Mutations¶

To initialise a slime simulation with mutations, you make a MutationTypes object and feed it into your RecentHistory object via the mutations parameter.

Note

If you are appending your SLiM simulation to a msprime simulation, there’s no need to code neutral mutations into your RecentHistory object, as they are more easily generated later using recapitate.

Fixed selection coefficients¶

Say we wish to specify 2 different types of mutations to occur:

Deleterious mutations with selection coefficient 0.2. These will occur with relative proportion 0.2, and have a dominance coefficient of 0.7.
Weakly beneficial mutations with selection coefficient 0.6. These will occur with a relative proportion 0.8, and have a dominance coefficient of 0.4.

The following code initialises a MutationTypes object that specifies these types of mutations to occur in our forward-in-time simulation.

>>> muts = slime.MutationTypes(mutation_rate=.005,
...     selection_coeffs=[0.2,0.6], proportions=[0.2, 0.8],
...     dominance_coeffs=[0.7, 0.4])

We’ll then use this MutationTypes object to initialize a RecentHistory object via the mutations parameter.

>>> config = slime.PopulationConfiguration(initial_size=10)
>>> script = slime.RecentHistory(final_gen=20, chrom_length=100,
...     reference_configs=[config, config], adm_configs=config,
...     prop=[0.3,0.7], mutations=muts)

Random selection coefficients¶

Coming soon.