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.

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.

Biological invasions represent a major global concern, intensifying major environmental and socio-economic challenges, including biodiversity loss, food insecurity, and risks to public health. In West Africa, however, the ecological and socio-economic impacts of biological invasions remain largely under-recognized by academic, policy, and socio-economic stakeholders. This highlights an urgent need for enhanced awareness, capacity building, and coordinated regional action. To address this gap and foster policy-relevant dialogue on biological invasions in the region, the West African Network on Biological Invasions (Wan@bi) was established in 2018 as a transdisciplinary and collaborative platform. Supported by the French National Research Institute for Sustainable Development (IRD), Wan@bi brings together academic and applied research institutions from France and four West African countries: Benin, Mali, Niger, and Senegal. The network promotes joint research initiatives, capacity-building programs, and outreach activities targeting both scientific and non-scientific audiences. Invasive alien rodents and insects serve as focal biological models that structure the network’s research themes and operational activities. Since its creation, Wan@bi has worked to strengthen scientific and technical capacities, raise awareness among diverse stakeholders, and contribute to the development of evidence-based management strategies and policy frameworks addressing biological invasions. These efforts have contributed to enhanced regional cooperation, improved visibility of invasive alien species (IAS) issues, and early engagement with policy processes. Key achievements include: contribution to the establishment of the first environmental surveillance platform at the Autonomous Port of Cotonou (Benin), designed as a multi-stakeholder system for monitoring and managing invasive alien species; organization of the first international conference dedicated to biological invasions and their socio-environmental impacts in Francophone Africa; development of a dedicated website (https://irnwanabi.wordpress.com/) that presents the network’s objectives and outputs while strengthening science–society interfaces through dissemination of outreach materials for the general public; and implementation of thematic capacity-building workshops for researchers, complemented by science communication and public engagement activities. contribution to the establishment of the first environmental surveillance platform at the Autonomous Port of Cotonou (Benin), designed as a multi-stakeholder system for monitoring and managing invasive alien species; organization of the first international conference dedicated to biological invasions and their socio-environmental impacts in Francophone Africa; development of a dedicated website (https://irnwanabi.wordpress.com/) that presents the network’s objectives and outputs while strengthening science–society interfaces through dissemination of outreach materials for the general public; and implementation of thematic capacity-building workshops for researchers, complemented by science communication and public engagement activities. Overall, Wan@bi illustrates the effectiveness of an integrated, multi-actor approach to addressing biological invasions in underrepresented regions. By consolidating long-term partnerships, strengthening local expertise, and fostering the emergence of an engaged regional scientific community, the network has positioned itself as a key actor in the field of invasion science in West Africa. Supporting and expanding such initiatives could facilitate their replication in other regions and enhance long-term global responses to biological invasions.

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.

In sub-Saharan Africa, agricultural intensification and urbanization have increased the risk of proliferation of rodents in rural and urban habitats. Management of rodent populations is a challenge in terms of food security and public health. However, conventional efforts to manage rodents are currently reactive and based on the inadequate use of synthetic chemical rodenticides, including first- and second-generation anticoagulants and acute rodenticides. This approach carries substantial environmental and health risks and has yielded limited success in terms of reduction of rodent populations sustainably. In this paper, which is the second part of a diptych, we advocate for a shift towards more sustainable and environmentally friendly approaches, such as Ecologically-Based Rodent Management (EBRM), as a realistic alternative to synthetic rodenticides. This method is based on a good knowledge of habitat use, species diversity and population dynamics of major rodent pests, and involves community-based interventions aimed at reducing rodent abundance to economically and hygienically acceptable levels in the long term. We present for the first time a comprehensive compilation of published and unpublished information derived from observational field studies conducted in Ethiopia, Niger, Nigeria, Benin, Mali, Mauritania and Senegal with the aim to provide an overview of EBRM case studies in these countries of sub-Saharan Africa. This paper intends to serve as a catalyst for change, encouraging the transformation of rodent management practices towards sustainable methods. We aim at stimulating further research and interventions that promote EBRM in Africa, ultimately fostering more environmentally conscious and effective solutions.

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.

Around 400 million people in the world are affected by zoonoses associated with rodents. In addition, at least 280 million cases of undernourishment could be avoided in the world by the effective management of populations of rodents which destroy crops and stores of crops. Consequently, managing rodent populations which are reservoirs of pathogenic agents or which destroy crops and stores of crops is a challenge both in terms of food security as well as public health. In terms of public policy, many African countries have established farming intensification programmes aiming to improve their food self-sufficiency, with the direct risk of the prolifera-tion of rodents. In this article, which is the first in a two-part series, we present the background to controlling rodents in Africa in rural and urban areas, followed by an overview of the regu-lations and uses of rodenticides. We will go on to document the problematic situations which result from this, illustrating them with case studies. The use of synthetic chemical rodenticidesis the most widely used method to control rodents and is not only toxic for humans, other animals and the environment, but also ineffective against rodent populations (for example, it is costly, leads to a build-up of resistance, and the avoidance of bait). The circulation and uncontrolled use of these rodenticides in many African countries is associated with conside-rable risks to health and the environment, without leading to any significant improvements in terms of rodent control or reducing the damage they cause.

The use of synthetic chemical rodenticides is the most commonly practiced rodent management method in sub-Saharan Africa which results in health and environmental risks without any significant improvement in terms of reducing rodent pest populations sustainably. In this paper, which is a second part of a diptych, we advocate for better control of the use of synthetic chemical rodenticides in urban and agricultural settings in sub-Saharan Africa, as well as a shift towards more sustainable and environment-friendly rodent management approaches, such as the Ecologically-Based Rodent Management (EBRM), as a realistic alternative to synthetic rodenticides. The EBRM approach relies on a solid knowledge of pest rodent biology, ecology and behavior as well as the use of a pool of rodent management actions implemented through community-based interventions to ensure sustained reduction of rodent pest populations down to economically and sanitary acceptable levels. EBRM is expected not only to ensure reducing the social impacts of pest rodents in cost-beneficial ways, but also the risks of rodents and synthetic rodenticides to human health and the environment.

In the context of food self-sufficiency, the River Senegal Valley has been undergoing profound environmental changes for several decades. Rice production has increased due to the development of vast irrigated perimeters, which has been accompanied by recurrent proliferations of rodent populations that are crop pests and reservoirs of zoonoses. The aim of our study was to determine the factors underlying these phases of increased rodent abundance over a ten-year (2008 to 2019) sampling period during the hot dry season (February-May). A total of 1,867 rodents of four species were captured, among which Arvicanthis niloticus and Mastomys huberti dominated. Our results showed that, during this season, rodent abundance (i) increases significantly with rainfall from the previous year, (ii) is higher in cultivated than in uncultivated plots, (iii) increases with plant cover, (iv) increases, for M. huberti, with the presence of open water. We showed that in an area that was first sparsely cultivated and then impacted by hydro-agricultural rehabilitation of irrigation and drainage infrastructure, the abundance of A. niloticus changed following this program, reaching the level of a nearby area that has been intensively cultivated for decades. Moreover, we showed that the proportion of adults among the captured individuals was lower in rice plots than in vegetable gardening fields and uncultivated plots. The breeding pattern of adult individuals was also affected by land use. Results suggest that uncultivated areas and vegetable gardening fields constitute refuge and breeding ground hotspots and would thus form a starting point for the invasion of rice fields. Following these results, we advocate for regular monitoring of rodent breeding and abundance patterns, with a special focus on these refuge areas, particularly during the hot dry season. We recommend implementing effective and sustainable science-based control strategies at national and community levels to keep rodent populations within tolerable limits.

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.

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.

Based on compiled small mammal trapping data collected over 12 years from Benin and Niger (3701 individual records from 66 sampling sites), located in mainland Africa, we here describe the small mammal community assemblage in urban habitats along the commercial axis connecting the two countries, from the seaport of Cotonou to the Sahelian hinterland, with a particular focus on invasive species. In doing so, we document extant species distributions, which highlight the risks of continuing the range expansion of three synanthropic invasive rodent species, namely black rats (Rattus rattus), brown rats (R. norvegicus), and house mice (Mus musculus). Using various diversity estimates and community ecology approaches, we detect a latitudinal gradient of species richness that significantly decreased Northward. We show that shrews (Crocidura) represent a very important component of micro-mammal fauna in West African towns and villages, especially at lower latitudes. We also demonstrate that invasive and native synanthropic rodents do not distribute randomly in West Africa, which suggests that invasive species dynamics and history differ markedly, and that they involve gradual, as well as human-mediated, long distance dispersal. Patterns of segregation are also observed between native Mastomys natalensis and invasive rats R. rattus and R. norvegicus, suggesting potential native-to-invasive species turn over. Consequences of such processes, especially in terms of public health, are discussed.

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.

Risks related to Toxoplasma gondii infection in humans remain poorly known in Senegal. Although rodent surveys could help to assess the circulation of T. gondii, they have seldom been set up in sub-Saharan Africa. The aim of this study was to examine Toxoplasma seroprevalence in rodents from villages and towns across Senegal. Rodents were sampled in 40 localities using a standardised trapping protocol. Detection of T. gondii antibodies was performed on 1205 rodents, using a modified agglutination test (MAT) technique. Seroprevalence data were analysed depending on geography, the local rodent community, and individual characteristics of the rodent hosts. We found 44 seropositive rodents from four different species (Mastomys erythroleucus, Mastomys natalensis, Mus musculus domesticus, Rattus rattus). Toxoplasma seroprevalence was low, averaging 4% in the localities. Higher Toxoplasma seroprevalence (up to 24%) was found in northern Senegal, a region known to be the heart of pastoral herding in the country.

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.

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.