#### Supplementary Text 1 - Simulation Commands ####


### simulated chromosomes

## msms neutral scenrio
# 4taxa
msms 40 1 -T -I 4 10 10 10 10 -ej 0.5 2 1 -ej 1 3 1 -ej 1.5 4 1 -m 2 3 0.1 -r 10000 1000000 | grep ";"  > msms_4of10_l1Mb_r10k.txt
# 5taxa
msms 30 1 -T -I 5 6 6 6 6 6 -ej 0.5 2 1 -ej 0.5 4 3 -ej 1 3 1 -ej 1.5 5 1 -m 2 3 0.1 -r 10000 1000000 | grep ";" | gzip > msms_5of6_l1Mb_r10k.txt


## msms adaptive introgression
#4 taxa
msms 40 1 -T -I 4 10 10 10 10 -ej 0.5 2 1 -ej 1 3 1 -ej 1.5 4 1 -m 2 3 0.1 -r 10000 1000000 -SAA 1000 -SAa 1000 -Sp 0.5 -SI 0.1 4 0 0 1 0 -N 100000 -threads 10 | grep ";"  > msms_4of10_l1Mb_r10k_sweep.txt
# 5 taxa
msms 30 1 -T -I 5 6 6 6 6 6 -ej 0.5 2 1 -ej 0.5 4 3 -ej 1 3 1 -ej 1.5 5 1 -m 2 3 0.1 -r 10000 1000000 -SAA 1000 -SAa 1000 -Sp 0.5 -SI 0.1 5 0 0 1 0 0 -N 100000 -threads 10 | grep ";" | gzip > msms_5of6_l1Mb_r10k_sweep.txt.gz

## msms barrier locus
#4 taxa
msms 40 1 -T -I 4 10 10 10 10 -ej 0.5 2 1 -ej 1 3 1 -ej 1.5 4 1 -m 2 3 5 -r 10000 1000000 -SAA -1000 -SAa -1000 -Sp 0.5 -SI 0.5 4 0 0 1 0 -N 100000 -threads 10 | grep ";"  > msms_4of10_l1Mb_r10k_island.txt
#5 taxa
msms 30 1 -T -I 5 6 6 6 6 6 -ej 0.5 2 1 -ej 0.5 4 3 -ej 1 3 1 -ej 1.5 5 1 -m 2 3 5 -r 10000 1000000 -SAA -1000 -SAa -1000 -Sp 0.5 -SI 0.5 5 0 0 1 0 0 -N 100000 -threads 10 | grep ";" | gzip > msms_5of6_l1Mb_r10k_island.txt.gz

##generate sequences with seq-gen (repeated for each simulation)

partitions=$(wc -l msms_4of10_l1Mb_r10k.txt)
seq-gen -mHKY -l 1000000 -s 0.01 -p $partitions < msms_4of10_l1Mb_r10k.txt > msms_4of10_l1Mb_r10k.seq_gen.phy


###Power analyses (Repeated with different split times as described)

#msms four populations
msms 40 1 -I 4 10 10 10 10 -ej 0.1 1 2 -ej 0.1 3 4 -ej 0.5 2 4  -T

#msms five populations
msms 50 1 -N 100000 -I 5 10 10 10 10 10 -ej 0.1 1 2 -ej 0.1 3 4 -ej 0.2 4 5 -ej 0.5 2 5 -T

#generate sequences
seq-gen -mGTR -l 600 -q < input.trees