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越来越多的植物和动物可利用的景观。城市生态学是一个相对较新的研究领域，主要研究城市扩张对本地和外来动植物物种的影响。挪威鼠是最成功的入侵物种之一，它们利用全球各地的城市栖息地，同时破坏基础设施，污染食物储备，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运动；(2)在不同城市中，哪些特定因素对鼠的运动具有一致性影响。该项目将利用来自四个城市的老鼠基因数据来了解城市栖息地对四个城市的具体影响：巴西的萨尔瓦多；纽约市；新奥尔良;以及不列颠哥伦比亚省的温哥华。本研究将有助于更有效的鼠群控制工作和公共卫生运动。该奖学金将促进PI（普罗维登斯学院）和福特汉姆大学科学家之间的合作，后者为该项目提供DNA序列分析和专业统计方面的专业知识。PI和本科生在现代遗传分析方面的训练将成为研究社区的研究人员的资源。美国的司法管辖区。该项目将结合来自萨尔瓦多、巴西、纽约、新奥尔良和温哥华的下一代空间序列数据，调查入侵挪威鼠的城市扩散情况。该研究团队将在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。有了这些数据，研究小组将：(A)估计每个城市样本区域之间的基因流动；(B)利用地理信息系统（GIS）中的空间统计分析来汇编和识别相关的地理空间数据；(C)构建景观抗性模型，以隔离限制或促进大鼠基因流动的特定城市变量；(D)通过平行分析直接比较四个城市的老鼠，以确定哪些环境和景观变量持续影响老鼠的运动。这项工作的意义是广泛的，并将填补城市生态学（即城市物种的运动）和景观遗传学（复制研究设计）的重要空白。这将是第一次对多个城市景观的运动和基因流动进行比较。

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.