UBC Research Data

Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities Combs, Matthew; Byers, Kaylee A.; Ghersi, Bruno M.; Blum, Michael J.; Caccone, Adalgisa; Costa, Federico; Himsworth, Chelsea G.; Richardson, Jonathan L.; Munshi-South, Jason

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Abstract
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.; Usage notes
PLINK .map file for New Orleans rat SNP GenotypesPLINK .map file for New Orleans SNP genotypes. The genotypes themselves are in the .ped file of the same name, and the .map file contains the chromosomal coordinates for each SNP.NOL.plink.map
PLINK .ped file for New Orleans rat SNP GenotypesPLINK .ped file for New Orleans SNP genotypes. The genotypes themselves are in the .ped file, and the .map file contains the chromosomal coordinates for each SNP.NOL.plink.ped
PLINK .map file for New York City rat SNP GenotypesPLINK .map file for New York City SNP genotypes. The genotypes themselves are in the .ped file of the same name, and the .map file contains the chromosomal coordinates for each SNP.NYC.plink.map
PLINK .ped file for New York City rat SNP GenotypesPLINK .ped file for New York City SNP genotypes. The genotypes themselves are in the .ped file, and the .map file contains the chromosomal coordinates for each SNP.NYC.plink.ped
PLINK .map file for Salvador, Brazil rat SNP GenotypesPLINK .map file for Salvador, Brazil SNP genotypes. The genotypes themselves are in the .ped file of the same name, and the .map file contains the chromosomal coordinates for each SNP.SAL.plink.map
PLINK .ped file for Salvador, Brazil rat SNP GenotypesPLINK .ped file for Salvador, Brazil SNP genotypes. The genotypes themselves are in the .ped file, and the .map file contains the chromosomal coordinates for each SNP.SAL.plink.ped
PLINK .map file for Vancouver rat SNP GenotypesPLINK .map file for Vancouver SNP genotypes. The genotypes themselves are in the .ped file of the same name, and the .map file contains the chromosomal coordinates for each SNP.VAN.plink.map
PLINK .ped file for Vancouver rat SNP GenotypesPLINK .ped file for Vancouver SNP genotypes. The genotypes themselves are in the .ped file, and the .map file contains the chromosomal coordinates for each SNP.VAN.plink.ped

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