Example ms lines for the 7 models simulated in the simulation study. For all simulation scripts the --options argument was used with msABC to specify the statistics calculated during the simulations. Model A: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -em Tgf 1 2 Nm -em Tgf+Tdur 1 2 0.0 -ej T1 3 2 -ej T2 2 1 Model B: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -em Tgf 1 3 Nm -em Tgf+Tdur 1 3 0.0 -ej T1 3 2 -ej T2 2 1 Model C: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -ej T1 3 2 -em T1 1 2 Nm -ej T2 2 1 Model D: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -em Tgf 2 1 Nm -em Tgf+Tdur 2 1 0.0 -ej T1 3 2 -ej T2 2 1 Model E: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -em Tgf 3 1 Nm -em Tgf+Tdur 3 1 0.0 -ej T1 3 2 -ej T2 2 1 Model F: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -ej T1 3 2 -em T1 2 1 Nm -ej T2 2 1 Model ISO: msABC #ind #loci -t THETA -I 3 2 2 2 0.0 -ej T1 3 2 -ej T2 2 1 Example ms lines for the 7 models simulated in our analysis of the B. pallida dataset Note: Gene flow in these models is represented as instantaneous admixture, rather than migration over a period of time at a particular rate (as above). Also, MYmsABC is a modified verison of msABC that disables calculation of several statistics that are not obtainable from a single sampled chromosome. For all simulation scripts the --options argument was used with msABC to specify the statistics calculated during the simulations. Model A: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -es Tgf 1 (1-F) -ej Tgf 4 2 -ej T1 3 2 -ej T2 2 1 Model B: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -es Tgf 1 (1-F) -ej Tgf 4 3 -ej T1 3 2 -ej T2 2 1 Model C: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -ej T1 3 2 -es Tgf 1 (1-F) -ej Tgf 4 2 -ej T2 2 1 Model D: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -es Tgf 2 (1-F) -ej Tgf 4 1 -ej T1 3 2 -ej T2 2 1 Model E: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -es Tgf 3 (1-F) -ej Tgf 4 1 -ej T1 3 2 -ej T2 2 1 Model F: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -ej T1 3 2 -es Tgf 2 (1-F) -ej Tgf 4 1 -ej T2 2 1 Model ISO: MYmsABC 5 1080 -t THETA -I 3 2 2 2 -ej T1 3 2 -ej T2 2 1