Mendel's Accountant and SLiM

Science
(S. Joshua Swamidass) #1

Continuing the discussion from Ratio of Beneficial Mutations to Others:

So, I found a place to download Mendel’s accountant. http://mendelsaccount.sourceforge.net/

MA is a “forward simulator”. In the past, we have pointed people to slim (Messer Lab — SLiM | Messer Lab, Mantha: Genetics for Dummies) another forward simulator.

It would be interesting to see if the results from MA and SLiM correspond on parallel experiments. Perhaps someone (@jordan?) wants to give it a shot.

(Blogging Graduate Student) #2

Here’s somewhere to start for SLiM:

initialize() {
	initializeMutationRate(2.7e-8);
	initializeMutationType("m1", 0.5, "f", 0.0);
	initializeMutationType("m2", 0.5, "e", -0.01);
	initializeMutationType("m3", 0.5, "e", 0.001);
	m2.convertToSubstitution = F;
	m3.convertToSubstitution = F;
	initializeGenomicElementType("g1", c(m1,m2,m3), c(1,1,1));
	initializeGenomicElement(g1, 0, 3000000);
	initializeRecombinationRate(1e-8);
}
1 { sim.addSubpop("p1", 1000); }
{
	meanFitness = mean(p1.cachedFitness(NULL));
	newSize = asInteger(1000 * meanFitness);
	p1.setSubpopulationSize(newSize);
}
10000 late() { sim.outputFull(); }
2 Likes
(Mikkel R.) #3

To give some related context, I remembered that Joe Felsenstein and Michael Lynch responded in a forum post on TheSkepticalZone, to one of Basener and Sanford’s papers on the topic of MA and simulations run using it, here: Does Basener and Sanford’s model of mutation versus selection show that deleterious mutations are unstoppable? | The Skeptical Zone

Bill Basener and John Sanford then responded to that post here:
http://theskepticalzone.com/wp/defending-the-validity-and-significance-of-the-new-theorem-fundamental-theorem-of-natural-selection-with-mutations-part-i-fishers-impact/

And Joe responds to that here:
http://theskepticalzone.com/wp/rejoinder-to-basener-and-sanfords-reply-part-i/

And finally Basener and Sanford again:
http://theskepticalzone.com/wp/defending-the-validity-and-significance-of-the-new-theorem-fundamental-theorem-of-natural-selection-with-mutations-part-i-fishers-impact-2/