Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil

Kajdacsi B, Costa F, Hyseni C, Porter F, Brown J, Rodrigues G, Farias H, Reis MG, Childs JE, Ko AI, Caccone A

Date Published: July 17, 2013

DOI: http://dx.doi.org/10.5061/dryad.hd300

 

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Title RatDemographics-ARLEQUIN
Downloaded 15 times
Description 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.
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Title RatDemographics-ARLEQUIN-PL8sep
Downloaded 9 times
Description 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.
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Title RatDemsPL8sep
Downloaded 10 times
Description 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.
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Title RatDemsPL8sep
Downloaded 10 times
Description 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.
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Title RatDemographics-GENECLASS-PL8sep
Downloaded 14 times
Description 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.
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Title RatDems-GENECLASS-POP NAMES-PL8sep
Downloaded 13 times
Description Population names for the Geneclass file of rat microsatellite genotypes.
Download RatDems-GENECLASS-POP NAMES-PL8sep.txt (129 bytes)
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Title RatDemographics-GENEPOP-PL8sep
Downloaded 21 times
Description 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.
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Title RatDems-GENEPOP-POP NAMES-PL8sep
Downloaded 16 times
Description Population names for the Genepop file of rat microsatellite genotypes.
Download RatDems-GENEPOP-POP NAMES-PL8sep.txt (130 bytes)
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Title Cluster1RatMsatIBD
Downloaded 14 times
Description 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).
Download Cluster1RatMsatIBD.txt (266 bytes)
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Title RatDemographics-STRUCTUREPL8sep
Downloaded 17 times
Description 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.
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Title RatMsat17LociClean-STRUCTURE
Downloaded 16 times
Description 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.
Download RatMsat17LociClean-STRUCTURE.txt (21.47 Kb)
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Title RatDems-Clusters-LDNE
Downloaded 6 times
Description 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.
Download RatDems-Clusters-LDNE.gen (12.43 Kb)
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Title RatDems-Clusters-LDNE-POP NAMES
Downloaded 11 times
Description Population (cluster) names for the LDNe file of rat microsatellite genotypes.
Download RatDems-Clusters-LDNE-POP NAMES.txt (46 bytes)
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Title RatDems-ML-RELATE-full
Downloaded 11 times
Description 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.
Download RatDems-ML-RELATE-full.txt (18.64 Kb)
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Title RatDems-ML-RELATE-PL1-V1
Downloaded 14 times
Description 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.
Download RatDems-ML-RELATE-PL1-V1.txt (3.339 Kb)
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Title RatDems-ML-RELATE-PL2-V2
Downloaded 12 times
Description 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.
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Title RatDems-ML-RELATE-PL6-V4
Downloaded 13 times
Description 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.
Download RatDems-ML-RELATE-PL6-V4.txt (2.459 Kb)
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Title RatDems-ML-RELATE-PL8-V2
Downloaded 11 times
Description 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.
Download RatDems-ML-RELATE-PL8-V2.txt (3.095 Kb)
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Title RatDems-ML-RELATE-PL9-V3
Downloaded 13 times
Description 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.
Download RatDems-ML-RELATE-PL9-V3.txt (1.576 Kb)
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Title RatDems-ML-RELATE-SA3-V5
Downloaded 14 times
Description 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.
Download RatDems-ML-RELATE-SA3-V5.txt (3.959 Kb)
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Title RatDems-House5-ML-RELATE
Downloaded 12 times
Description 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.
Download RatDems-House5-ML-RELATE.txt (932 bytes)
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Title RatDems-House15-ML-RELATE
Downloaded 11 times
Description 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.
Download RatDems-House15-ML-RELATE.txt (1.059 Kb)
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Title RatDems-House16-ML-RELATE
Downloaded 12 times
Description 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.
Download RatDems-House16-ML-RELATE.txt (1.059 Kb)
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Title RatDems-House19-ML-RELATE
Downloaded 19 times
Description 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.
Download RatDems-House19-ML-RELATE.txt (1.694 Kb)
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Title SalvadorRatMsatGenotypes
Downloaded 77 times
Description 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).
Download SalvadorRatMsatGenotypes.xlsx (145.9 Kb)
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When using this data, please cite the original publication:

Kajdacsi B, Costa F, Hyseni C, Porter F, Brown J, Rodrigues G, Farias H, Reis MG, Childs JE, Ko AI, Caccone A (2013) Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil. Molecular Ecology 22(20): 5056-5070. http://dx.doi.org/10.1111/mec.12455

Additionally, please cite the Dryad data package:

Kajdacsi B, Costa F, Hyseni C, Porter F, Brown J, Rodrigues G, Farias H, Reis MG, Childs JE, Ko AI, Caccone A (2013) Data from: Urban population genetics of slum-dwelling rats (Rattus norvegicus) in Salvador, Brazil. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hd300
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