Simulated FST value ~1/4 of the expected theoretical value

[Boki Lai]

Hello everyone,

I'm currently using SLiM 5 to simulate population divergence under various migration rates. For each parameter set, I ran 100 replicate simulations and calculated the average FST values using calcFST().  When I'm comparing the resulting FST values to the theoretical expectations based on Wright’s island model. However, I’ve consistently found that the FST values produced by SLiM are approximately one-fourth of the expected values.

For example, with two populations of 10,000 diploid individuals and a symmetric migration rate of 0.001, the expected FST (using the formula FST = 1 / (4Nm + 1)) is ~0.024; however, SLiM consistently reports a value of around 0.006.

I would like to know if this is expected behavior in SLiM, or if I’m missing something important in the manual?


Bless,
Ariel

[Ben Haller]

Hi Ariel,

Step one would be for you to supply your complete SLiM script here, in a form that can be run directly in SLiMgui (i.e., not requiring any command-line arguments to be supplied).  Without that, it is hard to guess what you might be doing wrong.  See https://doi.org/10.1371/journal.pcbi.1010540.

Beyond that, there are several steps you can take to investigate this yourself:

- Output your simulation state into, say, VCF or MS, and use other existing tools to measure the FST in your model, to compare to the value you're getting from SLiM.

- Code up the same simulation in a different evolutionary simulation framework, to see whether you get the same or a different result.

- Look at the code for calcFST(), available in the Eidos terminal with functionSource("calcFST"), to see whether it is doing what you expect or not, as there are different ways of measuring FST; the documentation might also be informative on that count.

If you pursue any of those steps, you might report your findings back here.  But as I said, step one is to show us what you're actually doing by supplying your script.

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


Boki Lai wrote on 8/4/25 5:16 AM:

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[Boki Lai]

hello!
Below is my SLiM script. The first 20,000 generations are intended to allow FST values to stabilize under different migration rates, and after generation 20,000, I simulate alternating bottlenecks. The simulation tests three pairs of populations, each with a different migration rate (5e-4, 1e-4, and 1e-3).  

Bless,

Ariel

Ben Haller 在 2025年8月4日 星期一下午1:55:56 [UTC+8] 的信中寫道：

[Ben Haller]

Hi Ariel,

Took a quick look at your model.  My initial impression is that the runtime of the model doesn't look nearly long enough for it to equilibrate; I would guess that it is still building up genetic diversity, and that the FST values are still rising.  Do you have reason to believe otherwise?

As I wrote before, it would be helpful if you were to measure the FST using a different method, such as a VCF or MS dump from the simulation, to confirm that the calcFST() method is producing reasonable results.  I had a couple of other suggestions too.  Good luck!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University

Boki Lai wrote on 8/4/25 10:04 AM:

To view this discussion visit https://groups.google.com/d/msgid/slim-discuss/6605c805-6e1a-4f63-a9a2-32e49e29d53cn%40googlegroups.com.

[Jose Luis Mijangos]

Hi Ariel,

Attached is a document that might be helpful in getting the correct expected FST value.

Cheers,

Luis 

To view this discussion visit https://groups.google.com/d/msgid/slim-discuss/7d24b66c-1cc2-9779-547e-341f6e67ed3d%40mac.com.

[Boki Lai]

Thank you for the information and advice! It's very helpful. 

Blessings,

Ariel

Jose Luis Mijangos <luis.m...@gmail.com> 於 2025年8月4日 週一 下午6:28寫道：