X chromosomes in SLiM 5

[Filip Ruzicka]

Hi,

I just wanted to clarify the default behaviour with recombination and sex chromosomes in SLiM 5, when using options initializeChromosome(..., type="X") and initializeRecombinationRate(...). 

On the one hand, initializeChromosome() with "type="X" assumes haploidy in males ("an X chromosome that is diploid (XX) in females, haploid (X–) in males." per the manual), which I assume means no recombination in males. On the other hand, initializeRecombinationRate() without using the sex option assumes recombination in both sexes ("the supplied recombination rate map will be used for both sexes", per the manual). 

My guess is that the default initializeChromosome("type=X") behaviour "overrides" the default initializeRecombinationRate() behaviour? And there is in fact no recombination on an X chromosome in males? I just wanted to double-check if this is true. Below I paste my initialisation set-up. 

Thanks!

Filip

initialize() {
if (exists("slimgui")){
defineConstant("LO",999999); // number of bp
defineConstant("N",500); // population size of individuals
defineConstant("ST",N*10); // start time at which beneficial mutation is introduced
defineConstant("END",N*110); // end simulation 
defineConstant("MU",1e-8); // mutation rate
defineConstant("R",1e-8); // recombination rate
defineConstant("HB",0.5); // dominance coefficient for the beneficial mutation
defineConstant("SB",0.01); // selection coefficient for the beneficial mutation
defineConstant("SD",-0.02); // selection coefficient for the deleterious mutation
defineConstant("C",0.05); // fraction of constrained sites
defineConstant("HD",0.5); // dominance coefficient for the deleterious mutation
defineConstant("R_RATIO",1); // X/A ratio of recombination rates
defineConstant("MU_RATIO",1); // X/A ratio of mutation rates
}
initializeSex();

// m1 mutation type: neutral
initializeMutationType("m1", 0.5, "f", 0.0);
// m2 mutation type: deleterious
initializeMutationType("m2", HD, "f", SD);

// g1 genomic element type containing neutral and deleterious alleles
initializeGenomicElementType("g1", c(m1,m2), c(1-C,C));
// initialise an X chromosome
initializeChromosome(1, LO, type="X", symbol="X");
// initialise genomic element
initializeGenomicElement(g1);
// initialise mutation rate
initializeMutationRate(MU*MU_RATIO);
// initialise recombination rate
initializeRecombinationRate(R*R_RATIO);

// m3 mutation type: beneficial
initializeMutationType("m3", HB, "f", SB);

}

[Peter Ralph]

Hello, Filip - yes, this is correct. (There's no other chromosome for it to recombine with!)

Happy slimulating,

  Peter

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From: slim-d...@googlegroups.com <slim-d...@googlegroups.com> on behalf of Filip Ruzicka <ruzick...@gmail.com>
Sent: Thursday, March 26, 2026 2:09 AM
To: slim-discuss <slim-d...@googlegroups.com>
Subject: X chromosomes in SLiM 5

 

Hi, I just wanted to clarify the default behaviour with recombination and sex chromosomes in SLiM 5, when using options initializeChromosome(. . . , type="X") and initializeRecombinationRate(. . . ). On the one hand, initializeChromosome() with "type="X"

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