RII Track-4: Comparative cityscape genomics of rats in four major cities

随着越来越多的人口居住在城市，城市栖息地也代表了植物和动物可利用的景观的越来越大的部分。城市生态学是一个相对较新的领域，研究本地和外来动植物物种如何受到城市扩张的影响。挪威鼠是最成功的入侵物种之一，它们在地球仪上利用城市栖息地，同时破坏基础设施，污染食物库存，传播疾病。该项目将确定：（1）城市栖息地、基础设施和社会经济因素如何影响城市老鼠的活动;（2）哪些特定因素持续影响不同城市的老鼠活动。PI将使用来自四个城市的大鼠遗传数据，以了解四个城市的城市栖息地的具体影响：巴西的萨尔瓦多;纽约市;新奥尔良;和不列颠哥伦比亚省的温哥华。这项研究将使更有效的老鼠种群控制工作和公共卫生运动。该研究金将促进PI（在普罗维登斯学院）和福德姆大学的科学家之间的合作，他们在DNA序列分析和该项目所需的专门统计方面提供专门知识。PI和本科生获得的现代遗传分析培训将成为研究人员研究社区的资源。s home jurisdiction. 技术说明本项目将通过结合来自萨尔瓦多、巴西、纽约市、新奥尔良和温哥华的下一代空间序列数据来调查入侵性挪威鼠的城市扩散。研究团队将在Illumina平台上使用双消化限制性位点相关DNA测序（ddRAD-seq）和策划的生物信息学管道来生成单核苷酸多态性（SNP）数据。利用这些数据，该小组将：（A）估计每个城市内抽样地区之间的基因流动;（B）利用地理信息系统中的空间统计分析来汇编和确定相关的地理空间数据;（C）建立景观阻力模型，以隔离限制或促进老鼠基因流动的特定城市变量;以及（D）通过平行分析直接比较来自四个城市的大鼠，以确定哪些环境和景观变量始终影响大鼠的运动。这项工作的影响是广泛的，并将填补城市生态学的重要空白（即，城市物种的运动）和景观遗传学（重复研究设计）。这将是第一次比较多个城市景观的运动和基因流。

Non-technical DescriptionWith an increasing majority of the human population residing in cities, urban habitats also represent an increasing portion of the landscapes available to plants and animals. The relatively new field of urban ecology studies how both native and invasive plant and animal species are impacted by expanding cities. Norway rats are one of the most successful invasive species, exploiting urban habitats across the globe, while damaging infrastructure, contaminating food stocks, and transmitting diseases. This project will determine: (1) how city habitats, infrastructure and socioeconomic factors, shape the movement of urban rats; and (2) which specific factors consistently influence rat movement across different cities. The PI will use genetic data on rats from four cities to understand the specific effects of urban habitat in four cities: Salvador, Brazil; New York City; New Orleans; and Vancouver, British Columbia. This study will enable more effective rat population control efforts and public health campaigns. The fellowship will promote collaboration between the PI (at Providence College) and scientists at Fordham University, who contribute expertise in DNA sequence analysis and specialized statistics required for this project. The training in modern genetic analysis gained by the PI and undergraduates students will be a resource for the research community in the researcher?s home jurisdiction. Technical DescriptionThis project will investigate urban dispersal of invasive Norway rats by combining next-generation spatial sequence data from Salvador, Brazil, New York City, New Orleans and Vancouver. The research team will use double-digest restriction-site associated DNA sequencing (ddRAD-seq) on the Illumina platform and curated bioinformatics pipelines to generate single nucleotide polymorphism (SNP) data. With these data, the team will: (A) estimate gene flow among the sampled areas within each city; (B) use spatial statistical analyses in geographic information systems (GIS) to compile and identify relevant geospatial data; (C) construct landscape resistance models to isolate particular urban variables that either constrain or promote gene flow in rats; and (D) directly compare rats from the four cities through parallel analyses to determine which environmental and landscape variables consistently impact the movement of rats. The implications of this work are broad, and will fill important gaps in urban ecology (i.e., movement of an urban species) and landscape genetics (replicated study design). This will be the first time that movement and gene flow will be compared for multiple urban landscapes.