Quickstart

SLiM scripts can be created from slime.RecentHistory objects. The following code shows a simple, minimal demographic history of admixture:

>>> ref_pops = [slime.PopulationConfiguration(initial_size=100),
...      slime.PopulationConfiguration(initial_size=100)]

>>> adm_pop = slime.PopulationConfiguration(initial_size=50)

>>> script = slime.RecentHistory(final_gen=100, chrom_length=1e7,
...    recombination=1e-8, reference_configs=ref_pops, adm_configs=adm_pop,
...    prop=[0.3, 0.7])

For example, in the code below, I specify two ancestral populations, each with population size 100 at the time of admixture. Our admixed population has initial population size 50, and is initially created with a single-pulse of admixture between the two reference populations that occurred 100 generations ago. Each reference population contributes migrants to the admixed population with proportions of 0.3 and 0.7 respectively. The simulated chromosome contains 1e7 bases, and recombination occurs at a uniform rate of 1e-8 per base per generation.

At minimum, your history of admixture should involve:

• some number of discrete ancestral populations
• a present-day admixed population
• the age of the admixed population, in generations
• an admixture proportion
• the number of bases in the genomic segment being simulated
• a recombination rate

The sections below explain how more complicated admixtures can be represented with slime.

Generating a SLiM script

Use the dump_script() method:

>>> script.dump_script('recent-history.slim')

You should then have a file called recent-history.slim in your root directory.

You can also view the SLiM script corresponding to your RecentHistory object at any stage using the print_script() method:

>>> script.print_script()