Population genomics of Paris brown rat
The brown rat (Rattus norvegicus) is a common synanthropic species, distributed worldwide, and living alongside humans for several centuries. While populations of brown rats have been extensively studied in the Americas, European cities have received less attention, despite their longer history of human-rat coexist-ence. To fill this gap, we focused on the inner city of Paris, France, and whole-genome sequenced 23 individuals sampled throughout the city. Fine-scale popu-lation structure analyses revealed a differentiation between the center of Paris, the Left and the Right Banks. Consistently, resistance maps incorporating several environmental features suggested that the Seine River acts as a geographic barri-er, while green areas facilitate gene flow. When integrating individual based iso-lation-by-distance analyses and population density we found that rats are capable of dispersing across an area of ~10 000 m² per generation, equivalent to the size of a small park. Urbanization significantly transforms ecosystems, forcing spe-cies to adapt to anthropic environments. Indeed, we found footprints of positive selection in several genomic regions and specific to the Paris sample. We further focused on genes involved in the vitamin-K cycle, which is targeted by common-ly used rodenticides. Two genes, VKORC1 and GGCX, displayed signatures of positive selection, suggesting the emergence of resistance to rodenticides in the population and underscoring the prevalence of polygenic adaptation in natural populations. These findings will contribute to more effective management strate-gies for controlling rat populations and may serve as a model for understanding the impacts of urbanization on other species.