Complex Models

NB: Complex scenario is sometimes called ‘Drosophila’ in scripts.

Programs

We used the following program versions:

  1. SLiM v4.0.1
  2. pyslim v1.0.3
  3. tskit v0.5.5

Demographic models

  1. No migration (nomig)
  2. Migration P1 -> P2 (p1_p2)
  3. Migration P2 -> P1 (p2_p1)

Distributions of Fitness Effects

  1. Neutral
    (neutral-nomig, neutral-p1_p2)
  2. Background Selection
    (bgs-nomig, bgs-p1_p2)
  3. Selective Sweep in P1
    (linkedp1-nomig, linkedp1-p1_p2)
  4. Selective Sweep in the ancestor
    (linkedancestor-nomig, linkedancestor-p1_p2)
  5. Balancing Selection (balancing-nomig, balancing-p1_p2)
  6. Adaptive Introgression
    (adaptiveint-p1_p2)

Simulating the data

Step 1: Sample parameters

To sample parameters, use this python script.
Parameters:

"-s","--slimfile", help="SLiM script to use for simulation", type="string"
"-r","--numreps", help="Number of replicates to simulate", default=1, type="int"
"-d","--divtime", help="Divergence time to use for simulations. Use scaled values.", type="int"

Example usage:

python sample_parameters_slim.py -s p1_p2_neutral_drosophila.slim -r 10000 -d 5000

Step 2: Simulate data

To simulate data, use this python script. Note: To run this, you must also have available the selRegionsFromAnnot_MLS.py script, along with the folder ‘drosophilaAnnotations’.

Parameters:

"-s","--slimfile", help="SLiM script to use for simulation", type="string"
"-r","--numreps", help="Number of replicates to simulate", default=1, type="int"
"-p","--paramsfile", help="Migration model parameters, if relevant. Default is None for divergence only.", type="string"
"-d","--divtime", help="Divergence time to use for simulations. Use scaled values.", type="int"
"-x","--slimexecutable", help="Path to slim executable", default="slim", type="str"
"-c","--processors", help="Number of processors to use", default=1, type="int"
"-f","--dfe", help="What DFE was used? neutral, bgs, or sweep", type="string"
"-o","--previous", help="Number of replicates previously simulated", default=0, type="int"
"--prefix", help="Prefix for naming file", type="string"
"--trees", help="Path to slim tree sequences without overlaid mutations.", action="store", type="string", dest="trees", default=None
"--scale", help="Factor by which to scale mutation rates, etc.", action="store", type="int", dest="scale", default=1
"--overlaidtrees", help="Path to slim tree sequences with overlaid mutations.", action="store", type="string", dest="overlaidtrees", default=None
"--seed", help="Seed for drawing mutation rate, recombination rate, fragments.", action="store", type="int", dest="seed", default=1

Example usage for a migration model:

python tskit_Drosophilamaps_to_msout_v3.py -d 5000 -r 10000 -s p1_p2_neutral_drosophila.slim --prefix p1_p2_neutral_drosophila -p p1_p2_neutral_drosophila_params_5000.txt -c 24 -f neutral -x slim --scale 100

Example usage for a no migration model:

python tskit_Drosophilamaps_to_msout_v3.py -d 5000 -r 10000 -s nomig_neutral_drosophila.slim --prefix nomig_neutral_drosophila -p None -c 24 -f neutral -x slim --scale 100

SLURM scripts used to simulate data on the IU HPC

All SLURM scripts used to simulate data on the IU HPC can be found here.

Output files (ms-style)

All simulated data, stored as ms-formatted output files, are available from Figshare (DOI: 10.6084/m9.figshare.24354277). Parameters files are also available from Figshare (DOI: 10.6084/m9.figshare.24354277).