example for serial sampling through bottleneck

[sameo...@gmail.com]

Hi Laurent,

I am having trouble formulating an input file to simulate a simple scenario. I have a single population that experienced a bottleneck in the past (at generation 18). I would like to sample sequences from the population at the present time (generation 0), and well before the bottleneck (generation 35).

I have read the manual and find the examples are not descriptive enough.

Can you provide a .par file that sets up this simulation? Any explanation for the choices would also be useful.

Here I attach the code of what I have come up with, but fsc25221 seems to go into an infinite loop when reading the file, and the .simparams output file goes on forever with nonsense, creating 100s of demes of size 0, etc.:

//Number of population samples (demes)
3
//Population effective sizes (number of genes)
2000
0
0
//Sample sizes
26
0 18
22 35
//Growth rates : negative growth implies population expansion
0
0
0
//Number of migration matrices : 0 implies no migration between demes
0
//historical event: time, source, sink, migrants, new size, growth rate, migr. matrix
2 historical events
18 2 1 1 3 0 0
35 1 0 1 1 0 0
//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 100000 0.000000013 0.00000002 0.33

[Laurent Excoffier]

Hi,

sorry i'm out of lab and with no access to my computer. 

However, your input file is pretty inconsistent.

I see several problems, the first one being the deme sizes set to zero, as a resize on a deme of size zero has no effect.

Then you seem to move all lineages of deme 2 to deme 1 at generation 18, but this deme will only be active at generation 35, whichmeans that your historical event has no effect.

Finally, making some acrive at a given generation create new historical events, which are added to the current ones. But since you have set up the time of your historical event to the same generation as the activation of some demes, it means that the classical events will be executed first, and then the ancient lineages in demes 0 and 1 will be activated. Therefore the historical event might have no effect.

Try to revise your par file, taking these information into account

best

laurent

[sameo...@gmail.com]

Laurent, thank you for your advice.

I re-created my par file using your tips as well as an example of a working par file from elsewhere in the google group. I find that now the simulations run, but I am unsure if the desired model is being implemented. Will you have a look?

Again, I have a very simple scenario: A single population experienced a bottleneck in the past (at generation 18). I would like to sample sequences from the population at the present time (generation 0), and well before the bottleneck (generation 35).

par file:

//Number of population samples (demes)
3
//Population effective sizes (number of genes)
20000
0
0
//Sample sizes
26
0 18
22 35
//Growth rates : negative growth implies population expansion
0
0
0
//Number of migration matrices : 0 implies no migration between demes
0
//historical event: time, source, sink, migrants, new size, growth rate, migr. matrix
2 historical events

18 1 0 1 3 0 0
35 2 0 1 1 0 0

//Number of independent loci [chromosome]
1 0
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters

DNA 130681887 0.000000013 0.00000002 0.33