smc++ split time

[zhidaobuzhidao]

Hi, I really want to learn how to calculate the split time of two groups in your article fig3d? Could you tell me which command I can get a series of split times after using smc++ to plot fig3d? Looking forward to your reply!

[mishaploid]

Hello! Thanks for this question, it prompted me to properly update this git repo and add more information on the analysis and results for this project. I've added a markdown file that walks through calculating split times from smc++ results and creating a plot with the bootstrapped and point estimates of divergence time.

General steps required to create a similar plot:

• Obtain marginal estimates of population size history for each population using smcpp estimate or smcpp cv
  • To assess uncertainty, also run this on a set of parametric bootstraps for each population; these can be generated by chunking up the genome and resampling (I used 10 bootstrap replicates per population)
• Fit a clean split model using smcpp split to estimate joint demography for population pairs
• Each split model output will have a model.final.json file that will contain values for N0 and split, you can use these values to convert from coalescent scaling to generations by multiplying 2 * N0 * split. Carrot has a generation time of two years, so I multiplied by two to get the time in years: 2 * N0 * split * 2. See discussion here for more context.