DOI: 10.5061/dryad.3r651
title: Data from: Evaluating methods for estimating local effective population size with and without migration

description: Effective population size is a fundamental parameter in population
 genetics, evolutionary biology and conservation biology, yet its
 estimation can be fraught with difficulties. Several methods to estimate
 Ne from genetic data have been developed which take advantage of various
 approaches for inferring Ne. The ability of these methods to accurately
 estimate Ne, however, has not been comprehensively examined. In this
 study, we employ seven of the most cited methods for estimating Ne from
 genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator
 including LDNe) across simulated datasets with populations experiencing
 migration or no migration. The simulated population demographies are an
 isolated population with no immigration, an island model metapopulation
 with a sink population receiving immigrants, and an isolation by distance
 stepping stone model of populations. We find considerable variance in
 performance of these methods, both within and across demographic
 scenarios, with some methods performing very poorly. The most accurate
 estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each
 of these approaches is outperformed by another in a differing demographic
 scenario. Knowledge of the approximate demography of population as well as
 the availability of temporal data largely improves Ne estimates.
description: Ne500_IdealRawPopulationFilesThese 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.Ideal500_Raw.zipNe5000_IdealRawPopulationFilesThese 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.Ideal5000_Raw.zipNe50_Generation0_IdealRawPopulationFilesThese 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.Ideal50_Gen0.zipNe50_Generation1_IdealRawPopulationFilesThese 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.Ideal50_Gen1.zipEstimationPrograms_FormattedInputFilesSee the ReadMe for further details. These are the input files formatted for each analysis program and are the population samples under analysis.Program_InputFiles.zipProgramOutputFilesFor_Colony_Estim_MLNe_NeEstimator_ONeSamp_TMVPThese 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.Colony_Estim_MLNe_NeEstimator_ONeSamp_TMVP_OutputFiles.zipCoNe_Ideal_OutputFilesThese are outputs for Cone Ideal (isolation) population cases. See the Readme for file naming conventions.CoNe_Mig50_OutputFilesCoNe Ne estimation output files for Migration scenarios with true Ne = 50. See the same readme for other input/output files for naming conventions.CoNe_Mig500_OutputFilesCoNe Ne estimation output files for Migration scenarios with true Ne = 500. See the same readme for other input/output files for naming conventions.CoNe_IBD50_OutputFilesCoNe Ne estimation output files for IBD scenarios with true Ne = 50. See the same readme for other input/output files for naming conventions.CoNe_IBD500_OutputFilesCoNe Ne estimation output files for IBD scenarios with true Ne = 500. See the same readme for other input/output files for naming conventions.ParamFiles_ConversionAndAnalysisScriptsSee the Readme files contained within each subfolder. These are the input files used for nemo simulations (Migration and IBD raw simulation files were &gt;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