GuppySV

Scripts for Lin, Y., van der Bijl, W., Mank, J. E. Sexual selection maintains ancient structural polymorphisms across natural populations. 2026, PLOS Biology, in press

1. Genotyping and SNP filtering with female reference genome using BWA MEM, BCFtools and VCFtools

   sh 01.genotyping.sh
   

2. Running localPCA using lostruct

   # plot all pops 
   Rscript 02.1.plot_lostrcut.R
   # or do one population one chromosome for a single run
   Rscript 02.2.single_lostruct.R [pop] [chr]
   

3. PCA and admixture using PLINK2.0

   sh 03.run_pca_admixture.sh 
   

4. Inferring demogrphic history using PSMC

   sh 04.run_psmc.sh
   

5. Calculating Fst and nucleotide diversity using VCFtools

   sh 05.calc_fst_pi.sh 
   

6. Calculating SV age using pixy

   sh 06.cal_inv_age.sh
   

7. Simulation, check the ./simulation folder for details.

8. Permutation test

   sh run_perm_test.sh
   

9. Breakpoint verification using Longranger and Loupe 2.1.2

10. Plotting, see details in Fig*.ipynb or SuppleFig*.ipynb.