DOI: 10.5061/dryad.6wwpzgn9w
title: Simulated genotype data from: Effective population size estimation in large marine populations: Considering current challenges and opportunities when simulating large datasets with high-density genomic information

description: Next-generation sequencing has broadened perspectives regarding the
 estimation of the effective population size (Ne) by providing high-density
 genomic information. These technologies have expanded data collection and
 analytical tools in population genetics, increasing understanding of
 populations with high abundance, such as marine species with high
 commercial or conservation priority. Several common methods for estimating
 Ne are based on allele frequency spectra or linkage disequilibrium between
 loci. However, their specific constraints make it difficult to apply them
 to large populations, especially with confounding factors such as
 migration rates, complex sampling schemes, or non-independence between
 loci. Computer simulations have long represented invaluable tools to
 explore the influence of biological or logistical factors on Ne estimation
 and to assess the robustness of dedicated methods. Here, we outline
 several Ne estimation methods and their foundational principles,
 requirements, and likely caveats regarding application to populations of
 high abundance. Thereafter, we present a simulation framework built upon
 recent computational genomic tools that combine the possibility to
 generate biologically realistic datasets with realistic patterns of
 long-term neutral genetic diversity. This framework aims at reproducing
 and tracking the main critical features of data derived from a large
 natural population when running a simulation-based population genetics
 study, e.g., evaluating the strengths and limitations of various Ne
 estimation methods. We illustrate this framework by generating genotype
 datasets with varying sample sizes and locus numbers and analyzing them
 with three software tools (NeEstimator2, GONE, and GADMA). Detailed and
 annotated simulation scripts are provided to ensure reproducibility and to
 support future research on Ne estimation. These resources can support
 method comparisons and validations, particularly for nonspecialists, such
 as conservation practitioners and students.
description: # Simulated genotype data from: Effective population size estimation in
 large marine populations: Considering current challenges and opportunities
 when simulating large datasets with high-density genomic information
 Dataset DOI: [10.5061/dryad.6wwpzgn9w](10.5061/dryad.6wwpzgn9w) ##
 Description of the data and file structure This repository contains
 genotype data, in the "genepop" format, obtained from the
 simulation framework described in the related article "Effective
 population size estimation in large marine populations: Considering
 current challenges and opportunities when simulating large datasets with
 high-density genomic information" published in *Evolutionary
 Applications*. A total of 108 genotypic data subsets (9 folders X 12 data
 files) were derived from 3 independent simulations conducted with gene
 flows '*m*' between 2 populations set at 0.01, 0.05, or 0.10,
 respectively, each simulation repeated 3 times (leading to 3 replicates
 for each value of '*m*').  Each .zip file corresponds to a
 simulation from a given combination of 'm' and replicate, and
 contains 12 genepop files with varying sample sizes (14, 50, 56 or 140)
 and loci numbers (1000, 10000 or 30000) from the simulated data. ### Files
 and variables #### File: gen_output_5000_m001_simR_1.zip
 **Description:** contains 12 genepop files derived from a simulation with
 gene 'm' = 0.01 (replicate 1) #### File:
 gen_output_5000_m001_simR_2.zip **Description:** contains 12 genepop files
 derived from a simulation with gene 'm' = 0.01 (replicate 2)
 #### File: gen_output_5000_m001_simR_3.zip **Description:** contains 12
 genepop files derived from a simulation with gene 'm' = 0.01
 (replicate 3) #### File: gen_output_5000_m005_simR_1.zip
 **Description:** contains 12 genepop files derived from a simulation with
 gene 'm' = 0.05 (replicate 1) #### File:
 gen_output_5000_m005_simR_2.zip **Description:** contains 12 genepop files
 derived from a simulation with gene 'm' = 0.05 (replicate 2)
 #### File: gen_output_5000_m005_simR_3.zip **Description:** contains 12
 genepop files derived from a simulation with gene 'm' = 0.05
 (replicate 3) #### File: gen_output_5000_m010_simR_1.zip
 **Description:** contains 12 genepop files derived from a simulation with
 gene 'm' = 0.10 (replicate 1) #### File:
 gen_output_5000_m010_simR_2.zip **Description:** contains 12 genepop files
 derived from a simulation with gene 'm' = 0.10 (replicate 2)
 #### File: gen_output_5000_m010_simR_3.zip **Description:** contains 12
 genepop files derived from a simulation with gene 'm' = 0.10
 (replicate 3)