Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.在全球发展中地区，遍布棚户区的城市中心正快速扩张，并不断侵占此前的森林生态系统。棚户区的典型特征为无人清理的垃圾、明沟排污以及过度滋生的植被，这些都会助长啮齿动物滋生泛滥。褐家鼠（*Rattus norvegicus*）是多种具有公共卫生重要性的人畜共患病原体的流行性传播宿主。深入了解褐家鼠的种群生态学，对于制定高效的啮齿动物防控策略至关重要，因为相关数据有助于评估种群的时间稳定性与空间连通性。本研究以巴西萨尔瓦多市9个采样点的146只褐家鼠为研究对象，利用17个微卫星位点筛选遗传变异、解析种群遗传结构，并评估城市景观中基因流的程度与模式。这些采样点分属该市的3个街区，各街区间距平均为2.7公里。令人意外的是，我们在同一采样点捕获的个体间几乎未检测到亲缘关系，同时发现了高水平的遗传多样性，以及小地理尺度下的遗传结构分化。多数采样点间的FST比较均具有统计学显著性，甚至包括间距不足400米的采样点。贝叶斯分析将样本划分为3个遗传簇，每个簇均对应来自不同街区或街区内部不同山谷的独特采样点。上述数据表明，萨尔瓦多市褐家鼠种群存在复杂的遗传结构，且该结构与异质性的城市景观密切相关。未来的啮齿动物防控措施需结合遗传数据揭示的萨尔瓦多市褐家鼠种群的空间与时间连通性，以制定科学合理的根除策略。