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International audience; 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.

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.

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.

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.

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.

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.

Whipworms were collected from rodents (Muridae) from six West African countries: Burkina-Faso, the Islamic Republic of Mauritania, and the Republics of Benin, Guinea, Mali and Senegal. Molecular sequences (ITS-1, 5.8S and ITS-2 of the ribosomal DNA gene) and morphometric characters were analysed in Trichuris (Nematoda: Trichuridae) specimens found in seven host species: Arvicanthis niloticus, Gerbilliscus gambianus, Gerbillus gerbillus, G. tarabuli, Mastomys erythroleucus, M. huberti and M. natalensis. Phylogenetic analyses revealed three clades, one recognised as Trichuris mastomysi, previously recorded in M. natalensis from Tanzania, and the other two previously undescribed. A new species named Trichuris duplantieri n. sp., found in Gerbillus spp. from Mauritania, was characterised using molecular and morphometric methods.

Although they are known to sometimes infect humans, atypical trypanosomes are very poorly documented, especially in Africa where one lethal case has yet been described. Here we conducted a survey of rodent-borne Trypanosoma in 19 towns and villages of Niger and Nigeria, with a special emphasis on Niamey, the capital city of Niger. The 1298 rodents that were captured yielded 189 qPCR-positive animals from 14 localities, thus corresponding to a 14.6% overall prevalence. Rats, especially black rats, displayed particularly elevated prevalence (27.4%), with some well sampled sites showing 40–50% and up to 68.8% of Trypanosoma -carrying individuals. Rattus were also characterized by significantly lower Ct values than in the other non- Rattus species. DNA sequences could be obtained for 43 rodent-borne Trypanosoma and corresponded to 41 T. lewisi (all from Rattus ) and 2 T. microti (from Cricetomys gambianus ). These results, together with data compiled from the available literature, suggest that Rattus may play a particular role for the maintaining and circulation of Trypanosoma , especially T. lewisi , in Africa. Taken into account its strong abilities to invade coastal and inland regions of the continent, we believe that this genus deserves a particular attention in regards to potentially under-looked but emerging atypical trypanosome-related 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 cytochrome b 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.

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.

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.

Understanding why some exotic species become widespread and abundant in their colonized range is a fundamental issue that still needs to be addressed. Among many hypotheses, newly established host populations may benefit from a parasite loss (“enemy release” hypothesis) through impoverishment of their original parasite communities or reduced infection levels. Moreover, the fitness of competing native hosts may be affected by the acquisition of exotic taxa from invaders (“parasite spillover”) and/or by an increased transmission risk of native parasites due to their amplification by invaders (“parasite spillback”). We focused on gastrointestinal helminth communities to determine whether these predictions could explain the ongoing invasion success of the commensal house mouse (Mus musculus domesticus) and black rat (Rattus rattus), as well as the associated drop of native Mastomys species, in Senegal. For both invasive species, our results were consistent with the predictions of the enemy release hypothesis. A decrease of helminth overall prevalence and individual species richness was observed along the invasion gradients as well as lower specific prevalence/abundance (Aspiculuris tetraptera in M. m. domesticus, Hymenolepis diminuta in R. rattus) on the invasion fronts. Conversely, we did not find strong evidence of helminth spill-over or spill-back in invasion fronts, where native and invasive rodents co-occurred. Further experimental research is needed to determine whether and how the loss of helminths and reduced infection levels along invasion routes may result in any advantageous effects on invader fitness and competitive advantage.

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.

Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillus gerbillus, Gerbillus andersoni, Gerbillus nanus, Gerbillus amoenus, Gerbillus perpallidus and Gerbillus pyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillus nanus (Asian origin) and Gerbillus amoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillus perpallidus and Gerbillus pyramidum, specimens considered as belonging to one Gerbillus pyramidum subspecies (Gerbillus pyramidum floweri) appeared closer to Gerbillus perpallidus suggesting that they (Gerbillus pyramidum floweri and Gerbillus perpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillus floweri. Furthermore, the three other Gerbillus pyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest.

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North-West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

Ndiaye, A., Bâ, K., Aniskin, V., Benazzou, T., Chevret, P., Konecný, A., Sembene, M., Tatard, C., Kergoat, G.J. & Granjon, L. (2011). Evolutionary systematics and biogeography of endemic gerbils (Rodentia, Muridae) from Morocco: an integrative approach. —Zoologica Scripta, 41, 11–28. Gerbils of the genus Gerbillus represent an important part of small mammal diversity in arid regions of North Africa, but their taxonomy and evolutionary systematics and biogeography are still poorly known. Based on the recent collection of a series of gerbils in southern Morocco, including at the type localities of three endemic species, we gathered morphological, chromosomal and molecular data on a number of specimens that we compared with other available results. These data provide new insights into the geographical distribution of the endemic species known to date and suggest that an additional and previously undetected species may exist within this area. Multivariate analyses of morphometrical skull data validated the criteria used in the description of some of these species, while confirming the morphological similarity of a set of medium to large-sized species with hairy feet that can be considered sibling species. Karyotypes were useful for the specific assignation of a number of specimens. Molecular phylogenetics and divergence time estimates allow us to draw the first picture of the evolutionary relationships between endemic Gerbillus species from Morocco and related species of North Africa, and to estimate their respective timing of diversification. Most of the lineage emergence events took place during the Pleistocene, a period characterised by a global aridification of North Africa, but more importantly by important climatic and eustatic variations that may have played a role in species differentiation and subsequent expansion. This integrative approach proved to be essential in such species group including morphologically similar species. It also enables to propose testable hypotheses as to possible scenarios of emergence and evolution of these species along the western margin of the Sahara desert.

The Mediterranean Basin is an acknowledged hotspot for biodiversity, yet historical processes that shaped this biodiversity in North Africa remain poorly understood. This study aimed to elucidate the phylogeographic pattern of an endemic species of Mediterranean areas of North Africa, the Greater Egyptian Jerboa, Jaculus orientalis. The extent of phylogeographic patterns and molecular genetic diversity (mitochondrial cytochrome b gene) were addressed in a survey of 45 jerboas from 24 localities. Our phylogeographical analyses show a strong genetic subdivision into three areas along a west-east axis, corresponding to (1) Morocco and western Algeria; (2) eastern Algeria, Tunisia and western Libya; (3) eastern Libya and Egypt. Demographic analyses revealed different modalities of population expansion since the last glacial age depending on geographic areas. The dating using relaxed molecular clock analyses revealed that most splits occurred during the Quaternary (

Jerboas belonging to the genus Jaculus are widely distributed rodents inhabiting Palearctic desert and semi-desert areas. Previous studies on the lesser Egyptian jerboa Jaculus jaculus showed the existence of various morphological forms of controversial taxonomic status. They were sometimes related to two different species, J. jaculus and Jaculus deserti, although this has not been recognized in recent taxonomic updates. To clarify the systematic status of J. jaculus in Tunisia, we performed molecular (phylogenetic analyses of cytochrome b sequences), morphological (multivariate analyses of 13 skull measurements) and karyotypic (standard preparations from bone marrow cells) analyses on a number of specimens collected from ten localities. Our analyses revealed two monophyletic, well differentiated clades, with a mean genetic divergence value (K2P = 10.9 ± 0.01%), which is within the range of distances generally observed between rodent species. Morphometric analyses clearly separated populations of the two genetic clades from each other. However, karyotypes of individuals from both clades appeared similar. Individuals from both molecular clades/morphometric groups were found in sympatry in most of the localities sampled. These results, as obtained from a restricted area of the total distribution, suggest that there are two separate species within the currently accepted J. jaculus in Tunisia. Alternative hypotheses such as the occurrence of a strong, ancient phylogeographic structure, or the presence of pseudogenes, are also considered to account for the results obtained. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 673–686.

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

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., Author Summary We surveyed rodent-borne Leptospira in rodents from Niamey, the capital town of Niger, using bacterial metabarcoding, RT-PCR, sequencing, VNTR typing and GIS-based geostatistics. Two new serovars of Leptospira kirschneri were identified in Arvicanthis niloticus and Cricetomys gambianus, two species that inhabit exclusively urban irrigated gardens. Since no rodent-borne leptospires could be found in the core city, our results point towards the importance of urban agriculture in the maintaining and the circulation of these bacteria in cities from semi-arid regions where they are usually poorly documented and even hardly looked for. Accordingly, this is one of the very rare mentions of these zoonotic agents in Sahel, and the first one in Niger. Keeping in mind the critical role of urban gardening for food security in extensively growing West African cities, we believe that leptospirosis should be more closely scrutinized in Sahelian countries where numerous cases of human fevers are of unknown origin.

Times Cited: 0; International audience; Invasive rodents have been responsible for the diffusion worldwide of many zoonotic agents, thus representing major threats for public health. Cities are important hubs for people and goods exchange and are thus expected to play a pivotal role in invasive commensal rodent dissemination. Yet, data about urban rodents' ecology, especially invasive vs. native species interactions, are dramatically scarce. Here, we provide results of an extensive survey of urban rodents conducted in Niamey, Niger, depicting the early stages of rodent bioinvasions within a city. We explore the species-specific spatial distributions throughout the city using contrasted approaches, namely field sampling, co-occurrence analysis, occupancy modelling and indicator geostatistics. We show that (i) two species (i.e. rural-like vs. truly commensal) assemblages can be identified, and that (ii) within commensal rodents, invasive (Rattus rattus and Mus musculus) and native (Mastomys natalensis) species are spatially segregated. Moreover, several pieces of arguments tend to suggest that these exclusive distributions reflect an ongoing native-to-invasive species turn over. The underlying processes as well as the possible consequences for humans are discussed.

Background Leptospirosis is the most common bacterial zoonoses and has been identified as an important emerging global public health problem in Southeast Asia. Rodents are important reservoirs for human leptospirosis, but epidemiological data is lacking. Methodology/Principal Findings We sampled rodents living in different habitats from seven localities distributed across Southeast Asia (Thailand, Lao PDR and Cambodia), between 2009 to 2010. Human isolates were also obtained from localities close to where rodents were sampled. The prevalence of Leptospira infection was assessed by real-time PCR using DNA extracted from rodent kidneys, targeting the lipL32 gene. Sequencing rrs and secY genes, and Multi Locus Variable-number Tandem Repeat (VNTR) analyses were performed on DNA extracted from rat kidneys for Leptospira isolates molecular typing. Four species were detected in rodents, L. borgpetersenii (56% of positive samples), L. interrogans (36%), L. kirschneri (3%) and L. weilli (2%), which were identical to human isolates. Mean prevalence in rodents was approximately 7%, and largely varied across localities and habitats, but not between rodent species. The two most abundant Leptospira species displayed different habitat requirements: L. interrogans was linked to humid habitats (rice fields and forests) while L. borgpetersenii was abundant in both humid and dry habitats (non-floodable lands). Conclusion/Significance L. interrogans and L. borgpetersenii species are widely distributed amongst rodent populations, and strain typing confirmed rodents as reservoirs for human leptospirosis. Differences in habitat requirements for L. interrogans and L. borgpetersenii supported differential transmission modes. In Southeast Asia, human infection risk is not only restricted to activities taking place in wetlands and rice fields as is commonly accepted, but should also include tasks such as forestry work, as well as the hunting and preparation of rodents for consumption, which deserve more attention in future epidemiological studies., Author Summary Leptospirosis is the most prevalent bacterial zoonosis worldwide. Rodents are believed to be the main reservoirs of Leptospira, yet little epidemiological research has been conducted on rodents from Southeast Asia. Previous studies suggest that activities which place humans in microenvironments shared by rodents increase the probability of contracting leptospirosis. We therefore investigated the circulation of leptospiral species and strains in rodent communities and human populations in seven localities scattered throughout Southeast Asia; in Thailand, Lao PDR and Cambodia. Molecular typing assays were used to characterize leptospiral species and strains in both rodents and humans, which demonstrated common strains between humans and rodents. Additionally, we observed that the two most abundant leptospiral species; L. borgpetersenii and L. interrogans, have different habitat requirements, which supposes different modes of transmission. Lastly, in Southeast Asia, the risk of leptospiral transmission to humans is not solely limited to wetlands and rice paddy fields, but is also linked to forested areas, and activities such as the hunting and/or preparation of rodents for consumption.

International audience; An understanding of the evolutionary history and dynamics of invasive species is required for the construction of predictive models of future spread and the design of biological management measures. The black rat (Rattus rattus) is a major vertebrate invader with a worldwide distribution. Despite the severe ecological, economic and health impacts of this species, its evolutionary history has been little studied. We carried out extensive specimen sampling in Senegal, West Africa, and used microsatellite markers to describe the pattern and processes of invasion in this large continental area. The genetic data obtained were combined with historical knowledge concerning the presence of this species in Senegal. Data were analysed by a combination of Bayesian clustering and approximate Bayesian computation methods. The invasion pathways closely paralleled the history of human trade routes in Senegal. In several places, we detected the occurrence of multiple introductions from genetically different sources. Long-distance migration between towns and villages was also observed. Our findings suggest that genetic bottlenecks and admixture have played a major role in shaping the genetics of invasive black rats. These two processes may generate genetic novelty and favour rapid evolution along the invasion pathways.

A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.

The systematics of the African rodent genus Gerbilliscus is still a matter of debate. At the genus level it has been said toinclude the related genus Gerbillurus, and at the species level some species still need to be definitely recognized as dis-tinct. To tackle these questions, we gathered and analyzed mitochondrial (cytochrome b) and nuclear (BRCA1) gene se-quences in a number of specimens representing ten species of Gerbilliscus and three species of Gerbillurus. Phylogeneticreconstructions confirm that Gerbillurus should be considered a synonym of Gerbilliscus. They also clearly show that spe-cies diversity in this group is spatially organized, with geographically well-defined species groups covering major areasof sub-Saharan Africa, namely Southern, Eastern and Western Africa. In the latter area, a well-supported genetic lineageappears to correspond to a hitherto overlooked species, also characterized by a distinctive karyotype. This species is char-acterized by an overall large size, a relatively long tail, a distinct karyotype, and represents a well-differentiated geneticcluster. It ranges from Benin to Guinea in Sudano-Guinean forest-savanna mosaic habitats, where it can be sympatric withthe congeneric species G. kempi and G. guineae. Detailed body and skull morphological and biometrical analyses per-formed on samples of the West African species, including type specimens described in this region, suggest that this speciesmay correspond to G. kempi. If confirmed, this would imply that what is currently named G. kempi would deserve another species name, the most likely of which would be G. giffardi.

International audience; Scrub typhus is an acute febrile zoonotic disease and worldwide more than a billion people may be at risk for infection. Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium. Rodents are reported to be the primary reservoir hosts of the disease and according to the most recent surveys, all species within the Rattus sensu lato complex of the tribe Rattini are carriers of scrub typhus. There is no evidence that any of mouse (Mus) species serves as the primary reservoir of the bacterium even when occurring in sympatry with wild infected rats. This contrast in the host/syndecan-4 interactions between Rattini and Asian Murini may be due to intrinsic (i.e., genetic) differences. Herein we compare the sequence and expression levels of syndecan-4 (the putative cell receptor of O. tsutsugamushi) between Rattini species that are known to be natural reservoirs for the typhus agents, and Murini species that are not. Although it was not possible to conclusively link the structural variations detected in syndecan-4 with carrier status in either Rattini and Murini, our findings indicate the absence of a strong Orientia-mediated selective regime acting on gene structure. In contrast, variable spleen-specific syndecan-4 expression levels show a strong correlation between under-expression of syndecan-4 in Murini and seropositive Rattini, compared to seronegative Rattini rodents. We postulate that two divergent responses may be at work in Murini and Rattini, both linked with differential expression of syndecan-4: (i) reduced syndecan-4 transcription in Murini decreases the likelihood that the host cells will become infected by the Orientia bacterium, while (ii) reduced syndecan-4 expression in seropositive Rattini limits the pathogenicity of Orientia and consequently improves the longevity of the rat hosts. These patterns may underpin the poor carrier status of wild mice on the one hand, and the effective role of wild rats as reservoir hosts on the other. (C) 2012 Elsevier B.V. All rights reserved.

Contact: fax: +33 4 9962 3345. E-mail address: carine.brouat@ird.fr; International audience; Contrasting host and parasite population genetic structures can provide information about the population ecology of each species and the potential for local adaptation. Here, we examined the population genetic structure of the nematode Neoheligmonella granjoni at a regional scale in southeastern Senegal, using 11 microsatellite markers. Using the results previously obtained for the two main rodent species of the host community, Mastomys natalensis and Mastomys erythroleucus, we tested the hypothesis that the parasite population structure was mediated by dispersal levels of the most vagile host. The results showed similar genetic diversity levels between host and parasite populations, and consistently lower levels of genetic differentiation in N. granjoni, with the exception of one outlying locus with a high F. The aberrant pattern at this locus was primarily due to two alleles occurring at markedly different frequencies in one locality, suggesting selection at this locus, or a closely linked one. Genetic differentiation levels and isolation by distance analyses suggested that gene flow was high and random in N. granjoni at the spatial scale examined. The correlation between pair-wise genetic differentiation levels in the parasite and its main host was consistent with the hypothesis tested. Models of local adaptation as a function of the dispersal rates of hosts and parasites suggest that opportunities for local adaptation would be low in this biological system. (C) 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Contact: gauthier.dobigny@ird.fr; International audience; Invading rodent species can harbor parasites with potential transmission to native rodents and/or humans. To investigate trypanosomes prevalence in rodents, the spleen of 76 rodents from Niger identified by their karyotype was used as a DNA source for Trypanosoma detection using a newly developed qPCR assay. Of the invasive black rat, Rattus rattus, 71% (10/14) were PCR positive as well as 6% (4/62) of native African rodents. Sequences of 400 bp of the SSU rDNA gene identified phylogenetically close Trypanosoma lineages. Trypanosoma lewisi was present in all positive black rats and the sequences displayed 100% similarity with T. lewisi-infected humans in Senegal. T. lewisi was also detected in one Acomys johannis, suggesting a possible transmission to native species. In addition to improved knowledge of Trypanosoma diversity in rodents, our data underscore the introduction of the potentially pathogenic T. lewisi kinetoplastid through the human-mediated invasion of black rats all over West Africa

Rodent diagnosis has long remained obscured by the co-existence of cryptic species in many lineages. However, alternative and accessible methods, such as cytotaxonomy and DNA-based methods, are now available that allow biologists to accurately monitor biodiversity through the production of well documented lists of unambiguously species-specific identifications. As a continuation of our previous surveys of West African rodents, we here present the first rodent inventory of rodents from Northern Cameroon (as well as one locality in Western Chad) that fully relies on karyotypic and/or sequencing data. Doing so, we assess the presence of 18 species in this poorly documented region. Among them, we found several African spiny mice that could be referred as to A. johannis, a poorly documented species. Moreover, several Arvicanthis individuals could be aggregated with previously studied but still enigmatic specimens of ANI-2 and ANI-4 sensu Volobouev et al., 2002a , Volobouev et al., 2002b , thus suggesting that they may all belong to one single species, namely A. rufinus. In addition, one specimen was shown to belong to a new biological species (Praomys sp.) that will deserve further taxonomic investigations. Finally, several Taterillus specimens were found with 2n = 28–30 chromosomes and a XX/XY1Y2 sex chromosome system. On the basis of these new results as well as a reinterpretation of previously published data, we propose to refer these individuals as to the poorly documented Taterillus lacustris. Altogether, our data suggest that Northern Cameroon is a “phylogeographical node” for several rodent lineages which may be at least partly explained by the past changes within the Lake Chad basin. Keeping this in mind, there is little doubt that biodiversity will undergo important modifications in the coming decades, following the increasing aridity and the drastic reduction of Lake Chad.

The African pygmy mouse, Mus minutoides, displays extensive Robertsonian (Rb) diversity. The two extremes of the karyotypic range are found in South Africa, with populations carrying 2n = 34 and 2n = 18. In order to reconstruct the scenario of chromosomal evolution of M. minutoides and test the performance of Rb fusions in resolving fine-scale phylogenetic relationships, we first describe new karyotypes, and then perform phylogenetic analyses by two independent methods, using respectively mitochondrial cytochrome b sequences and chromosomal rearrangements as markers. The molecular and chromosomal phylogenies were in perfect congruence, providing strong confidence both for the tree topology and the chronology of chromosomal rearrangements. The analysis supports a division of South African specimens into two clades showing opposite trends of chromosomal evolution, one containing all specimens with 34 chromosomes (karyotypic stasis) and the other grouping all mice with 18 chromosomes that have further diversified by the fixation of different Rb fusions (extensive karyotypic reshuffling). The results confirm that Rb fusions are by far the predominant rearrangement in M. minutoides but strongly suggest that recurrent whole-arm reciprocal translocations have also shaped this genome.

Correspondance: gauthier.dobigny@ird.fr; International audience; By suppressing recombination and reducing gene flow, chromosome inversions favor the capture and protection of advantageous allelic combinations, leading to adaptive polymorphisms. However, studies in non-model species remain scarce. Here we investigate the distribution of inversion polymorphisms in the multimammate rat Mastomys erythroleucus in West Africa. More than 270 individuals from 52 localities were karyotyped using G-bands and showed widespread polymorphisms involving four chromosome pairs. No significant deviations from Hardy–Weinberg equilibrium were observed either through space or time, nor were differences retrieved in viability or sex contribution between cytotypes. The distribution of chromosomal variation, however, showed perfect congruence with that of mtDNAbased phylogeographic clades. Thus, inversion diversity patterns in M. erythroleucus appeared more related to historical and/or demographic processes than to climatebased adaptive features. Using cross-species chromosome painting and G-banding analyses to identify homologous chromosomes in related out-group species, we proposed a phylogenetic scenario that involves ancestral-shared polymorphisms and subsequent lineage sorting during expansion/ contraction of West African savannas. Our data suggest that long-standing inversion polymorphisms may act as regions in which adaptation genes may accumulate (nucleation model)