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

Providence College, Providence RI

Investigators

Abstract

Non-technical Description With 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 Description This 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.