Dissertations, Theses, and Capstone Projects

Date of Degree

9-2015

Document Type

Dissertation

Degree Name

Ph.D.

Program

Biology

Advisor

Jason Munshi-South

Committee Members

Ana C. Carnaval

Michael J. Hicke

Stephane Boissinot

Steven J. Franks

Subject Categories

Bioinformatics | Biology

Keywords

Evolution; Historical Demography; Local Adaptation; Population Genomics; Transcriptome; Urban Ecology

Abstract

Urbanization significantly alters natural ecosystems. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC's forest fragments, and isolated populations may adapt in response to novel urban ecosystems. Using pooled transcriptome-wide RNAseq data, individually barcoded transcriptome-wide RNAseq data, and genome-wide RADseq data, I found genetic differentiation between urban and rural P. leucopus populations and evidence suggestive of local adaptation. I compared genome and transcriptome-wide SNP data in P. leucopus from relatively large urban parks surrounded by dense urban infrastructure to large rural sites representative of native habitat. First, I built a publicly available genomic resource for P. leucopus, and then looked at patterns of genetic differentiation in protein-coding DNA sequences that showed divergence between urban and rural populations. I also looked at the unique demographic history of urban and rural populations of P. leucopus using coalescent simulations and the site frequency spectrum (SFS). Historical demographic inference supported a scenarios of post-glacial sea level rise that led to isolation of mainland and Long Island populations. I also found that several urban parks in NYC represent distinct P. leucopus populations, and the estimated divergence times for these parks are consistent with patterns of urbanization in NYC. I then looked at transcriptome sequences within urban P. leucopus to look for signatures of genetic differentiation and selective sweeps due to positive selection, and then associated outliers with environmental measures of urbanization. The majority of candidate genes were involved in metabolic functions, especially dietary specialization. Candidate loci I identified suggest that populations of P. leucopus are using novel food resources in urban habitats or metabolizing nutrients differently. Ultimately, the data indicate that cities may represent novel ecosystems with selective pressures from urbanization leading to adaptive responses in populations of Peromyscus leucopus.

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