Subways, zoning and social factors influence the dispersal and genetic connectivity of an iconic urban pest, the brown rat (Rattus norvegicus) across a complex cityscape

Cities present unique ecological challenges and opportunities for species that have adapted to human-dominated environments. To understand how urban landscape heterogeneity shapes the movements of an iconic urban animal, the brown rat (Rattus norvegicus), we investigated the factors influencing rat genetic connectivity across Manhattan, New York City. We generated genome-wide SNP data from rats sampled throughout Manhattan as well as paired surface-subway locations, created a habitat suitability model using systematic municipal rat survey data, and employed landscape genetic approaches to identify urban features influencing rat gene flow. Our models revealed that underground subway tunnels were the strongest facilitator of rat gene flow, with municipal zoning also strongly influencing connectivity, particularly through low / medium-density residential areas. Habitat suitability analysis showed that high human population density, old building ages, and lower median household income were the strongest predictors of rat presence. Subterranean sampling revealed that rats in subway stations exhibited greater genetic relatedness than surface rats at short distances but lower inbreeding coefficients, suggesting underground tunnels facilitate longer-distance dispersal while maintaining some connectivity to surface populations. These findings demonstrate that physical infrastructure, political, and socioeconomic factors shape urban rat ecology, with implications for more targeted approaches to pest management in complex urban environments. This study is the first comprehensive analysis of rat dispersal and genetic connectivity in relation to complex cityscape heterogeneity.