Hi Guillaume,
You did not specify how do you calculate expected Fis. I guess you are
using Fis=s/(2-s). That is the expected value for an equilibrium model.
None of the models you present seem to to be in equilibrium (with
recapitation or forward period without selfing). Try simulating 20*N
generation in forward with the desired selfing rate from the beginning,
I think this should get you observed Fis values around to the expectation.
Best,
Miguel
On 23/11/2021 16:31, Guillaume Lan-Fong wrote:
> Hello everyone,
>
> I would like to ask for some help regarding an issue I have with some
> simulations and I don't seem to understand what is the problem. But
> first a little question before the "main issue".
>
> *- Adding a set number of SNPs afterwards -*
>
> First - and in order to not create a second thread for a kind of related
> question - I have a little question : would it be possible to create a
> SLiM simulation running forward, output the trees, sample some
> individuals and add mutations afterwards on them and their corresponding
> trees *but with a set number S of SNP across the genomes and the trees*
> i.e, a population of Ne individuals simulated forward during g
> generations of selfing, n individuals are sampled and we want the
> corresponding sequences and genealogies (in regard to the branches
> length) of these n individuals to *only contain a number S of SNP*.
>
> *- Underestimate Fis - *
>
> *Overall context* : I'm trying to simulate a quite simple population
> with selfing for some generations, sample a few individuals and compute
> the corresponding Fis.
>
> Here are the set of _parameters used for the simulations_ :
>
> * Ne = 500
> * µ = [1e-5, 1e-6, 1e-7, 1e-8]
> * L = 100 kb
> * r = 1e-6
> * s = [0, 0.1, 0.2, 0.3, ... , 0.9, 1.0]
>
>
> *1) SLiM + recap*
> I first run SLiM simulations for a 2 000 generations, save the .trees
> corresponding files, recap and add mutations afterward with pyslim.
> Then, I use a python script to compute the Fis - so the pipeline is
> something like this : _SLiM -> recap -> mutate -> Fis_.
>
> However, *the observed Fis were usually a bit lower than expected,
> especially for high value of Fis*.
>
> In order to see if something might have gone wrong with the recapitation
> or the "mutation" process, I then run some fully forward simulations.
> *
> *
> *2) Fully forward SLiM*
>
> This time, I first let the simulation run for 10.Ne generations without
> selfing before setting s to the desired value and I let the simulation
> run for about 2000 generations.
> I then output in ms format a sample and compute the corresponding Fis -
> so this time, we've got something like this : _SLiM -> msOutput -> Fis_.
>
> The results seems to be a bit better with this approach (which bugs me -
> things should be more or less the same no matter what method I'm using)
> but the *Fis are still too low compared to the expected value*.
>
> Here's the *SLiM script* :
> *Here's a plot of the results* :
>
> Fis_too_low.png
>
> /x = expected Fis, y = simulated Fis. Different colors show different
> value of µ. Dots are the average value of Fis. The red line is the
> "perfect" simulated = expected case./
>
> So it seems that a lower mutation rate would be better, but my issue is
> more that I don't understand why I have an underestimation of Fis ? It
> might be an issue with my SLiM script itself that cause this, but having
> the same results with 2 different approaches seems a bit strange to me.
>
> Once again, thanks in advance for your time and your answers,
>
> G. L-F
>
> --
> SLiM forward genetic simulation:
http://messerlab.org/slim/
> <
http://messerlab.org/slim/>
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--
Miguel de Navascués
UMR CBGP, INRAE
Centre de Biologie pour la Gestion des Populations
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