Population Genomics of Urban White-Footed Mice (Peromyscus leucopus) in NYC
Urbanization in NYC has created fragmented habitats with dense populations of white footed deer mice. These habitats are in the form of NYC parks and due to the restriction of migration between parks because of the urban matrix, environmental alteration, including introduced pollutants, and the removal of natural predators and competitors, it is likely that urban Peromyscus leucopus populations are adapting and gaining micro-evolutionary changes in the process. Similar ecological factors have been linked to quantitative trait changes in the past, but few underlying genes, and their mutations leading to phenotypic variation, have been discovered. My lab is using 454 pyro-sequencing to sequence portions of Peromyscus leucopus brain, liver, and gonad transcriptomes. We have assembled preliminary sequence data from several NYC mouse populations de novo, and have mapped the reads to reference mouse and rat genomes. We have scanned the transcriptomes for SNP differences between urban and rural populations for use in tests for selection, and results suggest multiple regions are undergoing strong positive selection. My work involves identifying specific genes undergoing selection and trying to determine the phenotypic traits involved. Ultimately, we plan to identify local adaptation in NYC P. leucopus populations and the associated microevolutionary changes caused by urbanization.