Re: [sfscode-users] question about simulation selection with sfs_code

[Ryan H. <rya...@uc...>]

Hi Miguel,

Unfortunately, I don't think your plan will do what you want.  The scenario you lay out below would still introduce new mutations under selection, there would just be a background level of diversity.  This is the same as doing the simulation with only a single population.  Selection on standing variation refers to the situation where an allele segregates in the population for a while (either neutral or even deleterious) until some time at which it becomes beneficial.  Sadly, SFS_CODE does not yet simulate selection on standing variation.  I have plans to implement such features soon, but have not yet started.  

Sorry!  Let me know if you have other questions.

Best,

Ryan

On Nov 26, 2013, at 11:28 AM, Miguel Navascues wrote:

> Dear Ryan and sfs_code users,
> 
> I would like to simulate some adaptive process from standing variation in one population with sfs_code. My idea is to use a similar trick that the one used to obtain samples at several times. I will simulate one population in which all mutations are neutral, then, at a given time I will create a second population for which mutations had some selective coefficient and terminate the first population. That is (values not necessary realistic in any way) :
> 
> ./sfs_code 2 1 -W P 0 0 -W P 1 1 5 1 0 -TS 1 0 1 -TE 1 0 -TE 5 -n 0 10
> 
> new non-synonymous mutations are neutral in population 0:
> -W P 0 0
> 
> new non-synonymous mutations are advantageous (with gamma=5) in population 1 :
> -W P 1 1 5 1 0
> 
> create population 1 from population 0 at time 1 (*2N):
> -TS 1 0 1
> 
> terminate population 0 at time 1 (*2N):
> -TE 1 0
> 
> terminate simulation at time 5 (*2N):
> -TE 5
> 
> sample 10 individuals in population 1 (at time 5*2N) and none in population 0:
> -n 0 10
> 
> 
> So my question is whether I got it right or I misunderstood how sfs_code works.
> 
> Also, is there a way to do the same but with the option --mutation? The way I understood it with mutation the gamma is fixed for all populations, isn't it? Could it be done in combination with --neutPop?
> 
> Sincerely,
> 
> Miguel
> 
> 
> -- 
> Miguel NAVASCUÉS, PhD
> 
> Chargé de Recherche (CR2) INRA
> 
> UMR CBGP Centre de Biologie pour la Gestion des Populations
> Institut National de la Recherche Agronomique
> Campus International de Baillarguet, CS 30016
> 34988 Montferrier-sur-Lez (France)
> 
> phone:  +33(0)4.99.62.33.70
> fax:    +33(0)4.99.62.33.45
> e-mail: miguel.navascues AT supagro.inra.fr
> e-mail: m.navascues AT gmail.com
> Skype:  m.navascues
> web:    http://www1.montpellier.inra.fr/cbgp/
> web:    http://sites.google.com/site/navascuesresearch/