Carine Brouat

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.

Spatial and social population structures can influence intra- and interspecific genetic processes. We investigated the spatial and social genetic structure of two sister species and evaluated whether there was evidence of hybridisation between them at a microgeographic scale, in syntopy. Our study models were Rhabdomys bechuanae (Rbech) and Rhabdomys dilectus dilectus (Rdil). We generated population genetic data using microsatellite markers and cross-referenced some of these results with published behavioural data from a prior study, reanalysed here. We compared genetic diversity and gene flow both in sympatry and allopatry, we tested for hybridisation between the sister species in sympatry and assessed the relationship between kinship and fine-scale spatial and social organisation. Genetic diversity was high within all populations of the two species. Population genetic substructure was more pronounced in Rbech than in Rdil, consistent with stronger group cohesion reported for Rbech. STRUCTURE and NEWHYBRIDS analyses suggested that sympatric individuals, 5% in Rbech, and 2% in Rdil, might have hybrid ancestry. Our results indicate social fences may limit gene flow within and between species. Further, limited hybridisation suggests that, despite syntopy, only rare events of hybridisation may occur, possibly at phases of density troughs and/or that F1 hybrids have a relatively low fitness.

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 such a context, this study aims at investigating the genetic diversity and temporal structure of R. rattus populations at a fine geographical scale. Methodology/Principal findings: Sampling was conducted in six villages of the Ankazobe district, both inside houses and outside villages. A total of 480 individuals, captured in March - May 2019 and 2020, were genotyped at 17 microsatellite loci. Our results show that genetic diversity levels were relatively homogeneous 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: An integrated approach combining flea control within houses together with measures to reduce human-rodent contact would thus appear more appropriate than rodent control only to limit plague transmission.

Previous field-based studies have evidenced patterns in gastrointestinal helminth (GIH) assemblages of rodent communities that are consistent with “enemy release” and “spill-back” hypotheses, suggesting a role of parasites in the ongoing invasion success of the exotic house mouse (Mus musculus domesticus) in Senegal (West Africa). However, these findings came from a single invasion route, thus preventing to ascertain that they did not result from stochastic and/or selective processes that could differ across invasion pathways. In the present study, we investigated the distribution of rodent communities and their GIH assemblages in three distinct zones of Northern Senegal, which corresponded to independent house mouse invasion fronts. Our findings first showed an unexpectedly rapid spread of the house mouse, which reached even remote areas where native species would have been expected to dominate the rodent communities. They also strengthened previous insights suggesting a role of helminths in the invasion success of the house mouse, such as: (i) low infestation rates of invading mice by the exotic nematode Aspiculuris tetraptera at invasion fronts—except in a single zone where the establishment of the house mouse could be older than initially thought, which was consistent with the “enemy release” hypothesis; and (ii) higher infection rates by the local cestode Mathevotaenia symmetrica in native rodents with long co-existence history with invasive mice, bringing support to the “spill-back” hypothesis. Therefore, “enemy release” and “spill-back” mechanisms should be seriously considered when explaining the invasion success of the house mouse—provided further experimental works demonstrate that involved GIHs affect rodent fitness or exert selective pressures. Next steps should also include evolutionary, immunological, and behavioral perspectives to fully capture the complexity, causes and consequences of GIH variations along these invasion routes.

Toxoplasma gondii is a zoonotic protozoan with a worldwide occurrence, but the determinants of the current pattern in the geographical distribution of T. gondii lineages and strains remain poorly understood. To test the influence of human trade on T. gondii populations, we conducted a population genetic study of 72 T. gondii animal isolates from Senegal, a West African country in which the ongoing inland progress of invasive murine hosts (introduced in port cities of Senegal since the 16^th century by European sailors) is well described. Isolates were mainly collected on free-range poultry, which are considered as relevant bioindicators of T. gondii strain diversity in the domestic environment. Sampling was conducted in two port cities of Senegal (Dakar and Saint-Louis) and in one inland region (Kedougou). Population genetic analyses using 15 microsatellite markers revealed different patterns between port cities where lineages non-virulent for mice (type II, type III, and Africa 4) were predominant, and Kedougou where the mouse-virulent Africa 1 lineage was the most common. By considering the current spatial pattern in the inland progress of invasive rodents in Senegal, our results suggest that the invasive house mouse Mus musculus domesticus counter-selects the Africa 1 lineage in the invaded areas. The comparison of the microsatellite alleles of type II strains from Senegal to type II strains from other areas in Africa and Western Europe, using discriminant analysis of principal components and Network analysis, point to a mainly Western European origin of the type II lineage in Senegal. Collectively, these findings suggest that human-mediated intercontinental migrations of murine hosts are important vectors of T. gondii strains. Differential susceptibility of endemic and introduced murine hosts to various T. gondii strains probably determines the persistence of these strains in the environment, and therefore their availability for human and animal infection. Toxoplasma gondii is a zoonotic protozoan with a worldwide distribution and which can infects virtually all warm-blooded species, including human. Clinical expression of human toxoplasmosis, as well as T. gondii strains diversity, exhibit contrasting patterns across geographic regions. The determinants of this geographical structure are poorly understood, but a growing body of evidence supports an important role of human-mediated migrations of T. gondii hosts in the intercontinental dissemination of some parasite lineages. The results of our study conducted in Senegal suggest that the invasive house mouse—which was introduced in the port cities of this country through maritime trade since colonial times—has a dramatic influence on the T. gondii populations of invaded areas. This important T. gondii reservoir seems to be a vector for the intercontinental migrations of T. gondii. In addition, it may have a role in the selection (or the counter-selection) of local T. gondii populations found in invaded areas. This study provides insights into the mechanisms shaping T. gondii populations, thereby determining which strains will be available for human and animal infection.

A bstract: 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.

Background: Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment of introduced populations still remains unsolved. Here we explore the appealing assertion that invasion success relies on immune phenotypic traits that would be advantageous in recently invaded sites. Results: 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. Transcriptome analyses revealed respectively 364 and 83 differentially expressed genes along the mouse and rat invasion routes. Among them, 20.0% and 10.6% were annotated with functions related to immunity. All immune-related genes detected along the mouse invasion route were over-expressed in recently invaded sites. Genes of the complement activation pathway were over-represented. Results were less straightforward when considering the black rat as no particular immunological process was over-represented. Conclusions: We revealed changes in transcriptome profiles along invasion routes. Patterns differed between both invasive species. These changes potentially be driven by increased infection risks in recently invaded sites for the house mouse and stochastic events associated with colonization history for the black rat. These results provide a first step in identifying the immune ecoevolutionary processes potentially involved in invasion success.