Tracking Introgressed Variants

[Autumn Allemon]

Hi Everyone, 

I have been having trouble figuring out how to speed up my simulations when I need introgressed variants to remain neutral for about a hundred generations before being selected for in a subpopulation. 

I have tried scaling my model, but that ends up in a loop, with the variant being lost before selection can take place, most likely due to drift. 

I don't know if there is a way to keep track of the regions of introgressed variants and then pull them out to apply the selection coefficient to only one of them. 

27237 late() {

cat(" -- P2-P3 Introgression -- \n");

p3.setMigrationRates(c(p2, p1), c(intro_rate, 15.24422112e-5));

p1.setMigrationRates(c(p2, p3), c(0, 0));

} 

27333 early() {

sim.addSubpopSplit("p5", asInteger(round(312.8 * POP_SCALE)), p4);

cat("p5 is now in existence " + sim.cycle + "\n");

}

Is there a way to extract any of the introgressed variants that exist in my p5 from this point on, before applying selection to them? 

Can tree sequencing recording be used?

Maybe tagging all the variants unique to p2? 

Or is my best option to not scale and use the full model? 

(I am using SLiM 5 btw)

All the best,

Autumn Allemon

[Ben Haller]

Hi Autumn!

Each mutation has a subpopID property that provides the ID of the subpopulation in which the mutation arose, so probably the easiest way is to check mutations in p5 for a subpopID other than 5, and those will be introgressed.

I'm not sure what you're asking with respect to the scaling, but it sounds like maybe you don't need to do that if you can select an introgressed mutation, so I'll leave that alone.  :->

By the way, you could also use a mutation() callback to tag relevant mutations as you suggest, I think, but since subpopID already has the information you need, probably that is unnecessary.

Good luck and happy modeling!  Feel free to post again if this is unclear.  :->

Cheers,
-B.

--
SLiM forward genetic simulation: http://messerlab.org/slim/
---
You received this message because you are subscribed to the Google Groups "slim-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to slim-discuss...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/slim-discuss/7b0ef5c1-872b-45c1-a158-a11ee32e0809n%40googlegroups.com.