MinimalWalkthrough
1 Introduction
In this walkthrough we quickly introduce the usage of MimicrEE2 using small toy examples.
We focus on diploids. Haploids will be treated in later walkthroughs.
2 Minimal walkthrough
Minimal simulations with MimicrEE2 require solely a haplotype file [HaplotypeFile].
haplotypes
We first generate a minimal haplotype file. We will simulate 10 SNPs and provide 20 haplotypes (thus N=10 diploid individuals).
We store the following toy example of diploid haplotypes in file: mini.mimhap
2L 1 G A/G AG AA AA AG AA AA AA AA AA AA 2L 2 G A/G AG AA AA AA AA AA AA AA AA AA 2L 3 G A/G AG AA AA AA AA AA AA AA AA AA 2L 4 G A/G AG AA AA AA AA AA AA AA AA AA 2L 5 G A/G AG AA AA AG AA AA AA AA AA AA 2L 6 G A/G AG AA AA AA AA AG AA AA AA AA 2L 7 G A/G AG AA AA AA AA AA AA AA AA AA 2L 8 G A/G AG AA AA AA AA AA AA AA AA AA 2L 9 G A/G AG AA AA AG AA AG AA AG AA AA 2L 10 G A/G AG AA AA AG AA AA AA AA AA AA
This file may also be obtained here: https://sourceforge.net/projects/mimicree2/files/walkthrough_for_wmode/data/mini.mimhap/download
minimal simulations
Now we can start the minimal simulations. We use 1 replicate and as output we want to obtain the allele frequencies.
Simulations will be performed for 50 generations.
java -jar mim2.jar w --replicate-runs 1 --haplotypes-g0 mini.mimhap --snapshots 50 --output-sync allele-freqs.txt
output from minimal simulations
We may view the content of the resulting sync file (it basically contains the allele frequencies) with the following command
> gzip -cd allele-freqs.txt
and may for example obtain:
2L 1 G 18:0:0:2:0:0 20:0:0:0:0:0 2L 2 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 3 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 4 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 5 G 18:0:0:2:0:0 20:0:0:0:0:0 2L 6 G 18:0:0:2:0:0 20:0:0:0:0:0 2L 7 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 8 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 9 G 16:0:0:4:0:0 6:0:0:14:0:0 2L 10 G 18:0:0:2:0:0 20:0:0:0:0:0
The above sync file contains the allele frequencies of the start population (column 4) and the evolved population (column 5), in the form A:T:C:G:N:del (for details see [OutputFiles]; this file can be used directly for downstream analysis with tools such as PoPoolation2 https://sourceforge.net/projects/popoolation2/).
In this example all segregating SNPs - except one - got fixed during the neutral simulations.
3 Minimal simulations with recombination and selection
In this walkthrough we introduce the usage of MimicrEE2 with recombination and selected loci.
We use the haplotype file specified above and additionally provide a recombination map as well as a selected locus.
recombination map
We specify that in the region between base 1 and 10 of chromosome 2L on the average 0.1 recombination should occur. We save the following content in file recrate.txt
[lambda] 2L:1..10 0.1
For details on this file format see [RecombinationRate] . The file may also be obtained here https://sourceforge.net/projects/mimicree2/files/walkthrough_for_wmode/data/recrate.txt/download
selected loci
Finally we specify that the locus at position 5 is positively selected with a selection coefficient of s = 0.15 (and an additive effect of h=0.5). We store the following content in file selected.txt.
[s] 2L 5 A/G 0.15 0.5
For details on this file format see [SelectedLoci]. The file may also be obtained here https://sourceforge.net/projects/mimicree2/files/walkthrough_for_wmode/data/selected.txt/download
minimal simulations with recombination and selection
Having the input files we can proceed with the forward simulations. We use 1 replicate and simulate selection for 50 generations. As output we want to obtain the allele frequencies
java -jar mim2.jar w --replicate-runs 1 --haplotypes-g0 mini.mimhap --recombination-rate recrate.txt --fitness selected.txt --snapshots 50 --output-sync allele-freqs.txt
output: the allele frequencies (--output-sync)
The output is zipped and may be displayed with command gzip -cd allele-freqs.txt
2L 1 G 18:0:0:2:0:0 0:0:0:20:0:0 2L 2 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 3 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 4 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 5 G 18:0:0:2:0:0 0:0:0:20:0:0 2L 6 G 18:0:0:2:0:0 20:0:0:0:0:0 2L 7 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 8 G 19:0:0:1:0:0 20:0:0:0:0:0 2L 9 G 16:0:0:4:0:0 0:0:0:20:0:0 2L 10 G 18:0:0:2:0:0 14:0:0:6:0:0
We specified that the G at position 5 is positively selected. This file shows that the G went from a low frequency of 10% in the base population (18:0:0:2:0:0) to fixation in the evolved population (0:0:0:20:0:0).
With the exception of the SNP at position 10 all other SNPs where fixed. Individual number 4 contains a distinct haplotype that is linked to the positively selected variant. This haplotype has a distinct allele at positions 1, 9 and 10. The sync file demonstrates that the alleles at position 1 and 9 hitchhiked to fixation with the selected locus (at position 5). However the linked variant at position 10 did not get fixed.
4 Minimal simulations with several replicates and fitness as output
Using the input files generated above we perform forward simulations for 2 replicates and 50 generations. As output we want the allele frequencies and the fitness of the individuals.
java -jar mim2.jar w --replicate-runs 2 --haplotypes-g0 mini.mimhap --recombination-rate recrate.txt --fitness selected.txt --snapshots 50 --output-sync allele-freqs.txt --output-gpf pop-fitness.txt
output: the allele frequencies (--output-sync)
Drift is strong with a population size of N=10, so the results may differ between replicates (they actually differ in the following output):
2L 1 G 18:0:0:2:0:0 0:0:0:20:0:0 18:0:0:2:0:0 0:0:0:20:0:0 2L 2 G 19:0:0:1:0:0 20:0:0:0:0:0 19:0:0:1:0:0 0:0:0:20:0:0 2L 3 G 19:0:0:1:0:0 20:0:0:0:0:0 19:0:0:1:0:0 0:0:0:20:0:0 2L 4 G 19:0:0:1:0:0 20:0:0:0:0:0 19:0:0:1:0:0 20:0:0:0:0:0 2L 5 G 18:0:0:2:0:0 0:0:0:20:0:0 18:0:0:2:0:0 20:0:0:0:0:0 2L 6 G 18:0:0:2:0:0 20:0:0:0:0:0 18:0:0:2:0:0 20:0:0:0:0:0 2L 7 G 19:0:0:1:0:0 20:0:0:0:0:0 19:0:0:1:0:0 20:0:0:0:0:0 2L 8 G 19:0:0:1:0:0 20:0:0:0:0:0 19:0:0:1:0:0 20:0:0:0:0:0 2L 9 G 16:0:0:4:0:0 0:0:0:20:0:0 16:0:0:4:0:0 20:0:0:0:0:0 2L 10 G 18:0:0:2:0:0 0:0:0:20:0:0 18:0:0:2:0:0 20:0:0:0:0:0
- column 1: chromosome
- column 2: position
- column 3: reference character
- column 4: base population
- column 5: evolved population of replicate 1 (50 generations)
- column 6: base population
- column 7: evolved population of replicate 2 (50 generations)
For details on this output file see [OutputFiles]
Note the beneficial allele at position 5 got fixed in the first replicate (compare column 4 vs 5) but got lost in the second replicate (compare column 6 vs 7).
output: fitness (--output-gpf)
The following file contains the fitness (column 5) of all individuals in the base (column_2 = 0) and evolved (column_2 = 50) populations from both replicates (replicate is column 1). For details of this file format see [OutputFiles]
1 0 1.0 1.0 1.075 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.075 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 0 1.0 1.0 1.0 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 1 50 1.0 1.0 1.15 2 0 1.0 1.0 1.075 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.075 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 0 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0 2 50 1.0 1.0 1.0
Fom the fitness files we can also see that the beneficial locus got fixed in the first replicate (all 10 individuals have a fitness of 1.15 at generation 50) while it got lost in the second replicate (all ten individuals have a fitness of 1.0 at generation 50).
Related
Wiki: HaplotypeFile
Wiki: Home
Wiki: OutputFiles
Wiki: RecombinationRate
Wiki: SelectedLoci
