Data from: Evaluating methods for estimating local effective population size with and without migration

Gilbert KJ, Whitlock MC

Date Published: June 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.3r651

 

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Title Ne500_IdealRawPopulationFiles
Downloaded 42 times
Description These are the "true" population files for ideal (isolation) populations of size 500 simulated from Nemo. They contain all individuals and many extra loci, from which these were sampled to obtain the inputs used in analyses (see Program_InputFiles). Temporal samplers used two time points, from which the files here are identified as belonging to generation 0 or generation 1.
Download Ideal500_Raw.zip (518.1 Mb)
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Title Ne5000_IdealRawPopulationFiles
Description These are the "true" population files for ideal (isolation) populations of size 5000 simulated from Nemo. They contain all individuals and many extra loci, from which these were sampled to obtain the inputs used in analyses (see Program_InputFiles). Temporal samplers used two time points, from which the files here are identified as belonging to generation 0 or generation 1.
Download Ideal5000_Raw.zip (40.38 Mb)
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Title Ne50_Generation0_IdealRawPopulationFiles
Downloaded 1 time
Description These are the "true" population files for ideal (isolation) populations of size 50 simulated from Nemo. They contain all individuals and many extra loci, from which these were sampled to obtain the inputs used in analyses (see Program_InputFiles). Temporal samplers used two time points, from which the files here are identified as belonging to generation 0 or generation 1.
Download Ideal50_Gen0.zip (511.5 Mb)
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Title Ne50_Generation1_IdealRawPopulationFiles
Downloaded 1 time
Description These are the "true" population files for ideal (isolation) populations of size 50 simulated from Nemo. They contain all individuals and many extra loci, from which these were sampled to obtain the inputs used in analyses (see Program_InputFiles). Temporal samplers used two time points, from which the files here are identified as belonging to generation 0 or generation 1.
Download Ideal50_Gen1.zip (511.4 Mb)
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Title EstimationPrograms_FormattedInputFiles
Downloaded 4 times
Description See the ReadMe for further details. These are the input files formatted for each analysis program and are the population samples under analysis.
Download Program_InputFiles.zip (643.8 Mb)
Download README.docx (667.5 Kb)
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Title ProgramOutputFilesFor_Colony_Estim_MLNe_NeEstimator_ONeSamp_TMVP
Downloaded 5 times
Description These are the Ne estimates output by the various programs. See the readme for file naming conventions. Because of their large size, CoNe output files are stored separately.
Download Colony_Estim_MLNe_NeEstimator_ONeSamp_TMV...es.zip (80.76 Mb)
Download README.docx (667.5 Kb)
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Title CoNe_Ideal_OutputFiles
Downloaded 2 times
Description These are outputs for Cone Ideal (isolation) population cases. See the Readme for file naming conventions.
Download README.docx (667.5 Kb)
Download CoNe_Ideal_OutputFiles.zip (77.30 Mb)
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Title CoNe_Mig50_OutputFiles
Downloaded 1 time
Description CoNe Ne estimation output files for Migration scenarios with true Ne = 50. See the same readme for other input/output files for naming conventions.
Download CoNe_Mig50_OutputFiles.zip (813.6 Mb)
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Title CoNe_Mig500_OutputFiles
Downloaded 1 time
Description CoNe Ne estimation output files for Migration scenarios with true Ne = 500. See the same readme for other input/output files for naming conventions.
Download CoNe_Mig500_OutputFiles.zip (1.003 Gb)
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Title CoNe_IBD50_OutputFiles
Downloaded 2 times
Description CoNe Ne estimation output files for IBD scenarios with true Ne = 50. See the same readme for other input/output files for naming conventions.
Download CoNe_IBD50_OutputFiles.zip (729.5 Mb)
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Title CoNe_IBD500_OutputFiles
Downloaded 4 times
Description CoNe Ne estimation output files for IBD scenarios with true Ne = 500. See the same readme for other input/output files for naming conventions.
Download CoNe_IBD500_OutputFiles.zip (563.7 Mb)
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Title ParamFiles_ConversionAndAnalysisScripts
Downloaded 1 time
Description See the Readme files contained within each subfolder. These are the input files used for nemo simulations (Migration and IBD raw simulation files were >80GB in size when compressed, and may be requested from KJ Gilbert). Otherwise, these input files contain the parameters used in Nemo v2.2.0 to create the raw population files from which individuals were sampled. R scripts for file conversion to the various program inputs as well as for analyzing the various outputs are also included, but are also made public on GitHub at: https://github.com/kjgilbert/NeEstimation_Param-Conversion-Analysis_Files
Download ParamFiles_ConversionAndAnalysisScripts.zip (69.56 Kb)
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When using this data, please cite the original publication:

Gilbert KJ, Whitlock MC (2015) Evaluating methods for estimating local effective population size with and without migration. Evolution 69(8): 2210-2226. http://dx.doi.org/10.1111/evo.12713

Additionally, please cite the Dryad data package:

Gilbert KJ, Whitlock MC (2015) Data from: Evaluating methods for estimating local effective population size with and without migration. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3r651
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