Calculate Ne

[Prothama Manna]

Hello Ben,

I hope you’re doing well. I’m simulating a population bottleneck followed by expansion in SLiM and need to estimate its effective population size (Nₑ) over time. I first tried using SLiM’s calcHeterozygosity() function  but since it assumes a constant population size and weights all segregating sites equally, it misestimates both ancestral and bottleneck Nₑ.

Do you have any recommendation for a more suitable approach for non-equilibrium demography?

Best,

Pro

[Ben Haller]

Hi Prothama!

Section 9.11 of the manual has a little discussion of effective population size estimation.  Beyond that, it's a very large and complex subject; I'd recommend delving into the literature by Robin Waples, who has written quite a bit about the topic.  For example, here is a very recent paper: https://doi.org/10.1111/mec.17670.

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


Prothama Manna wrote on 5/21/25 12:24 AM:

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SLiM forward genetic simulation: http://messerlab.org/slim/
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