phylogeography, Geography, Africa, Genetic structure, Biological dispersal
Abstract: E-mail Addresses: brouat@mpl.ird.fr; International audience; Aim : To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub-Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species. Location Sahel and Sudan savannas, Africa. Methods : We sequenced the whole cytochrome b gene in 211 individuals from 59 localities distributed from Senegal to Ethiopia. Sequence data were analysed using both phylogenetic (several rooted tree-construction methods, median-joining networks) and population genetic methods (spatial analyses of molecular variance, mismatch distributions). Results : Haplotypes were distributed into four major monophyletic groups corresponding to distinct geographical regions across a west-east axis. Diversification events were estimated to have occurred between 1.16 and 0.18 Ma. Main conclusions : Vicariance events related to the fragmentation of savanna habitats during the Pleistocene era may explain the phylogeographical patterns observed. Genetic structure was consistent with a role of major Sahelian rivers as significant barriers to west-east dispersal. Recent demographic expansions probably occurred during arid phases of the Holocene with the southward expansion of savannas
Published: 2009
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50. Population genetic structure of two ecologically distinct multimammate rats: the commensal Mastomys natalensis and the wild Mastomys erythroleucus in southeastern Senegal

Author: Carine Brouat, Jean-Marc Duplantier, Anne Loiseau, Mamadou Kane, and Khalilou Bâ
Subjects: 0106 biological sciences, 0303 health sciences, Genetic diversity, education.field_of_study, biology, Ecology, Population, Zoology, Context (language use), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, Mastomys, Genetic structure, Genetics, Biological dispersal, Mastomys erythroleucus, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Using the same set of microsatellite markers, we compared the population genetic structure of two Mastomys species, one being exclusively commensal in southeastern Senegal, and the other being continuously distributed outside villages in this region. Both species were sampled in the same landscape context and at the same spatial scale. According to the expectations based on the degree of habitat patchiness (which is higher for commensal populations in this rural area), genetic diversity was lower and genetic differentiation was higher in commensal populations of Mastomys natalensis than in wild populations of Mastomys erythroleucus. Contrasting estimates of effective dispersal and current migration rates corroborates previous data on differences in social structure between the two species. Isolation-by-distance analyses showed that human-mediated dispersal is not a major factor explaining the pattern of genetic differentiation for M. natalensis, and that gene flow is high and random between M. erythroleucus populations at the spatial scale considered.
Published: 2007
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