DOI: 10.5061/dryad.hd300
title: Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

description: 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 &lt;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.
description: RatDemographics-ARLEQUINGenotype 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-PL8sepGenotype 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.RatDemsPL8sepGenotype 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.RatDemsPL8sepGenotype 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-PL8sepGenotype 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-PL8sepPopulation names for the Geneclass file of rat microsatellite genotypes.RatDemographics-GENEPOP-PL8sepGenotype 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-PL8sepPopulation names for the Genepop file of rat microsatellite genotypes.Cluster1RatMsatIBDMatrices 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-STRUCTUREPL8sepGenotype 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-STRUCTUREGenotype 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-LDNEGenotype 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 NAMESPopulation (cluster) names for the LDNe file of rat microsatellite genotypes.RatDems-ML-RELATE-fullGenotype 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-V1Genotype 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-V2Genotype 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-V4Genotype 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-V2Genotype 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-V3Genotype 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-V5Genotype 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-RELATEGenotype 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-RELATEGenotype 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-RELATEGenotype 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-RELATEGenotype 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.SalvadorRatMsatGenotypesRat 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).