Simulated data

##################################################Introduction##################################################
The data was simulated with ms (Hudson, Bioinformatics, 2002). The command that invoked ms (including the seed) and the simulated data are provided. For each simulation, the ms output was parsed into two files that are directly used for the analysis.100 unlinked loci were simulated, where each of them contains 100 SNPs. For each of the 100 demes, 20 chromosomes are simulated.
##################################################Folders and parameters##################################################
- Secondary contact models -
Parameters and files:mu mu_B t_C d t_s bottleneck_intensity archivename0.005 0.005 0 0.125 19 0.1 seccon.sim0.tgz 0.005 0.005 1 0.125 19 0.1 seccon.sim1.tgz 0.005 0.005 2 0.125 19 0.1 seccon.sim2.tgz 0.005 0.005 3 0.125 19 0.1 seccon.sim3.tgz 0.005 0.005 4 0.125 19 0.1 seccon.sim4.tgz 0.005 0.005 5 0.125 19 0.1 seccon.sim5.tgz 0.005 0.0005 1 0.125 19 0.1 seccon.sim31.tgz 0.005 0.0005 2 0.125 19 0.1 seccon.sim32.tgz 0.005 0.0005 3 0.125 19 0.1 seccon.sim33.tgz 0.005 0.0005 4 0.125 19 0.1 seccon.sim34.tgz 0.005 0.0005 5 0.125 19 0.1 seccon.sim35.tgz 0.005 0.005 1 0.125 19 0.25 seccon.sim51.tgz 0.005 0.005 1 0.125 19 0.5 seccon.sim52.tgz 0.005 0.005 1 0.25 19 0.1 seccon.sim61.tgz 0.005 0.005 1 0.375 19 0.1 seccon.sim62.tgz 0.01 0.01 1 0.125 19 0.1 seccon.sim71.tgz 0.05 0.05 1 0.125 19 0.1 seccon.sim72.tgz 
main text (fig 3): sim0-sim5SI:- bottleneck intensity (fig S3): sim1, sim51-52- expansion speed (fig S4): sim1, sim61-62- migration rate (fig S5): sim1, sim71-72- secondary contact model with barrier (fig S6): sim0, sim31-35

- Stepping stone models -
Parameters and files:mu mu_B archivename0.005 0.005 step.sim10.tgz0.005 0.0005 step.sim11.tgz0.005 0.00005 step.sim12.tgz0.005 0.001 step.sim13.tgz0.005 0.0001 step.sim14.tgz0.005 0.00001 step.sim15.tgz0.01 0.00002 step.sim71.tgz0.05 0.0001 step.sim72.tgz
main text (fig 3): sim10-sim15SI: - migration rate (fig S5): sim15, sim71-72

############################################Files: ############################################
- Filenames -
sim* (see archivename) + number of the replicate (1-100)
- Filetypes - 
- *.mscmd: Command that invoked ms.- *.posout: Positions of the segregating sites.One line per unlinked locus. For each locus, the positions of the 100 SNPs on a scale of (0, 1) are given, separated by blanks. - *.parseout: Segregating sites.One line per chromosome. Each line consists of the number of the deme (1-100, i. e. there are 20 lines per deme) followed by a sequence of 0s, and 1s, 0 for the ancestral and 1 for the derived allele at each polymorphic site, separated by blanks.