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，城市栖息地在动植物可利用的景观中所占的比例也越来越大。城市生态学是一个相对较新的领域，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，在破坏基础设施、污染食物储备和传播疾病的同时，利用全球各地的城市栖息地。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塑造城市老鼠的活动；以及(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老鼠的基因数据来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鼠类控制工作和公共卫生运动成为可能。该奖学金将促进国际和平研究所(普罗维登斯学院)和福特汉姆大学的科学家之间的合作，他们提供了DNA序列分析方面的专业知识和该项目所需的专门统计数据。该研究所和本科生在现代遗传分析方面的培训将成为S研究员家乡辖区研究界的一种资源。本项目将结合来自萨尔瓦多、巴西、纽约市、新奥尔良和温哥华的下一代空间序列数据，调查入侵挪威鼠的城市扩散情况。研究小组将在Illumina平台上使用双酶切限制位点相关DNA测序(ddRAD-seq)和精心策划的生物信息学管道来产生单核苷酸多态(SNP)数据。利用这些数据，该团队将：(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确定相关的地理空间数据；(C)构建景观阻力模型，以分离出抑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移动。这项工作的影响是广泛的，将填补城市生态学(即城市物种的运动)和景观遗传学(重复研究设计)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.