MigrationWalkthrough
1 Introduction
In these walkthrough we introduce simulations with migration using a toy example.
We perform simulations with MimicrEE2 to demonstrate how different migration regimes can be integrated into the simulations. As output we request the haplotypes which allows us to monitor the evolution of the haplotypes.
2 Required input files
haplotypes of the base population
We save the following content in file basepop.mimhap
2L 1 G A/T AA AA AA AA AA AA AA AA AA AA 2L 2 G A/T AA AA AA AA AA AA AA AA AA AA 2L 3 G A/T AA AA AA AA AA AA AA AA AA AA 2L 4 G A/T AA AA AA AA AA AA AA AA AA AA 2L 5 G A/T AA AA AA AA AA AA AA AA AA AA 2L 6 G A/T AA AA AA AA AA AA AA AA AA AA 2L 7 G A/T AA AA AA AA AA AA AA AA AA AA 2L 8 G A/T AA AA AA AA AA AA AA AA AA AA 2L 9 G A/T AA AA AA AA AA AA AA AA AA AA 2L 10 G A/T AA AA AA AA AA AA AA AA AA AA
haplotypes of the source population
We save the following content in file sourcepop.mimhap
2L 1 G A/T TT TT TT TT TT TT TT TT TT TT 2L 2 G A/T TT TT TT TT TT TT TT TT TT TT 2L 3 G A/T TT TT TT TT TT TT TT TT TT TT 2L 4 G A/T TT TT TT TT TT TT TT TT TT TT 2L 5 G A/T TT TT TT TT TT TT TT TT TT TT 2L 6 G A/T TT TT TT TT TT TT TT TT TT TT 2L 7 G A/T TT TT TT TT TT TT TT TT TT TT 2L 8 G A/T TT TT TT TT TT TT TT TT TT TT 2L 9 G A/T TT TT TT TT TT TT TT TT TT TT 2L 10 G A/T TT TT TT TT TT TT TT TT TT TT
recombination rate
We save the following content in file recrate.txt
[lambda] 2L:1..10 1
Note: We specify that on the average 1 recombination event per zygote will take place on chromosome 2L between sites 1 and 10.
3 Simulations with migration
We start with a simple scenario.
migration regime
We store the following content in file migrationregime.txt
10 5 sourcepop.mimhap 20 5
This file specifies migration at generations 10 and 20 (column 1). At generation 10, five migrants (10 haplotypes) will move from the source population to the evolved population. At generation 20, another five migrants will move from the base population to the evolved population (if no source population is specified the base population is used as source).
For details on the migration regime file see [MiscInput]
run MimicrEE2
mkdir output java -jar mim2.jar w --haplotypes-g0 basepop.mimhap --migration-regime migrationregime.txt --recombination-rate recrate.txt --snapshots 9,10,19,20 --output-dir output
output haplotypes
haplotypes at generation 9
At generation 9 we find the haplotypes directly before the first migration event.
2L 1 G A/T AA AA AA AA AA AA AA AA AA AA 2L 2 G A/T AA AA AA AA AA AA AA AA AA AA 2L 3 G A/T AA AA AA AA AA AA AA AA AA AA 2L 4 G A/T AA AA AA AA AA AA AA AA AA AA 2L 5 G A/T AA AA AA AA AA AA AA AA AA AA 2L 6 G A/T AA AA AA AA AA AA AA AA AA AA 2L 7 G A/T AA AA AA AA AA AA AA AA AA AA 2L 8 G A/T AA AA AA AA AA AA AA AA AA AA 2L 9 G A/T AA AA AA AA AA AA AA AA AA AA 2L 10 G A/T AA AA AA AA AA AA AA AA AA AA
haplotypes at generation 10
At generation 10 we have the haplotypes directly following the first migration event
2L 1 G A/T TT TT TT TT TT AA AA AA AA AA 2L 2 G A/T TT TT TT TT TT AA AA AA AA AA 2L 3 G A/T TT TT TT TT TT AA AA AA AA AA 2L 4 G A/T TT TT TT TT TT AA AA AA AA AA 2L 5 G A/T TT TT TT TT TT AA AA AA AA AA 2L 6 G A/T TT TT TT TT TT AA AA AA AA AA 2L 7 G A/T TT TT TT TT TT AA AA AA AA AA 2L 8 G A/T TT TT TT TT TT AA AA AA AA AA 2L 9 G A/T TT TT TT TT TT AA AA AA AA AA 2L 10 G A/T TT TT TT TT TT AA AA AA AA AA
haplotypes at generation 19
At generation 19 we find the haplotypes directly before the second migration event
2L 1 G A/T TT TA AA TA AT AA AT AA TA AA 2L 2 G A/T TT TA AA TA AT AA AT AA TA AA 2L 3 G A/T AA AA TT TA TT AA AA AA AT TA 2L 4 G A/T TT TA AT AT AT AA TT TA TA AA 2L 5 G A/T AT TA TA AT AT AA TA AA TA AT 2L 6 G A/T TT AA TT TT TT AA TT TA TT TT 2L 7 G A/T TT TA TT TT TT TA TT TT TT TT 2L 8 G A/T TT TT TT TT TT TT TT TT TT TT 2L 9 G A/T TT AA TT TT TA AA TT TT TT TT 2L 10 G A/T TT TT AT TT TT TT TT TT TT TA
haplotypes at generation 20
At generation 20 we have the haplotypes directly after the second migration event
2L 1 G A/T AA AA AA AA AA TT AA AA TA AA 2L 2 G A/T AA AA AA AA AA TT AA AA TA AA 2L 3 G A/T AA AA AA AA AA AT TA AA AA TA 2L 4 G A/T AA AA AA AA AA TT AA AT TT AA 2L 5 G A/T AA AA AA AA AA AT AA AT AT AA 2L 6 G A/T AA AA AA AA AA TT TA AT TT TA 2L 7 G A/T AA AA AA AA AA TT TA AT TT TA 2L 8 G A/T AA AA AA AA AA TT TT TT TT TT 2L 9 G A/T AA AA AA AA AA TA TA AT TT TA 2L 10 G A/T AA AA AA AA AA TT TT TT TT TT
4 Simualtions with migration and selection
In this example we simulate competition between two beneficial haplotypes. Both haplotypes carry a beneficial mutation, but no haplotype carries both. This situation is, at least in the beginning, similar to clonal interference. The major difference however is that recombination may eventually join both beneficial alleles at the same haplotype.
Initially only one haplotype is present, the second haplotype is introduced at generation 10 by migration.
For this walkthrough we will use the same base population, source population and recombination rate as in the previous example.
We will however use a novel migration regime file and additionally specify a selected locus
migration regime file
We store the following content in the file migrationregime.txt
10 5 sourcepop.mimhap
At generation 10 we introduce 5 individuals from the source population to the evolving population.
selected locus
We store the following content in the file sellocus.txt
[s] 2L 2 A/T 1.0 0.5 2L 9 T/A 1.0 0.5
For the locus at position 2 the allele T is beneficial and for the locus at position 9 the allele A is beneficial. Both alleles have the same selection coefficient (1.0) and heterozyous effect (0.5 additive effect).
run MimicrEE2
mkdir output java -jar mim2.jar w --haplotypes-g0 basepop.mimhap --migration-regime migrationregime.txt --recombination-rate recrate.txt --snapshots 9,10,20,30,40,50 --output-dir output
output haplotypes
haplotypes at generation 9
At generation 9 we have the haplotypes directly before the migration event
2L 1 G A/T AA AA AA AA AA AA AA AA AA AA 2L 2 G A/T AA AA AA AA AA AA AA AA AA AA 2L 3 G A/T AA AA AA AA AA AA AA AA AA AA 2L 4 G A/T AA AA AA AA AA AA AA AA AA AA 2L 5 G A/T AA AA AA AA AA AA AA AA AA AA 2L 6 G A/T AA AA AA AA AA AA AA AA AA AA 2L 7 G A/T AA AA AA AA AA AA AA AA AA AA 2L 8 G A/T AA AA AA AA AA AA AA AA AA AA 2L 9 G A/T AA AA AA AA AA AA AA AA AA AA 2L 10 G A/T AA AA AA AA AA AA AA AA AA AA
haplotypes at generation 10
At generation 10 we have the haplotypes directly after migration
2L 1 G A/T TT TT TT TT TT AA AA AA AA AA 2L 2 G A/T TT TT TT TT TT AA AA AA AA AA 2L 3 G A/T TT TT TT TT TT AA AA AA AA AA 2L 4 G A/T TT TT TT TT TT AA AA AA AA AA 2L 5 G A/T TT TT TT TT TT AA AA AA AA AA 2L 6 G A/T TT TT TT TT TT AA AA AA AA AA 2L 7 G A/T TT TT TT TT TT AA AA AA AA AA 2L 8 G A/T TT TT TT TT TT AA AA AA AA AA 2L 9 G A/T TT TT TT TT TT AA AA AA AA AA 2L 10 G A/T TT TT TT TT TT AA AA AA AA AA
haplotypes at generation 20
Recombination quickly generates novel haplotypes linking both beneficial alleles
2L 1 G A/T TT TT AT TA TA TT TT TT TA TA 2L 2 G A/T TT TT AT TA TA TT TT TT TA TA 2L 3 G A/T TA AA AT TA AA TA TT TA TA AA 2L 4 G A/T TA TA AT TA TA TA TT TA TA AA 2L 5 G A/T TA TA AT TA TA TA TT TA TA AA 2L 6 G A/T TA TT AT TA TA TA TT TT TA AA 2L 7 G A/T AT TT AA AT AT AT AA AT AT TA 2L 8 G A/T AA AT AA AT AA AA AA AT TT AA 2L 9 G A/T AA AT AA AT AA AA AA AT TT AA 2L 10 G A/T TT TT TT TT TT TT TT TT TT TT
haplotypes at generation 50
By generation 50 both beneficial alleles (T at site 2 and A at site 9) got fixed
2L 1 G A/T TT TT TT TT TT TT TT TT TT TT 2L 2 G A/T TT TT TT TT TT TT TT TT TT TT 2L 3 G A/T AA AA AA AA AA AA AA AA AA AA 2L 4 G A/T AA AA AA AA AA AA AA AA AA AA 2L 5 G A/T AA AA AA AA AA AA AA AA AA AA 2L 6 G A/T AA AA AA AA AA AA AA AA AA AA 2L 7 G A/T TT TT TT TT TT TT TT TT TT TT 2L 8 G A/T TT TT AT AA TA TA AA TA TT TA 2L 9 G A/T AA AA AA AA AA AA AA AA AA AA 2L 10 G A/T TT TT TT TT TT TT TT TT TT TT
