jaatha (version 2.7.0)

dm.addMigration: Add migration/gene flow between two populations to a demographic model

Description

This function adds the assumption to the model that some individuals 'migrate' from one sub-population to another, i.e. they leave the one and become a member of the other. This is usually used to model ongoing gene flow through hybridisation after the populations separated.

Usage

dm.addMigration(dm, lower.range, upper.range, fixed.value, pop.from, pop.to,
  time.start = "0", par.new = T, new.par.name = "M", parameter)

Arguments

dm

The demographic model to which recombination events should be added.

lower.range

If you want to estimate the migration parameter (see note

upper.range

Same as lower.range, but the largest possible value.

fixed.value

If specified, the migration rate will not be estimated, but assumed to have the given value.

pop.from

The population from which the individuals leave.

pop.to

The population to which the individuals move.

time.start

The time point at which the migration with this rate starts.

par.new

If 'TRUE' a new parameter will be created using the arguments 'lower.range' and 'upper.range' or 'fixed.value'. It will be named 'new.par.name'. If 'FALSE' the argument 'parameter' will be evaluated instead.

new.par.name

The name for the new parameter.

parameter

Instead of creating a new parameter, you can also set the mutation rate to an expression based on existing parameters. For example setting this to "M" will use an parameter with name M that you have previously created. You can also use R expression here,

Value

• The demographic model with migration

Details

You can enter a time ('time.start') at which the migration is assumed to start (looking backwards in time). From that time on, a fixed number of migrants move from population 'pop.from' to population 'pop.to' each generation. This number is given via this feature's parameter, which equals 4*N0*m, where m is the fraction of 'pop.to' that is replaced with migrants each generation. If 'pop.to' has also size Ne, than this is just the expected number of individuals that migrate each generation.

You can add different mutation rates at different times to your model. Then each rate will be used for the period from its time point to the next. Migration from and to an population always ends with the speciation event in which the population is created.

Examples

# Constant asymmetric migration
dm <- dm.createThetaTauModel(c(25,25), 100)
dm <- dm.addMigration(dm, 0.01, 5, pop.from=1, pop.to=2, time.start="0")

# Stepwise decreasing mutation
dm <- dm.createThetaTauModel(c(25,25), 100)
dm <- dm.addMigration(dm, 0.01, 5, pop.from=1, pop.to=2, new.par.name="M",
                      time.start="0")
dm <- dm.addMigration(dm, pop.from=1, pop.to=2, par.new=FALSE,
                      parameter="0.5*M", time.start="0.5*tau")