DOI: 10.6084/m9.figshare.14339618
title: Data for: Comment on “Individual heterozygosity predicts translocation success in threatened desert tortoises”

description: # translocation_load<br>## Data and code to reproduce individual-based simulations with SLiM presented in Hansson, Morales and van Oosterhout (2021). Science<br>This repo includes SLiM3 v3.4 (Haller and Messer, 2019) code to replicate our simulations of the genetic load and genetic diversity outcomes of translocating individuals under different sampling regimes to investigate the effect of the recommendation from Scott et al. (2020) of translocating only the most genetically diverse individuals.<br>## Translocation regimes- Random: individuals are selected at random from the metapopulation- Diversity: individuals in the highest 20% of nucleotide diversity are selected- Load: individuals in the bottom 20% of genetic load are selected (Genetic load = the sum of selection coefficients in homozygous condition plus the sum of selection coefficients multiplied by their dominance coefficients in heterozygous condition)- Load+Diversity: two-step approach, first individuals in the bottom 30% of genetic load distribution are selected followed by selection of individuals in the top 50% distribution of individual’s genetic uniqueness score (Uind) is calculated as U[ind]=∑(1-q), where q is the allelic frequency<br>## SimulationsWe simulated a 1Mb chromosome with a mutation rate = 1e-7 and recombination rate = 1e-8. The ratio of deleterious to neutral mutations is 0.2:1.First, four populations with Ne=500 accumulate mutations for 5000 generations (burn-in), followed by individuals selection to be translocated to an admixed population were they mate randomly.To assess the load that causes inbreeding depression in future generations, we plotted only the part of the load that is in heterozygous condition (∑h.s) in the figures, and not the load that is already fixed (∑s), i.e. the sum of selection coefficients across all loci that are homozygous in an individual.<br>## FiguresThe main figure, included in the published version, represents a set of parameters where the metapopulation effective population sizes (Ne) are fixed (Ne = 500) and there is no migration between demes before translocation. Alternative figures are presented here that represent variants of these parameters, with variable metapopulation sizes (Ne = 50, 100, 500 or 1000) or different migration rates between demes within the metapopulation before migration. For all variants, qualitatively results are the same as in our main figure.Please refer to the SLiM code for varying any of these parameters further.Please see the published version for the full legend for the main figure<br><br>## References:Haller, B. C., & Messer, P. W. (2019). SLiM 3: forward genetic simulations beyond the Wright–Fisher model. Molecular biology and evolution, 36(3), 632-637.Scott, P. A., Allison, L. J., Field, K. J., Averill-Murray, R. C., & Shaffer, H. B. (2020). Individual heterozygosity predicts translocation success in threatened desert tortoises. Science, 370(6520), 1086-1089.<br>## DependenciesThe only dependency is SLiM 3.4 or higher. The code has not been tested with the most recent version of SLiM 3.5 which introduce syntax changes that might not be back-compatible with this code.SLiM software can be found in: https://messerlab.org/slim/