A single population with population size change such as bottleneck?

[Sang Chul Choi]

Hi,

I wonder if popABC allows analyses of a single population.  If so, is it possible to analyze a single population with bottleneck?  I have one more question about setting a prior file in popABC; what is Model marker in the prior file, examples/1pop.prs? Is it related with model comparison?

So, what is difference between 0 and 3 9?

examples/1pop.prs

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>topology:       0 - uniform distribution;

                     3 - uniform distribution (and choose a Model marker);

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Thank you for your answers.

Best,

SangChul

 

[Joao Sollari Lopes]

Hi SangChul,

1) popABC does allow for analyses of a single population, but only to infer a constant effective population size (Ne). I guess you can produce a 2-populations splitting model with a ghost population, so that you can infer:
- Ne before the false splitting (NeAnc)
- Ne after the false splitting (Ne1)
- time of the false splitting, aka bottleneck (tev).
[Ne2 would be the Ne of a ghost population for which you would have no sample data. Also you should set migration to zero]

2) Indeed, the Model Marker is to be used when comparing different models.
If you set this option to be 0, then the first parameter of the .dat files (top, the Model Marker) will be 0. If you want to give it a different value you can use the option 3 and then the marker that you want (an integer).
This option is important when you want to create .dat files with different conditions (e.g. different patterns of migration) which you want later to join so that you can perform a model-choice analysis.

Hope this was clear. Let me know if you have more questions,
Joao
 
 This way you can  that splits from the previous one this does not

[Sang Chul Choi]

Thank you! -SCC