Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most FST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.
RatDemographics-ARLEQUIN
Genotype data from 146 trapped individuals formatted for Arlequin, with animals grouped by sampling site and year. "RatDemographics" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDemographics-ARLEQUIN-PL8sep
Genotype data from 146 trapped individuals formatted for Arlequin, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDemsPL8sep
Genotype data from 146 trapped individuals formatted for FSTAT, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDemsPL8sep
Genotype data from 146 trapped individuals formatted for sex-biased dispersal tests in FSTAT, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDemographics-GENECLASS-PL8sep
Genotype data from 146 trapped individuals formatted for Geneclass, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-GENECLASS-POP NAMES-PL8sep
Population names for the Geneclass file of rat microsatellite genotypes.
RatDemographics-GENEPOP-PL8sep
Genotype data from 146 trapped individuals formatted for Genepop, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-GENEPOP-POP NAMES-PL8sep
Population names for the Genepop file of rat microsatellite genotypes.
Cluster1RatMsatIBD
Matrices of pairwise Fst and distance in meters between sites in Pau da Lima with site 8 separated into two populations based on sampling year for use in Genepop to perform Mantel tests of isolation by distance (IBD).
RatDemographics-STRUCTUREPL8sep
Genotype data from 146 trapped individuals formatted for STRUCTURE, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatMsat17LociClean-STRUCTURE
Genotype data from 146 trapped individuals formatted for STRUCTURE, with animals grouped by sampling site and year. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-Clusters-LDNE
Genotype data from trapped individuals formatted for LDNe, with animals grouped by structure clusters. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex. Juveniles have been removed from datasets used in Ne analyses.
RatDems-Clusters-LDNE-POP NAMES
Population (cluster) names for the LDNe file of rat microsatellite genotypes.
RatDems-ML-RELATE-full
Genotype data from 146 trapped individuals formatted for ML-Relate. All 146 animals are included in this file to test for pairwise relatedness across animals from different sites. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-PL1-V1
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 1 in Pau da Lima (valley 1) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-PL2-V2
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 2 in Pau da Lima (valley 2) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-PL6-V4
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 6 in Pau da Lima (valley 4) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-PL8-V2
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 8 in Pau da Lima (valley 2) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-PL9-V3
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 9 in Pau da Lima (valley 3) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-ML-RELATE-SA3-V5
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 3 in Sete de Abril (valley 5) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-House5-ML-RELATE
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 5 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-House15-ML-RELATE
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 15 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-House16-ML-RELATE
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 16 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
RatDems-House19-ML-RELATE
Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 19 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
SalvadorRatMsatGenotypes
Rat microsatellite genotypes for 17 loci in 146 individuals captured in Salvador, Brazil. Individuals are grouped by sites and sampling year or by cluster in different sheets in the workbook. All data files used in analyses were converted for specialized software from these excel sheets in CREATE (Coombs, Letcher, & Nislow 2009).