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

Abstract
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. (2020-06-30)

Usage notes
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.zip
Ne5000_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.zip
Ne50_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.zip
Ne50_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.zip
EstimationPrograms_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.zip
ProgramOutputFilesFor_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.zip
CoNe_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 >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 (2020-06-30)