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Spatial population genomics of the brown rat ( Rattus norvegicus ) in New York City
Author(s) -
Combs Matthew,
Puckett Emily E.,
Richardson Jonathan,
Mims Destiny,
MunshiSouth Jason
Publication year - 2018
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.14437
Subject(s) - biological dispersal , biology , population , population genomics , isolation by distance , gene flow , ecology , evolutionary biology , spatial ecology , genetic structure , spatial heterogeneity , rodent , genomics , genetic variation , genome , genetics , demography , gene , sociology
Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially explicit population genomic methods provide insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genomewide variation in brown rats ( Rattus norvegicus ) across Manhattan, New York City ( NYC ), using 262 samples and 61,401 SNP s to understand (i) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; (ii) the geographic origin of NYC rats, using a large, previously published data set of global rat genotypes; and (iii) heterogeneity in gene flow across the city, particularly deviations from isolation by distance. We found that rats separated by ≤200 m exhibit strong spatial autocorrelation ( r = .3, p = .001) and the effects of localized genetic drift extend to a range of 1,400 m. Across Manhattan, rats exhibited a homogeneous population origin from rats that likely invaded from Great Britain. While traditional approaches identified a single evolutionary cluster with clinal structure across Manhattan, recently developed methods (e.g., fineSTRUCTURE, sPCA , EEMS ) provided evidence of reduced dispersal across the island's less residential Midtown region resulting in fine‐scale genetic structuring ( F ST = 0.01) and two evolutionary clusters (Uptown and Downtown Manhattan). Thus, while some urban populations of human commensals may appear to be continuously distributed, landscape heterogeneity within cities can drive differences in habitat quality and dispersal, with implications for the spatial distribution of genomic variation, population management and the study of widely distributed pests.