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Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size

Citation

Andrello, Marco; Noirot, Christelle; Débarre, Florence; Manel, Stéphanie (2020), Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size, Dryad, Dataset, https://doi.org/10.5061/dryad.jq2bvq87d

Abstract

Multi-locus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multi-locus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, MetaPopGen 2.0, to model multi-locus population genetic processes in subdivided populations of arbitrarily large size. It allows for spatial and temporal variation in demographic parameters, age structure, adult and propagule dispersal, variable mutation rates and selection on survival and fecundity. We developed MetaPopGen 2.0 in the R environment to facilitate its use by non-modeler ecologists and evolutionary biologists. We illustrate the capabilities of MetaPopGen 2.0 for studying adaptation to water salinity in the striped red mullet Mullus surmuletus.

Usage Notes

This dataset contains the scripts and data to run the simulations presented in the paper, namely:

  • the simulations used to validate MetaPopGen 2.0 against theoretical expectations (the Wright-Fisher model and the two-locus Slatkin model);
  • the simulations used to compare the computation times of Nemo 2.2.0 and MetaPopGen 2.0;
  • the simulations to study adaptation to water salinity in the striped red mullet Mullus surmuletus.

Data structure:

  • Dispersal_SC.RData # Dispersal probabilities for Mullus surmuletus, used in MullusSimulations.R
  • IslandModelMetaPopGen.R # R code to run the island model simulation (section "Computation time")
  • IslandModelNemo.ini # Ini file for Nemo 2.2.0 to run the island model simulation (section "Computation time")
  • MullusSimulations.R # R code to run the Mullus simulation (section "Example: adaptation to water salinity in the red mullet Mullus surmuletus")
  • Salinity_data.RData # Salinity, used in MullusSimulations.R
  • Simulation_parameters.RData # Other simulation parameters used in MullusSimulations.R
  • SlatkinModel.R # R code to run the Slatkin model simulation (section "Theoretical validation")
  • SlatkinModelFunctions.R # R functions to used in SlatkinModel.R
  • WrightFisher.R # R code to run the Wright-Fisher model simulation (section "Theoretical validation")

Funding

Université de Recherche Paris Sciences et Lettres, Award: Resmod