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International audience; The cosmopolitan black rat, Rattus rattus, has invaded many cities throughout the world. Although the species is responsible for major damages to food stocks and crops and is involved in the maintenance, circulation and transmission of many zoonotic pathogens to humans and animals, a lot remains to be known about its eco-evolutionary characteristics, especially in highly modified environments like the urban habitat. In particular, very few studies were conducted on the genetic structure of urban black rat populations, which is yet a prerequisite for defining effective management units. Here, we focus on the population genetics of Rattus rattus in Cotonou, Benin. Forty different localities were sampled throughout the city and 457 individuals were genotyped using 18 microsatellite markers. Our results reveal two poorly distinguishable but significant genetic clusters, one of each side of Cotonou channel, that tend to homogenize into a single group due to probable gene flow between the two shores. Implications in terms of management units and rodent control are discussed.

Relationships between parasitism and invasion success are increasingly evidenced in the literature. However, the dynamic nature of the major parasite-related processes has been rarely taken into account until now, while the residence time of invaders in colonized regions was shown to be associated to crucial changes in parasite communities. Here, we strive to bridge this gap using a temporal survey of rodent populations along one invasion route of the exotic house mouseMus musculus domesticusthat currently invades North Senegal. In this study, we investigated whether gastrointestinal helminth (GIH) assemblages changed over time in native (Mastomys erythroleucus) and/or invasive (M. m. domesticus) rodent populations sampled at an invasion front, and whether these potential changes may be associated to the invasion success of the exotic mouse. Four years separated two rodent sampling campaigns (2013 and 2016/17) in six localities. Despite being relatively short, the timeframe considered here allowed to evidence significant patterns in rodent communities and their GIH assemblages. At the host community level, we showed that the exotic mouse was now established at all sites, becoming the dominant species in sites where it was not recorded before. At the GIH community level, increased infection of the single shared cestode (Mathevotaenia symmetrica) in both rodent species brought support to the "spill-back" hypothesis. Infection levels of GIH that remained low at the invasion front in invading mice over time also supported the "enemy release" hypothesis. Both hypotheses should deserve further experimental work to demonstrate their role in the invasion success of the house mouse in Senegal.

Gerbillus nigeriae is a sand-dwelling and semi-arid adapted rodent species restricted to the West African Sahel where it causes extensive damages to cereal crops such as millet and sorghum. It also displays one of the most extensive floating chromosomal polymorphisms currently known in mammals, showing a non-random spatial distribution of diploid numbers (2N). We combined population dynamics and genetics to determine dispersal and mobility parameters of G. nigeriae in the species distribution range characterized by low 2N. To do so, we performed a three-year long population survey at Gangara, in the central east Niger. We used both time-dependent monitoring trough capture-mark-recapture (CMR) methods and genetic analyses performed on the 134 monitored individuals. CMR results showed low to very low population densities (maximum 27.5 individuals/ha) throughout the study. Abundance cycle was single-phased and strongly dependent on rainfall patterns. Mobility parameters showed very low individual mobility, with means of distance between successive (re) captures (DRS) and maximal distance between (re) captures (DMR) of 7.8 and 14.4 meters, respectively. Genetic analyses revealed significant isolation by distance as well as spatial structuration, thus confirming poor dispersal capacity. Our results are discussed in terms of rodent pest control in arid areas of Niger where cereal crops production is crucial for human food security.

Bioinvasion is a major public health issue because it can lead to the introduction of pathogens in new areas and favours the emergence of zoonotic diseases. Rodents are prominent invasive species, and act as reservoirs in many zoonotic infectious diseases. The aim of this study was to determine the link between the distribution and spread of two parasite taxa (Leishmania spp. and Trypanosoma lewisi) and the progressive invasion of Senegal by two commensal rodent species (the house mouse Mus musculus domesticus and the black rat Rattus rattus). M. m. domesticus and R. rattus have invaded the northern part and the central/southern part of the country, respectively. Native and invasive rodents were caught in villages and cities along the invasion gradients of both invaders, from coastal localities towards the interior of the land. Molecular diagnosis of the two trypanosomatid infections was performed using spleen specimens. In the north, neither M. m. domesticus nor the native species were carriers of these parasites. Conversely, in the south, 17.5% of R. rattus were infected by L. major and 27.8% by T. lewisi, while very few commensal native rodents were carriers. Prevalence pattern along invasion gradients, together with the knowledge on the geographical distribution of the parasites, suggested that the presence of the two parasites in R. rattus in Senegal is of different origins. Indeed, the invader R. rattus could have been locally infected by the native parasite L. major. Conversely, it could have introduced the exotic parasite T. lewisi in Senegal, the latter appearing to be poorly transmitted to native rodents. Altogether, these data show that R. rattus is a carrier of both parasites and could be responsible for the emergence of new foci of cutaneous leishmaniasis, or for the transmission of atypical human trypanosomiasis in Senegal., Author summary Biological invasions (the introduction and adaptation of living organisms to a new environment) are increasingly frequent due to worldwide intensification of human-associated exchanges. They can lead to the introduction of pathogens in new areas and favour the emergence of diseases. Rodents are prominent invasive species, and act as reservoirs in many infectious diseases. The aim of our study was to determine the link between the distribution and spread of two parasites, Leishmania spp. and Trypanosoma lewisi, and the progressive invasion of Senegal by two commensal rodent species, the house mouse Mus musculus domesticus, and the black rat Rattus rattus. We identified R. rattus as a potential reservoir for Leishmania major and T. lewisi in the southern part of Senegal. The presence of these two pathogens in R. rattus may be of different origins. The invader R. rattus could have been locally contaminated with L. major. Conversely, T. lewisi infection could have been introduced in Senegal by R. rattus, and seems to be poorly transmitted to native rodents. Altogether, these data show that R. rattus is a carrier of both parasites, and could be responsible for the emergence of new foci of cutaneous leishmaniasis or for the transmission of atypical human trypanosomiasis in Senegal.

Changes in host-parasite ecological interactions during biological invasion events may affect both the outcome of invasions and the dynamics of exotic and/or endemic infections. We tested these hypotheses, by investigating ongoing house mouse (Mus musculus domesticus) and black rat (Rattus rattus) invasions in Senegal (West Africa). We used a 16S gene rRNA amplicon sequencing approach to study potentially zoonotic bacterial communities in invasive and native rodents sampled along two well-defined independent invasion routes. We found that individual host factors (body mass and sex) were important drivers of these bacterial infections in rodents. We observed that the bacterial communities varied along invasion routes and differed between invasive and native rodents, with native rodents displaying higher overall bacterial diversity than invasive rodents. Differences in prevalence levels for some bacterial Operational Taxonomic Units (OTUs) provided support for ecological processes connecting parasitism and invasion success. Finally, our results indicated that rodent invasions may lead to the introduction of exotic bacterial genera and/or to changes in the prevalence of endemic ones. This study illustrates the difficulty of predicting the relationship between biodiversity and disease risks, and advocate for public health prevention strategies based on global pathogen surveillance followed by accurate characterization of potential zoonotic agents.

Biological invasions provide unique opportunities for studying life history trait changes over contemporary time scales. As spatial spread may be related to changes in parasite communities, several hypotheses (such as the evolution of increased competitive ability (EICA) or EICA-refined hypotheses) suggest immune changes in invasive species along invasion gradients. Although native hosts may be subject to similar changes in parasite selection pressures, their immune responses have been rarely investigated in invasion contexts. In this study, we evaluated immune variations for invasive house mice Mus musculus domesticus, invasive black rats Rattus rattus and native rodents Mastomys erythroleucus and Mastomys natalensis along well-characterised invasion gradients in Senegal. We focused on antibody-mediated (natural antibodies and complement) and inflammatory (haptoglobin) responses. One invasion route was considered for each invasive species, and environmental conditions were recorded. Natural-antibody mediated responses increased between sites of long-established invasion and recently invaded sites only in house mice. Both invasive species exhibited higher inflammatory responses at the invasion front than in sites of long-established invasion. The immune responses of native species did not change with the presence of invasive species. These patterns of immune variations do not support the EICA and EICA refined hypotheses, and they rather suggest a higher risk of exposure to parasites on the invasion front. Altogether, these results provide a first basis to further assess the role of immune changes in invasion success.

International audience; Microorganisms comprise the majority of earth's biodiversity and are integral to biosphere processes. Biological invasions are no exception to this trend. The success of introduced macroorganisms can be deeply influenced by diverse microorganisms (bacteria, virus, fungus and protozoa) occupying the whole range of species interaction outcomes, from parasitism to obligate mutualism. This large range of interactions, often coupled with complex historical and introduction events, can result in a wide variety of ecological dynamics. In this chapter, we review different situations in which microorganisms affect biological invasions. First, we consider outcomes of microorganism loss during the introduction of alien species. Second, we discuss positive effects of microorganisms on the invasiveness of their exotic hosts. Third, we examine the influence of microorganisms hosted by native species on the success of introduced species. Finally, in an applied perspective, we envisage how microorganisms can be used (i) to better decipher invasion processes and (ii) as biological control agents.

Gerbillus nigeriae is a sand-dwelling and semi-arid adapted rodent species restricted to the West African Sahel where it causes extensive damages to cereal crops such as millet and sorghum. It also displays one of the most extensive floating chromosomal polymorphisms currently known in mammals, showing a non-random spatial distribution of diploid numbers (2N). We combined population dynamics and genetics to determine dispersal and mobility parameters of G. nigeriae in the species distribution range characterized by low 2N. To do so, we performed a three-year long population survey at Gangara, in the central east Niger. We used both time-dependent monitoring trough capture-mark-recapture (CMR) methods and genetic analyses performed on the 134 monitored individuals. CMR results showed low to very low population densities (maximum 27.5 individuals/ha) throughout the study. Abundance cycle was single-phased and strongly dependent on rainfall patterns. Mobility parameters showed very low individual mobility, with means of distance between successive (re) captures (DRS) and maximal distance between (re) captures (DMR) of 7.8 and 14.4 meters, respectively. Genetic analyses revealed significant isolation by distance as well as spatial structuration, thus confirming poor dispersal capacity. Our results are discussed in terms of rodent pest control in arid areas of Niger where cereal crops production is crucial for human food security.

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.

International audience; The worldwide intensification of human-associated exchanges favours the multiplication of biological invasions. Among mammals, rodent species, including the house mouse Mus musculus, are identified as major invaders with profound impacts on native biodiversity, human health and activities. Though contemporary rodent invasions are described on several islands, there are few data describing ongoing house mouse invasions in continental areas. We first outline the known picture of the distribution of the house mouse in Africa. We then describe the ongoing range expansion of the house mouse in Senegal, in order to update its distribution area, assess the location of the invasion front, describe the spatio-temporal dynamics of the invasion at the country scale and evaluate its impact on native small mammal communities. We briefly review the worldwide status of the house mouse, with special focus on its situation in Africa. Focusing on Senegal, we then use historical records and a large body of spatio-temporal indoor trapping data obtained from small mammal communities over the last 30 years to analyse the invasion dynamics of the subspecies at the scale of the country.The geographic range of the invasive house mouse is surprisingly poorly known in Africa. In Senegal, we document a large range expansion of the subspecies in human settlements over the whole country within the last 30 years. The invasion is still ongoing further east and south within the country, and has major consequences for small mammal communities and thus probably for risks associated with zoonotic diseases.

In order to evaluate the contribution of geological, environmental, and climatic changes to the spatial distribution of genetic variation of Mastomys natalensis, we analysed cytochromeb sequences from the whole distribution area of the species to infer its phylogeographic structure and historical demography. Six well-supported phylogroups, differentiated during the Pleistocene, were evidenced. No significant correlation between genetic and geographic distances was found at the continental scale, and the geographic distributions of the observed phylogroups have resulted from extensive periods of isolation caused by the presence of putative geographic and ecological barriers. The diversification events were probably influenced by habitat contraction/expansion cycles that may have complemented topographic barriers to induce genetic drift and lineage sorting. According to our results, we propose a scenario where climate-driven processes may have played a primary role in the differentiation among phylogroups.(c) 2013 The Linnean Society of London

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.

We studied patterns of variation in cestode communities of 3 abundant rodent species that live in sympatry in the Niayes of the Retba Lake, Western Senegal. We evaluated whether the host species have the same parasites and, within host species, whether the variability in parasite community is related to intrinsic (sex, age of the host individual) or extrinsic (habitat, season) factors. Arvicanthis niloticus was parasitized by 2 cestode species, namely Inermicapsifer madagascariensis and the highly dominant Raillietina trapezoides. henna baeri was the only cestode species found in Mastomys erythroleucus, and there was no cestode in M. huberti. Prevalence and abundance levels of cestodes were very high in A. niloticus, especially in adults. Seasonal and habitat effects were found in both cestode communities of M. erythroleucus and A. niloticus. Local host specificity and abundance/prevalence levels suggested variations in the interaction between rodents and cestode intermediate host species among habitats and seasons.

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecolres.com; International audience; This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides

Contact: Anne Loiseau, Fax: +33 (0)4 9962 3345; E-mail: loiseau@supagro.inra.fr; International audience; We isolated and characterized 10 microsatellite loci in the black rat Rattus rattus (Muridae, Rodentia), a widespread invasive species largely known to cause serious problems in agriculture and human health. Polymorphism was studied in two populations, one from Madagascar and one from Senegal. It ranged from three to 12 alleles in Madagascar, and from two to five alleles in Senegal. Together with the loci previously adapted from Rattus norvegicus, this set of markers should allow the conduct of thorough studies on the genetic structure of natural populations of R. rattus.

Two new species of heligmosomoid Trichostrongylina nematodes belonging to the genera Neoheligmonella Durette-Desset, 1970 and Heligmonina Baylis, 1928 are described. They are parasitic in the small intestine of three species of Mastomys from Senegal living in sympatry: M. natalensis (Smith, 1834), M. erythroleucus (Temminck, 1853) and M. huberti (Wroughton, 1909). Neoheligmonella granjoni n. sp. is closely related to three species from Senegal. They concern: N. bai Diouf & Durette-Desset, 2002 and N. dielmensis Diouf, Ba & Durette-Desset, 1998, both parasitic in Arvicanthis niloticus Geoffroy, 1903 and N. mastomysi Diouf et al., 1998, a parasite of M. erythroleucus. N. granjoni n. sp. differs from these species by having 15 cuticular ridges at mid-body versus 13, a large carene and spicules taking up 10-15 % of body length versus 5.3-7.1 %. Heligmonina kanei n. sp, differs from the most related species H. kotoensis Diouf, Daoudo & Durette-Desset 2005, a parasite of M. natalensis from Benin in the following features: spicules taking up 11.6 % of body length on average versus 16.8 %; a female fail three times longer than the distance anus-vulva versus a tail of equivalent size to this distance. In N. granjoni n. sp., where the material is abundant in all three hosts, the infro-specific variations observed (morphological or morphometrical) were not related to the host species. This is the first report of the genera Neoheligmonella and Heligmonina in M. huberti. The relevance of the phenomenon of host capture concerning the evolution of these two genera is confirmed.

Correspondance: akonecny@mail.muni.cz; International audience; The Praomys complex contains some of the most important agricultural pests of Africa, including Mastomys species. We describe the development of nine supplementary microsatellite markers isolated from Mastomys huberti . We show the potential utility of M. Huberti microsatellites as population markers for two other species of Mastomys , and two other species of the Praomys complex, Myomys daltoni And Praomys cf. rostratus

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.

International audience; 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.