Neutral modifiers in SLiM

[Dan Kehila]

Hi there

Thanks for accepting me into the group. And big thanks for developing such a versatile platform. It's obvious many people found how to use SLiM to ask their specific questions. 

I'm wondering if anyone used SLiM for modelling a neutral modifier allele, e.g., of recombination rate or mutational variance. I couldn't find anything in the manual on a cursory look.

My end goal is quite complex and I'm not sure if SLiM is the right platform, but I want to see the approaches that other people may have taken ,in hopes that one of them can point me in the direction I want to go.

Thanks for any such pointers or advice

Best

Dan

[Ben Haller]

Hi Dan!

I did a google scholar search on ""slim" modifier mutation affecting recombination rate" (quotes around "slim" so that that search term is required in the result), and do see some hits that look relevant.  I don't know those papers well, so I can't speak to them; but maybe some people on the list know more.  :->

I don't think there's anything in the manual about it, no; but the building blocks are there.  I think you could make a nonWF model, so that you have control over the generation of each offspring, and set the desired mutation/recombination rate just before calling addCrossed() to generate each individual.  A "big bang" reproduction strategy (see section 15.3) might be useful for a simple, clean, efficient model design.  If you want to have each gamete get generated with its own mutation/recombination rate, rather than choosing rates per diploid individual, you might want to model "alternation of generations", as in section 16.4 of the manual, so that you can control the mutation/recombination rate used in each meiosis event.  You could model a simple Mendelian modifier, such that the presence/absence of one specific mutation gives you a high/low rate; or you could model the modifier trait as a quantitative trait, as shown in chapter 13.

What you're proposing is a fairly advanced model; so rather than jumping right into the deep end of the pool, I'd recommend that you take the SLiM Workshop to learn more about SLiM first.  It's available for free online, including recorded lectures and PDF worksheets.  If you spend a couple of days to do the workshop, you'll end up with a much better idea of whether SLiM is the tool you want to use or not.  I think it probably is, but I might be biased.  :->  Happy modeling!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


Dan Kehila wrote on 7/18/25 8:53 AM:

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