2010
Antonio Carvajal Rodríguez
GenomePop2 allows for flexible migration model definition. Standard one dimensional Stepping Stone and Island models are predefined. Then, to run a stepping stone model of one dimension with migration rate of 1% just add the following lines to the file GP2Input.txt:
migration
0.01
flowmodel
steppingstone
Similarly, to run an island model with migration rate of 1%:
migration
0.01
flowmodel
island
However, we can define more complicated models. To do this we just put the following line in the file GP2Input.txt
flowmodel
user
Now we should include the model in a new file called MigrationModel.txt. For example:
Pop
2
0.01 2
0.001 3
Pop
1
0.01 1
Defines a model where the first population has 2 different migration levels i.e. 2 different migration rates. The first implies sending migrants at a rate 0.01 to population 2 and the second implies sending migrants at rate 0.001 to population 3. The second population has only 1 migration rate and sends migrant at a rate 0.01 to the first population. The third population does not appear and do not send migrants anyway. Formally, we should include the word "Pop" each time we want to consider a new population that sends emigrants. The number below "Pop" indicantes the different migration rates from this population. Below the migraton level, we should have as much as lines as different migration rates. Each of these lines having a first decimal number that is the migration rate followed by one or more integer numbers representing the target populations. Using this representation an island migration model between three populations with migration rate 0.01 will appear as:
Pop
1
0.01 2 3
Pop
1
0.01 1 3
Pop
1
0.01 1 2
As we can see there are only one migration level, 0.01, from each population. The population 1 sends migrants to populations 2 and 3, the population 2 to 1 and 3 and the population 3 to 1 and 2. Using this rules we can define any desired migration scheme.