Commensal mammals offer unique opportunities to study how human-mediated dispersal, admixture, and secondary contact shape genomic variation during range expansion, yet for one of the most successful invasive commensals globally, the western house mouse Mus musculus domesticus, invasion dynamics across Africa remain largely unexplored. Here, we present a large-scale population genomic analysis of 380 whole-genome sequences, including 303 newly sequenced low-coverage genomes, of which 216 are from 13 distinct African populations, enabling us to investigate how human-mediated dispersal and secondary contact with native species shape the genomic legacy of a commensal mammal invasion. Ancestry analyses reveal contributions from at least three major Eurasian source lineages contributing to African populations: an Iberian-West Asian lineage present in Morocco, Algeria, and Niger; a Mediterranean lineage represented in Tunisia; and a Northern European lineage dominant in West and Central Africa. Demographic inferences indicate both recent and ancient episodes of divergence and population contraction. In West and Central Africa, divergence times broadly overlap with European maritime expansion and colonial trade. In contrast, North African populations exhibit older coalescent signals, consistent with early participation in the western Mediterranean radiation. We also detect substantial introgression from the native Mus spretus into North African populations in regions of sympatry. Collectively, our results reveal that the African invasion of the house mouse was not a single demographic process but a mosaic of population-specific histories shaped by multiple introductions, shifting connectivity through time, admixture, and interspecific gene flow. These findings reinforce the importance of population-level perspectives in invasion genomics, especially for commensal mammals whose dispersal is closely tied to human movement, and establish the most extensive open genomic resource for wild African house mice.

BACKGROUND:Plague remains a major public health concern in Madagascar. In the Central Highlands, where the disease is still endemic, the black rat (Rattus rattus) is the main reservoir of the causative agent Yersinia pestis. Understanding its population dynamics and structure is therefore crucial to inform control strategies, as dispersal may greatly limit the effectiveness of local interventions during outbreaks. In this context, our study investigates the genetic structure of R. rattus populations at a fine geographical scale and across two different years. METHODOLOGY/PRINCIPAL FINDINGS:Sampling was conducted in six villages of the Azobenzene district, both inside houses and in habitat outside villages. A total of 480 individuals, captured in March - May 2019 and 2020, were genotyped at 18 microsatellite loci. Our results showed that genetic diversity levels were relatively similar among villages and years. However, subpopulations living outside villages displayed significantly higher genetic diversity and lower genetic differentiation levels than those from inside houses, indicating larger effective population sizes outside villages in the cultivated habitats. These findings suggest more restricted movement among rat subpopulations from the houses, and greater connectivity among subpopulations living outside villages. However, overall genetic differentiation was rather low, suggesting extensive dispersal of rats at the scale of the district, facilitating rapid recolonization after local control efforts. CONCLUSION:Because of the recolonization problem, an integrated approach combining flea control inside houses together with measures to reduce human-rodent contact would thus appear more appropriate than rodent control only to limit plague transmission.

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

Rodents are important reservoirs for numerous zoonotic parasites. Among them, Trypanosoma lewisi (subgenus Herpetosoma) has been introduced into many regions worldwide through its primary reservoir, Rattus, which has spread globally along human commercial routes. Several other Herpetosoma species have been reported to infect native rodents in Africa, although their zoonotic potential remains unclear. In rural areas of Gabon, R. rattus is widely distributed within villages, being largely dominant in rodent communities. Based on sampling conducted across 11 localities, we screened 528 rodents. Using qPCR targeting the 18S rDNA gene. The overall prevalence for this subgenus was 56.6% (n = 299). Trypanosoma spp. were detected at all sampling sites, with prevalence in R. rattus ranging from 21.6% to 85.7% in domestic localities. Infections were also observed in Praomys jacksoni (100%), Lophuromys roseveari (72%), Lemniscomys striatus (25%), and Hybomys univittatus (71%). To formally identify the circulating species, a 2100 bp fragment of the 18S rDNA gene was successfully sequenced from a subset of 21 qPCR-positive samples, revealing that all these characterized isolates belonged to the subgenus Herpetosoma and clustered tightly within the T. lewisi subclade (genotype AF05b), recognized as T. lewisi sensu stricto. Our findings confirm the occurrence of T. lewisi AF05b within invasive R. rattus populations in rural Gabon. While T. lewisi DNA was also detected in a few native rodents, the low trypanosome diversity observed in this study is likely driven by the overwhelming dominance of R. rattus in our sampling. This study underscores the widespread presence of the T. lewisi clade in invasive rats in Gabon and emphasizes the importance of monitoring invasive rodent populations as potential amplifiers of zoonotic trypanosomes, though further targeted studies with balanced sampling are required to clarify the exact epidemiological role of native African rodents in these transmission cycles.

The emergence of infectious diseases associated with land-use changes is well-documented. However, the presence and dynamics of zoonotic pathogens in small mammals within European forests, whether from rural development or urban greening, remain underexplored. To describe zoonotic hazards in these ecosystems, and to assess the influence of biotic and abiotic factors on their distribution, we analyzed 1549 individuals from 18 small mammal species sampled across forest types representing different levels of anthropization using both targeted and broad-spectrum serological and molecular methods. We detected nine bacteria and five Apicomplexa that are potentially pathogenic to humans. Zoonotic pathogen richness and community composition varied significantly across host species, sites, and sampling periods. Richness was lower in forested urban parks, possibly due to the absence of vectors or intermediate hosts within cities. It was higher in urban adapter species, even within a given forested habitat, emphasizing the important role of specific life-history traits. Pathogen community structure was shaped by forest anthropization and host ecology, with marked differences between urban and rural forested environments and between urban adapter and dweller species within forested urban parks. The seroprevalence of key pathogens (e.g., Bartonella, Orthopoxvirus, Neoehrlichia mikurensis, and Sarcocystidae) showed spatial, temporal, and host-specific variation. Epidemiological differences between sites often exceeded those between habitat types, in particular when comparing protected and managed forests, highlighting the importance of local ecological context. Nevertheless, some patterns reflected the influence of forest anthropization and species urban adaptation strategies for certain zoonotic agents. High anthropization in forests was associated with elevated Bartonella prevalence, driven by urban-adapter species rather than forest dwellers, emphasizing local ecological interactions between hosts and pathogens. Besides, higher levels of Orthopoxvirus seroprevalence were associated with adapter species in protected forests where they might be more abundant. Altogether, these findings underscore the need for integrated and multipathogen wildlife surveillance to anticipate and mitigate disease risks at the human-environment-animal interface.

BACKGROUND:The plague, caused by Yersinia pestis, remains a critical public health issue, particularly in endemic regions like Madagascar. Rapid and accurate detection of this pathogen is essential for effective outbreak management and timely intervention. Following the urban plague outbreak of 2017, a new molecular diagnostic algorithm was developed and introduced into routine use. However, certain cases required combining real-time and conventional polymerase chain reaction (PCR) methods. While effective, this approach often delayed obtaining conclusive results, an issue that can hinder swift outbreak responses. The aim of this study is to design and optimize a three-target real-time PCR assay (qPCR) for the detection of Y. pestis in clinical samples. METHODS:The assay targeted three genes: caf1, pla, and yopM, located on the plasmids pMT1, pPCP1, and pCD1, respectively. Conducted at the Institut Pasteur de Madagascar (IPM), the study evaluated the assay using both pure bacterial cultures and clinical samples, including 50 bubonic aspirates and 50 respiratory specimens. RESULTS:Using bacteriology technique as the reference standard, the triplex qPCR demonstrated a sensitivity of 100% (89-100%) and a specificity of 82%. The positive predictive value (PPV) was 73% and the negative predictive value (NPV) was 100% (91-100%). The coefficient of agreement kappa was 0.74, with a p-value of <0.0001. Notably, the new assay resolved 100% of previously inconclusive cases from the duplex qPCR test targeting only pla and caf1. DISCUSSION:While a new plague diagnostic algorithm has been set up after the outbreak in 2017, the present study suggests a real-time PCR assay based on three genes to improve the speed and accuracy of plague diagnostic. Furthermore, this new technique is a valuable tool for managing plague outbreaks and supporting field diagnostics not only in Madagascar but also in countries with plague. CONCLUSIONS:The developed triplex assay to molecularly diagnose Y. pestis in human samples improves the standard already in place and allows to resolve ambiguities previously associated with inconclusive results from duplex qPCR tests, thereby reinforcing the reliability and accuracy of this new technique. Implementing this new method into routine will enable a faster, more effective response to plague outbreaks by reducing the time needed to confirm plague cases and limiting the spread of the diseases. This new technique is also flexible and can be undertaken close to human cases with adequate biosecurity and biosafety measures.

Invasive species are increasingly recognized for their role in reshaping host-parasite dynamics. This study reports the first molecular detection of Plasmodium yoelii in the invasive black rat (Rattus rattus) in Gabon, based on a systematic molecular screening of 527 rodents captured in rural villages between 2021 and 2022. Two R. rattus individuals tested positive for P. yoelii, with phylogenetic analysis confirming identity with strains previously isolated from native rodents in the region. These findings challenge the traditional view that rodent malaria parasites are restricted to native hosts and highlight R. rattus as a potential, albeit likely incidental, host within local Plasmodium transmission networks. Despite a low infection prevalence (0.38 %), this result raises important questions about the capacity of invasive rodents to integrate into local parasite cycles and influence disease dynamics.

The emergence of infectious diseases associated with land-use changes is well-documented. However, zoonotic risks originating from European forests, whether from rural development or urban greening, remain underexplored. To assess and mitigate zoonotic hazards in these ecosystems, we analyzed 1,549 individuals from 18 small mammal species sampled along a forest anthropization gradient using both targeted and broad-spectrum serological and molecular methods. We detected nine bacteria and several Apicomplexa that are potentially pathogenic to humans. Zoonotic pathogen richness and community composition varied significantly across host species, sites and sampling periods. Richness was lower in forested urban parks, possibly due to the absence of vectors or intermediate hosts within cities. It was higher in urban adapter species, even within a given forested habitat, emphasizing the important role of specific life-history traits. Pathogen community structure was similarly shaped by forest anthropization and host ecology, with marked differences between urban and rural forested environments and between urban adapter and dweller species within forested urban parks. The (sero-)prevalence of key pathogens (e.g., Bartonella, Orthopoxvirus, Neoehrlichia mikurensis , Sarcocystidae) showed spatial, temporal, and host-specific variation. Site-level differences often exceeded those between general habitat types, highlighting the importance of local ecological context. Nevertheless, some patterns reflected the influence of forest anthropization and species urban adaptation strategies for certain zoonotic agents. Forest anthropization had a positive impact on Bartonella prevalence, for urban adapter species within parks, emphasizing a potential dilution effect of these pathogens. Besides, higher levels of Orthopoxvirus seroprevalence were associated with adapter species, in protected forests where they might be more abundant. Altogether, these findings underscore the need for integrated and multi-pathogen wildlife monitoring to anticipate and mitigate disease risks at the human– environment–animal interface. ### Competing Interest Statement The authors have declared no competing interest. 2018-2019 BiodivERsA joint call, BiodivERsA3 ERA-Net COFUND programme

A growing number of studies has highlighted the importance of coinfections in eco-evolutionary processes underlying host-parasite interactions and the resulting epidemiology of zoonotic agents. Small mammals, and particularly rodents, are known to be important reservoirs of many zoonotic pathogens, such as Toxoplasma gondii and Trypanosoma lewisi, that are responsible for toxoplasmosis and atypical trypanosomiasis in humans, respectively. Laboratory experiments on rodent models have shown that primary infection with T. lewisi increases the host sensitivity to other parasites, including T. gondii, following an alteration in the immune response. However, data on potential interactions between these parasites in wild small mammals remain scarce. In this study, we determined the T. lewisi prevalence in 553 small mammals from four localities of Cotonou city, Benin. The results were then combined with T. gondii data previously collected for the same individuals in order to investigate the influence of T. lewisi on T. gondii infection, and vice versa, using co-occurrence tests and generalized linear mixed models (GLMMs). Despite quite high overall prevalence (32.5% and 15.2% for T. lewisi and T. gondii, respectively), we observed a clear and significant segregation between the two parasites. This may be explained by (i) differences in the species-specific receptivity and/or sensitivity of small mammal host species to infection by these two parasites, with Rattus rattus (Rra), Rattus norvegicus (Rno), and Mastomys natalensis (Mna) being the main hosts of T. lewisi, while Crocidura olivieri (Cro) and Mus musculus domesticus (Mus) were the main hosts for T. gondii; and/or (ii) a possibly high mortality in coinfected animals in the wild. Although dedicated experimental studies are required to confirm this pattern, as they stand, our data fail to support that in nature, the infection of small mammals by one of these two parasites favors widespread infection by the second one.

Caliciviruses (Caliciviridae) and astroviruses (Astroviridae) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of Rattus rattus species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to Mamastrovirus genus in which they were genetically related to R. rattus related AstVs previously detected in Gabon or in Rattus spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.

International trade has been favouring the dissemination of a wide suite of invasive alien species. Upstream prevention through the monitoring of entry points is identified as an appropriate strategy to achieve control of bioinvasions and their consequences. Maritime transportation has been responsible for the introduction worldwide of exotic rodents that are major pests for crops and food stocks as well as reservoirs of many zoonotic pathogens. In order to limit further dissemination, the International Health Regulation constrains decisions makers and socio-economic stakeholders to manage ship-mediated import/export of rodents within seaports.Unfortunately, eco-evolutionary insights into rodent introduction events that could guide preventive actions in seaports are very scarce. In order to bridge this gap, we here describe the results of a 3 year-long survey of small mammals conducted in the Port of Cotonou, Benin.Our aim was to assess the spatiotemporal distribution, diversity and relative abundance of invasive and native rodents.960 small mammal individuals were captured in nine within-seaport sites. We found (i) a marked predominance of invasive species (84% of the individuals belonging to Mus musculus, Rattus rattus, R. norvegicus), (ii) with native species (i.e. Mastomys natalensis and the shrew Crocidura olivieri) essentially restricted to peripheral non-industrial areas, as well as (iii) a fine-scale spatial segregation stable over time between the invasive Norway rats and house mice on the one hand, and the black rats and shrews on the other hand.Furthermore, trapping before and after two successive rodent control campaigns indicates that they were ineffective and that subsequent rodent recolonisation occurred 6-12 months following intervention.Synthesis and applications. Our results are discussed in terms of ecological processes at play (e.g. interspecific interactions) and operational recommendations (e.g. assessment of proper eradication units, environmental modifications).

Abstract Urbanization processes are taking place at a very high rate, especially in Africa. At the same time, a number of small mammal species, be they native or invasive, take advantage of human‐induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try to understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences among house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co‐occurrence patterns were studied at the global and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever‐accelerating global changes.

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.

Crocidura olivieri is a large-sized shrew species showing a clear trend towards commensalism in West Africa, where it co-occurs and interacts with a number of rodent species in indoor small mammal communities. Among the rodents present is the house mouse Mus musculus , a major invasive species worldwide. We here test the hypothesis that M. musculus could be part of the diet of C. olivieri in a number of localities of Senegal where the two species are known to coexist. We use a metabarcoding approach based on the high-throughput sequencing of a 133 bp fragment of the COI gene, on DNA extracted from digestive tracts and faeces of a sample of 108 shrews. Beside insects of various groups (ants, beetles and cockroaches especially) representing usual items of shrew’s diet, and traces of domestic mammals and poultry that were probably scavenged, several species of rodents were evidenced. Among them, M. musculus was by far the best represented species, found in 17 of the 54 shrews where at least one prey taxon was identified. This finding tends to confirm the potential role of C. olivieri as predator of house mice, while highlighting the capacity of this species to adapt its diet to environmental conditions.

Leptospirosis is a zoonotic disease that is caused by spirochete bacteria of the genus Leptospira. Around the world, one million people each year are infected, leading to 60,000 deaths. Infection occurs through contact with environmental pathogens excreted by mammals (notably rodents). Data on Leptospira and leptospirosis in Africa are rather scarce, especially in urban habitats though these appear to be favourable environments for the pathogen circulation and human contamination. Using qPCR, DNA sequencing as well as MST/VNTR approaches, we examined Leptospira occurrence and genetic diversity in 779 commensal small mammals that were sampled over 2 years in the city centre of Cotonou, Benin, from three neighbourhoods with contrasting socio-environmental conditions. Overall prevalence reached 9.1%. However, very marked variations in both space and time were observed, with local peaks of high prevalence but no clear seasonal pattern. In most sites that could be regularly sampled, Leptospira-positive rodents were found at least once, thus confirming the widespread circulation of the pathogen within small mammal communities of Cotonou. Interestingly, an unusual diversity of small mammal-borne Leptospira species and genotypes was retrieved, with up to four species and three different genovars within the same neighbourhood, and even instances of two species and two genovars identified simultaneously within the same household. To our knowledge, such a high genetic diversity has never been described at such a fine scale, a fortiori in Africa and, more generally, within an urban environment. Altogether, our results underline that much remains unknown about leptospirosis as well as the associated infectious risk in African cities where the disease may be massively over-looked.

Trypanosoma lewisi belongs to the so-called atypical trypanosomes that occasionally affect humans. It shares the same hosts and flea vector of other medically relevant pathogenic agents as Yersinia pestis, the agent of plague. Increasing knowledge on the population structure (reproductive mode, population size, dispersal) of this parasite thus represents a challenging but important issue. The use of polymorphic genetic markers, together with suitable population genetics tools, is a convenient way to achieve such objectives. To date, the population biology of T. lewisi is poorly known and, to our knowledge, no population genetics studies have ever been conducted. Here, we present the development of nine microsatellite markers of this species. We investigated their polymorphism in different countries from Africa and South-East Asia from DNAs extracted from the spleen of their rodent reservoirs (essentially rat species). Several amplification problems arose, especially with South-East Asian individuals. This led to retain only those individuals with complete genotypes (most of them originating from West Africa, notably Cotonou, Benin) to ensure an optimal estimate of heterozygosity. Our results pointed towards a mainly (at least 95-99%) clonal mode of propagation, a strong subdivision at the smallest scale available (i.e., urban neighborhoods, i.e. 0.250 km²), and a generation time most probably shorter than 4 months. In future studies, more extensive sampling at smaller geographic scales (i.e., households), within a one- or two-months window and with improved amplification conditions, should lead to a more precise picture of the fine population structure of this parasite.

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.

Cercarial emission of schistosomes is a determinant in the transmission to the definitive host and constitutes a good marker to identify which definitive host is responsible for transmission, mainly in introgressive hybridization situations. Our goal was to test the hypothesis that micro-mammals play a role in Schistosoma haematobium, S. bovis, and/or S. haematobium x S. bovis transmission. Small mammal sampling was conducted in seven semi-lacustrine villages of southern Benin. Among the 62 animals trapped, 50 individuals were investigated for Schistosoma adults and eggs: 37 Rattus rattus, 3 Rattus norvegicus, 9 Mastomys natalensis, and 1 Crocidura olivieri. Schistosoma adults were found in four R. rattus and two M. natalensis, with a local prevalence reaching 80% and 50%, respectively. Two cercarial chronotypes were found from Bulinus globosus experimentally infected with miracidia extracted from naturally infected M. natalensis: a late diurnal and nocturnal chronotype, and an early diurnal, late diurnal, and nocturnal chronotype. The cytochrome C oxidase subunit I mtDNA gene of the collected schistosomes (adults, miracidia, and cercariae) belonged to the S. bovis clade. Eleven internal transcribed spacer rDNA profiles were found; four belonged to S. bovis and seven to S. haematobium x S. bovis. These molecular results together with the observed multi-peak chronotypes add M. natalensis as a new host implicated in S. haematobium x S. bovis transmission. We discuss the origin of the new chronotypes which have become more complex with the appearance of several peaks in a 24-h day. We also discuss how the new populations of offspring may optimize intra-host ecological niche, host spectrum, and transmission time period.

Describing patterns and testing hypotheses on processes driving biological invasions represent major issues in ecology. Addressing these questions requires building adequate data sets, i.e., covering areas and spanning periods adapted to the invasion processes studied. Rodents include major invasive species, among which the black rat Rattus rattus and the domestic mouse Mus musculus have nearly colonized the entire world, from their native Asian range. To do so, they have benefitted from their ability to cope with human-modified environments and to live in the immediate vicinity of Man, who served as a vector of their dispersal between regions and continents. In Senegal, both R. rattus and M. musculus, initially introduced by early West European colonizers some centuries ago, are currently expanding thanks to road traffic and infrastructure development and rampant urbanization that concerns even remote regions of the country. As part of projects aimed at studying (1) the role of invasive black rat populations in the emergence of zoonotic diseases in southeastern Senegal, and (2) the evolutionary consequences of parasites in R. rattus and M. musculus invasions in Senegal, we conducted a series of field campaigns throughout the southern half of the country, between May 2012 and September 2015. The objectives were to catch commensal small mammals using standard trapping procedures, identify them using morphological or molecular tools, and take samples from them upon autopsy, to look for zoonotic parasites and pathogens. Along with data on individual specimens, information on microhabitats was gathered at each trap position. This resulted in the constitution of a data set of more than 13,000 trapnights, which allowed the capture of more than 3,100 small mammals, all characterized by a series of associated biological, geographical, and environmental data. The small mammals concerned are mainly rodents (10 species), shrews, and hedgehogs. The two invasive rodent species were the most numerous, exceeding in numbers all the other species pooled. This data set makes it possible to study coarse to fine-scaled distribution of species of this commensal community in southern Senegal, as well as the possible determinants of this distribution in terms of habitat preferences and/or interspecific interactions. This data set can be freely used for non-commercial purposes and is licensed under a Creative Commons Attribution 4.0 International License.