Origin Count dependent on time when selection starts
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I'm using the -SI with the -oOC option to stimulate selection on standing variation. It seems like the lower I set t as part of the -SI option, the higher the origin count becomes, given that the rest of the options stay constant. I'm having trouble reasoning through why this dependency would occur, as I would think they were independent. Does anyone have any intuition behind this behavior? Thank you!
This is expected behavior. You are starting with standing variation, that is some fixed proportion of the population carries the mutation. At that time all lineages get a different mutation origin of the selected allele since they potently all have different backgrounds. If this is recent you have many lineages, if its a long way in the past you have only a few.
The problem is that -oOC gives an origin count. Not a true "recurrent mutation" count. This is the only way it can be implemented with the -SI option.