Data for: Comment on “Individual heterozygosity predicts translocation success in threatened desert tortoises”

# translocation_load ## Data and code to reproduce individual-based simulations with SLiM presented in Hansson, Morales and van Oosterhout (2021). Science This repo include 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. ## Translocation regimesRandom: 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 ## 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) ## FiguresThe main figure, included in the published version, represents a set of parameters were 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 furtherPlease refer to the published version to see the full legend for the main figure. ## 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. ## 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/# 易位负荷（translocation_load） ## 复现Hansson、Morales与van Oosterhout（2021）发表于《Science》的基于个体的SLiM模拟所用数据与代码。本仓库包含SLiM 3 v3.4（Haller与Messer，2019）代码，用于复现我们在不同采样策略下开展个体易位的遗传负荷与遗传多样性结果模拟，以探究Scott等人（2020）提出的「仅易位遗传多样性最高的个体」这一建议的效果。 ## 易位采样策略 随机策略：从集合种群（metapopulation）中随机选取个体 多样性策略：选取核苷酸多样性（nucleotide diversity）排名前20%的个体 负荷策略：选取遗传负荷（genetic load）排名后20%的个体（遗传负荷定义为：纯合状态下选择系数之和，加上杂合状态下选择系数与显性系数乘积之和） 负荷+多样性策略：采用两步法，首先选取遗传负荷分布排名后30%的个体，随后选取个体遗传独特性得分排名前50%的个体；个体遗传独特性得分的计算公式为 U[ind] = Σ(1-q)，其中 q 为等位基因频率（allelic frequency） ## 模拟设置 我们模拟了一条长度为1Mb的染色体，突变率设置为1e-7，重组率设置为1e-8。有害突变与中性突变的比例为0.2:1。 首先，4个有效种群大小（Ne）为500的种群经历5000代的突变积累（预演化期），随后选取个体易位至混合种群中进行随机交配。 为评估后续世代中导致近交衰退的负荷，我们仅在图中展示了杂合状态下的负荷（∑h.s），而非已固定的负荷（∑s） ## 图表说明 已发表版本中的主图对应如下参数设置：集合种群的有效种群大小（Ne）固定为500，且易位前亚种群（deme）间不存在迁移。本仓库还提供了其他参数变体的图表，包括可变的集合种群有效种群大小（Ne=50、100、500或1000），或集合种群内亚种群间的迁移率差异。所有参数变体的定性结果均与主图一致。 如需进一步调整上述任意参数，请参考SLiM代码。 主图的完整图例请参阅已发表文献。 ## 参考文献 Haller, B. C. 与 Messer, P. W. (2019). SLiM 3：超越赖特-费希尔（Wright–Fisher）模型的正向遗传模拟。《分子生物学与进化》，36(3)，632-637。 Scott, P. A. 等 (2020). 个体杂合性可预测受威胁沙漠陆龟的易位成功。《Science》，370(6520)，1086-1089。 ## 依赖项 本项目仅依赖SLiM 3.4及更高版本。当前代码尚未在最新的SLiM 3.5版本中测试，该版本引入了语法变更，可能与本代码不兼容。 SLiM软件可从以下网址获取：https://messerlab.org/slim/