Genomic element type without mutation + tree sequence recording?

[Jiseon Min]

Hi,

I am simulating a population with non-neutral sites flanked by neutral sites. Is there a way to make those arms mutation-free so that I can overlay neutral mutations on the tree sequence after the simulation? The simulation runs as it is, but I was wondering if I can do something about the warning about neutral mutations. Thanks in advance!

[Peter Ralph]

Hi, Jiseon! Well, here's an example of a chromosome with only selected mutations happening in a 10kb chunk in the middle:

initialize() {

      initializeMutationRate(c(0, 1e-7, 0), ends=c(50000, 60000, 100000));

      initializeMutationType("m1", 0.5, "f", 0.1);

      initializeGenomicElementType("g1", m1, 1.0);

      initializeGenomicElement(g1, 50000, 60000);

      initializeRecombinationRate(1e-8);

}

But, maybe I didn't understand the question? If not, a short, simplified script might help?

-peter

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From: slim-d...@googlegroups.com <slim-d...@googlegroups.com> on behalf of Jiseon Min <minjis...@gmail.com>
Sent: Friday, May 9, 2025 7:01 AM
To: slim-discuss <slim-d...@googlegroups.com>
Subject: Genomic element type without mutation + tree sequence recording?

 

Hi,

I am simulating a population with non-neutral sites flanked by neutral sites. Is there a way to make those arms mutation-free so that I can overlay neutral mutations on the tree sequence after the simulation? The simulation runs as it is, but I was wondering if I can do something about the warning about neutral mutations. Thanks in advance!

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