HaploidSimulations
1 Introduction
In this walkthrough we show how to simulate evolution of haploid organism. We show minimal simulations and simulations with recombination and selection.
2 Minimal simulations with haploid organism
In this toy example we demonstrate minimal simulations with haploid organism. Solely the haplotypes of the not evolved base population are required
haploid base population
2L 1 G A/T A T A A A A A A A A A A A A A A A A A T 2L 2 G A/T A T A A A A A A A A A A A A A A A A A T 2L 3 G A/T A T A A T A A A A A A A A A A A A A A T 2L 4 G A/T A T A A T A A A A A A A A A A A A A A T 2L 5 G A/T A T A A T A A A A A A A A A A A A A A T 2L 6 G A/T A T A A T A A A A A A A A A A A A A A T 2L 7 G A/T A T A A T A A A A A A A A A A A A A A T 2L 8 G A/T A T A A T A A A A A A A A A A A A A A T 2L 9 G A/T A T A A T A A A A A A A A A A A A A A T 2L 10 G A/T A T A A T A A A A A A A A A A A A A A T
neutral simulations
We perform neutral simulations for 20 generations.
Note the flag --haploid is absolutely necessary! If not provided diploid simulations would be performed, where the genotypes of the base population would be interpreted as homozygotes (e.g. A would be interpreted as AA and T as TT).
mkdir output java -jar mim2.jar w --haplotypes-g0 basepop.mimhap --snapshots 20 --output-dir output --haploid
evolved haplotypes
With the command gzip -cd output/haplotypes.r1.g20.mimhap.gz we may display the evolved haplotypes
2L 1 G A/T T A A A A T A A A A A A A A A A A A A A 2L 2 G A/T T A A A A T A A A A A A A A A A A A A A 2L 3 G A/T T A A A A T A A A A A A T A A A A A A A 2L 4 G A/T T A A A A T A A A A A A T A A A A A A A 2L 5 G A/T T A A A A T A A A A A A T A A A A A A A 2L 6 G A/T T A A A A T A A A A A A T A A A A A A A 2L 7 G A/T T A A A A T A A A A A A T A A A A A A A 2L 8 G A/T T A A A A T A A A A A A T A A A A A A A 2L 9 G A/T T A A A A T A A A A A A T A A A A A A A 2L 10 G A/T T A A A A T A A A A A A T A A A A A A A
3 Simulations with recombination and selection
For this walkthrough we use the same base population as in the previous example.
Additionally we specify a selected locus and recombination.
selected loci for haploid organism
We store the following content in the file sellocus.txt
[w] 2L 5 A/T 1.0 100.0 1.2
The file format is the same as for diploid organism; see [SelectedLoci]
With haploid organism however the heterozygous genotypes are ignored (in this case the ridiculously high fitness of 100.0).
The fitness of the haploid A is identical to the diploid AA and the fitness of the haploid T is identical to the fitness of the diploid TT
- w_A = w_AA = 1.0
- w_T = w_TT = 1.2
recombination rate for haploid organism
We store the following content in file recrate.txt
[lambda] 2L:1..10 1
start the simulations
mkdir output java -jar mim2.jar w --haplotypes-g0 basepop.mimhap --snapshots 5,10,20,30,40,50 --output-dir output --haploid --recombination-rate recrate.txt --fitness sellocus.txt
output haplotypes
generation 20
At generation 20 the beneficial allele at position 5 is still segregating
2L 1 G A/T T T T T T T T T T T T T T T T T T T T T 2L 2 G A/T T T T T T T T T T T T T T T T T T T T T 2L 3 G A/T A A T A A A A A A A A A A T T A A A A A 2L 4 G A/T A A A A A A A A A A A A A A A A A A A A 2L 5 G A/T T A A T A A T A A A T A T A A T A T T T 2L 6 G A/T A A A A A A A A A A A A A T A A A A A A 2L 7 G A/T A A A A A A A A A A A A A A A A A A A A 2L 8 G A/T A A A A A A A A A A A A A A A A A A A A 2L 9 G A/T A A A A A A A A A A A A A A A A A A A A 2L 10 G A/T A A A A A A A A A A A A A A A A A A A A
generation 30
At generation 30 the beneficial allele at position 5 got fixed
2L 1 G A/T T T T T T T T T T T T T T T T T T T T T 2L 2 G A/T T T T T T T T T T T T T T T T T T T T T 2L 3 G A/T A A A A A A A A A A A A A A A A A A A A 2L 4 G A/T A A A A A A A A A A A A A A A A A A A A 2L 5 G A/T T T T T T T T T T T T T T T T T T T T T 2L 6 G A/T A A A A A A A A A A A A A A A A A A A A 2L 7 G A/T A A A A A A A A A A A A A A A A A A A A 2L 8 G A/T A A A A A A A A A A A A A A A A A A A A 2L 9 G A/T A A A A A A A A A A A A A A A A A A A A 2L 10 G A/T A A A A A A A A A A A A A A A A A A A A
4 Sex and haploid organism
MimicrEE2 supports the simulation of sex for haploid organism.
haploid base population with sex
We store the following in file basepop.mimhap
#sex M F M F M F M F M F M F M F M F M F F F 2L 1 G A/T A T A A A A A A A A A A A A A A A A A T 2L 2 G A/T A T A A A A A A A A A A A A A A A A A T 2L 3 G A/T A T A A T A A A A A A A A A A A A A A T 2L 4 G A/T A T A A T A A A A A A A A A A A A A A T 2L 5 G A/T A T A A T A A A A A A A A A A A A A A T 2L 6 G A/T A T A A T A A A A A A A A A A A A A A T 2L 7 G A/T A T A A T A A A A A A A A A A A A A A T 2L 8 G A/T A T A A T A A A A A A A A A A A A A A T 2L 9 G A/T A T A A T A A A A A A A A A A A A A A T 2L 10 G A/T A T A A T A A A A A A A A A A A A A A T
Note in the first row (the comment starting with #) we provide the sex for each haploid organism
recombination rate for haploid organisms (!)
Note In order to generate progeny, haploid organism form a transient diploid stage where recombination takes place. Assignment of sex to this transient diploid stage is not possible, thus sex specific recombination rates do not make sense for haploid organism. So which recombination rate to use? MimicrEE2 uses the recombination rate of hermaphrodites for simulations of haploid organisms. We recommend to just provide the default recombination rate (which is valid for all sexes). See the example shown below.
[lambda] 2L:1..10 1
sex info
MimicrEE2 supports simulations with different sexes for haploid organism. Just as for diploids the fractions of males/females/hermaphrodites may be specified in the sex-info file.
If this file is not provided hermaphrodites will be simulated per default.
We store the following into the file sexinfo.txt
M=0.5 F=0.5 H=0.0 MC=1
Note hemizygous sex chromosomes do not make sense for haploid organisms. If a hemizygous sex chromosome is provided for haploid organism, MimicrEE2 will throw an Error!
haploid simulations with sex
We perform neutral forward simulations for 50 generations and store the output haplotypes in the folder output.
mkdir output java -jar mim2.jar w --haplotypes-g0 basepop.mimhap --snapshots 5,10,20,30,40,50 --output-dir output --haploid --recombination-rate recrate.txt --sex sexinfo.txt
haplotypes at generations
#sex M F F F M F F F F M M F F M F F M F M M 2L 1 G A/T A A A A A A A A A A A A A A A A A A A A 2L 2 G A/T A A A A A A A A A A A A A A A A A A A A 2L 3 G A/T A A A A A A A A A A A A A A A A A A A A 2L 4 G A/T A A A A A A A A A A A A A A A A A A A A 2L 5 G A/T A A A A A A A A A A A A A A A A A A A A 2L 6 G A/T T A T T T T A T A A A A A T A A A T A T 2L 7 G A/T A A A A A A A A A A A A A A A A A A A A 2L 8 G A/T A A A A A A A A A A A A A A A A A A A A 2L 9 G A/T A A A A A A A A A A A A A A A A A A A A 2L 10 G A/T A A A A A A A A A A A A A A A A A A A A
