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.

The Sahel has long been plagued by drought, which along with human pressure has caused ecosystem degradation, biodiversity loss, and increased poverty of local populations. Thus, in 2005 African heads of state set up a project, named the “Great Green Wall” (GGW), to restore Sahelian ecosystems. Establishment of the GGW led to the founding in 2009 of the “International Human-Environment observatory Téssékéré (OHMi Téssékéré)”, between France’s National Center for Scientific Research and Cheikh Anta Diop University (Dakar, Senegal), to assist decision-making by providing scientific information. The OHMi’s research is conducted in the Ferlo, northern Senegal. This paper summarizes knowledge of the region’s biodiversity and how the GGW may affect it. Semi-natural grazed parklands dominated by grasses with scattered trees occupy over 90% of the surface. Eighty-two woody plant species, representing 55 genera and 26 families, have been recorded. Forbs (non-graminoid herbs) are more diverse but account for a small proportion of vegetation cover. The study of arthropod biodiversity is just beginning. A first study showed that 427 insect morpho-species visit the flowers of a single common tree species, Balanites aegyptiaca . Vertebrate biodiversity includes seven species of amphibians, eleven species of reptiles and 217 bird species, among them palearctic migratory species (including 60 waterbirds) some of which are classified at high protection levels on the IUCN’s Red List. Four species of micromammals (in order of decreasing abundance, Gerbillus nigeriae , Arvicanthis niloticus , Taterillus pygargus and Mastomys erythroleucus ) occur in the area. Nine species of large wild mammals occur, of which eight are nocturnal.

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.

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.

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 increase in the incidence of zoonoses underlines the need for monitoring pathogens in wild animals. Recent studies have revealed the circulation of several microorganisms in rodents, in various geographic and environmental contexts, including African urban habitats. However, Mali, a landlocked country of West Africa, was not extensively studied for the circulation of the microorganisms in rodents. And this paucity of information puts the fight against rodent-borne zoonoses at a disadvantage. This is why we aimed through this study to improve knowledge of potentially zoonotic infectious agents carried by rodents in Mali (Bamako). Three hundred and seventy-one small mammal spleen samples taken from captures realized in 2021-2022 were analyzed by polymerase chain reaction. Eleven of them (i.e. 2.96%) were infected by microorganisms (Bartonella spp., Coxiella burnetii and Trypanosoma otospermophili). The most frequently detected microorganisms were Bartonella spp. (2.43%). We identified new genotypes of B. elizabethae (a species involved in some cases of infective endocarditis) and B. mastomydis. We also identified C. burnetii MS type 12, thus showing active circulation of a human-pathogenic genotype of Q fever agent in wild rodents. For the first time in Mali, Trypanosoma otospermophili was identified in a specimen of brown rat Rattus norvegicus.

Small mammals are regular inhabitants of urban centres worldwide. The house mouse Mus musculus and rats of the genus Rattus, major invasive alien species, are increasingly present, particularly in West Africa where house mice and black rats (Rattus rattus) are frequently met in commensal small mammal communities. We studied the case of Bamako the capital of Mali, through intensive city-wide trapping, and found a strong dominance of invasive alien species over native ones, with house mouse representing more than half and the brown rat (Rattus norvegicus) nearly one quarter of the captures. Shrews (Crocidura olivieri) and multimammate rats (Mastomys natalensis) represented the main native species still found in the city. The spatial and ecological determinants of these species’ distribution were analysed, showing segregation between species at different spatial scales. At the housing unit scale, M. musculus and M. natalensis appeared associated with inner parts of buildings, while R. norvegicus and C. olivieri occured at the interface between the indoor and outdoor environments. At the city scale, invasive species were more abundant in older quarters than in more recent peripheral ones. This was particularly true for the house mouse which probably colonized Bamako during the 21st century, while the brown and the black rats had done so a century before. This process of invasion of a native community of small mammals by cosmopolitan invasive species is discussed in a regional context, as are the potential consequences it may have in terms of public health and social well-being.

Monkeypox is an emerging infectious disease of unclear zoonotic origin in Africa although increasing evidence suggests that rope squirrels are reservoirs of the monkeypox virus (MPXV).Here, we describe new data on the systematics of rope squirrels (Sciuridae, Funisciurus). Our molecular phylogeny strongly supports the polyphyly of Funisciurus pyrropus, with a Central African clade sister to Funisciurus leucogenys and a West African clade sister to Funisciurus anerythrus. Museum specimens show that the two clades have distinct pelage patterns. We propose therefore to resurrect the name Funisciurus leucostigma for the West African clade. Using reliable taxonomic identifications of georeferenced squirrels, we inferred the ecological niches of the three species of interest. The Sanaga River in Cameroon appears to be the barrier separating both the sister species F. anerythrus and F. leucostigma as well as the sister MPXV clades I and II. This suggests that these two MPXV clades were isolated in Central and West Africa, respectively, due to allopatric squirrel speciation.

Long-term ecological data are of paramount importance to document the effects of global changes on biodiversity and dynamics of populations and communities. The site of Bandia, 70 km southeast of Dakar in western Senegal, has been the scene of numerous ecological studies since the 1970s. In the frame of projects led by researchers of the Institut de Recherche pour le Developpement (IRD), rodent populations were monitored at various periods using capture-mark-recapture (CMR) protocols on trapping grids that yielded important datasets on population dynamics and ecology of the main species present. Among them, the Guinea Multimammate Rat Mastomys erythroleucus proved to represent the dominant species. Thus, CMR data were collected on M. erythroleucus between (i) November 1975-March 1981, (ii) January 1983-October 1986, (iii) January 1997-April 2001, and (iv) June 2007-June 2012. Raw data from the 1975-1981 period were not available, but those from the three other periods are now in the IRD data repository DataSuds at . They represent 2556 (re)captures of 1296 M. erythroleucus individuals. They include the identity of each animal captured with some biological attributes (sex, weight at first capture, and reproductive activity), exact date and point of capture (via a trap-specific code) at each trapping occasion, and additional comments that may help to interpret the data. This dataset concerning one of the most widespread rodent species of the Sahelo-Sudanian bioclimatic belt provides information that can be used to address various questions such as outbreak prediction or effects of climate change.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

Schistosomiasis is a neglected tropical disease of public health significance. In view of its elimination as a public health problem by 2030, adopting a One Health approach is necessary, considering its multidimensional nature. Animal reservoirs, in particular, pose a significant threat to schistosomiasis control in Africa and beyond. In this study, we conducted a spatio-temporal survey of Schistosoma infections in small mammal communities and intermediate snail hosts in the vicinity of Lake Guiers in northern Senegal. Sampling campaigns were undertaken four times between April 2021 and August 2022 around eight villages. A total of 534 small mammals of four species, primarily Hubert’s multimammate mice Mastomys huberti, were captured. Out of 498 individuals examined, only 18 rodents (17 M. huberti and 1 Arvicanthis niloticus) were infected with schistosomes. The infection rates in M. huberti varied over time (prevalence range: 2.4% to 9.3%, intensity range: 4 to 132), and space (prevalence range: 3.1% to 40%, intensity range: 2 to 110) and were higher in adult hosts captured during or just after the rainy season, a time when older individuals dominate in rodent populations. Using a multi-locus molecular approach (cox1 and ITS) on Schistosoma larvae (cercariae and miracidia) and adult worms, we identified Schistosoma mansoni as the most widespread species. We also detected Schistosoma bovis and Schistosoma haematobium in M. huberti from one locality (Temeye). Although no Schistosoma hybrids were found, the discovery of a male S. mansoni and a female S. bovis pair raises concerns about potential hybridization patterns that could occur in rodents. Finally, three snail species were found infected (25 Biomphalaria pfeifferi, 3 Bulinus truncatus and 1 Bulinus senegalensis) including with S. mansoni, S. bovis, S. haematobium and S. haematobium x S. bovis hybrids. Our findings highlight the spatial-temporal variations of Schistosoma infections in rodents and emphasize the need for fine-scale monitoring over time and space for effective One Health measures and ensuring the sustainability of schistosomiasis control efforts.

In Senegal, Coxiella burnetii, which causes Q fever, has often been identified in ticks and humans near livestock, which are considered to be reservoirs and main sources of infection. We describe the emergence of C. burnetii in rodents, not previously known to carry this pathogen, and describe 2 new genotypes.

Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the PlioPleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.

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.

Zoonotic pathogens are responsible for most infectious diseases in humans, with rodents being important reservoir hosts for many of these microorganisms. Rodents, thus, pose a significant threat to public health. Previous studies in Senegal have shown that rodents harbour a diversity of microorganisms, including human pathogens. Our study aimed to monitor the prevalence of infectious agents in outdoor rodents, which can be the cause of epidemics. We screened 125 rodents (both native and expanding) from the Ferlo region, around Widou Thiengoly, for different microorganisms. Analysis, performed on rodent spleens, detected bacteria from the Anaplasmataceae family (20%), Borrelia spp. (10%), Bartonella spp. (24%) and Piroplasmida (2.4%). Prevalences were similar between native and the expanding (Gerbillus nigeriae) species, which has recently colonised the region. We identified Borrelia crocidurae, the agent responsible for tick-borne relapsing fever, which is endemic in Senegal. We also identified two other not-yet-described bacteria of the genera Bartonella and Ehrlichia that were previously reported in Senegalese rodents. Additionally, we found a potential new species, provisionally referred to here as Candidatus Anaplasma ferloense. This study highlights the diversity of infectious agents circulating in rodent populations and the importance of describing potential new species and evaluating their pathogenicity and zoonotic potential.

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.

Ornithodoros sonrai (O. sonrai) ticks are the only known vectors of Borrelia crocidurae, an agent of tick-borne relapsing fever (TBRF) borreliosis. Rodents serve as principal natural reservoirs for Borrelia. Our research objective was to detect TBRF Borrelia and other zoonotic bacterial infections in ticks and in house mice Mus musculus domesticus, an invasive species currently expanding in rural northern Senegal. Real-time and conventional PCR were utilized for detecting Borrelia and other bacterial taxa. The analyses were performed on 253 specimens of O. sonrai and 150 samples of brain and spleen tissue from rodents. Borrelia crocidurae was found in one O. sonrai tick and 18 Mus musculus domesticus samples, with prevalences of 0.39 percent and 12 percent, respectively, as well as Ehrlichia sp. in one Mus musculus domesticus. Further, we were able to detect the presence of a potentially infectious novel species belonging to the Anaplasmataceae family for the first time in O. sonrai ticks. More attention should be paid to the house mouse and O. sonrai ticks, as they can be potential hosts for novel species of pathogenic bacteria in humans.