Does .output() report sites that differ from the ancestral sequence but lack polymorphism in the sample?

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Chase W. Nelson

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Nov 2, 2021, 1:25:20 PM11/2/21
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Apologies if I missed this in the manual, but I am wondering if .output() reports sites that (a) differ from the ancestral sequence even if they are (b) not polymorphic in the sample (vector of genomes)?

The context is an explicit-nucleotide experiment with a long burn-in of one subpopulation (p1), after which it is split into two subpopulations (p1 and p2) that evolve independently for very many generations. Some mutations arise and fix (conceptually, albeit not in SLiM) in one subpopulation but not the other. For example, suppose the ancestral sequence contains a C at position 123. In only p1, a C>T change arises and fixes, but the ancestral sequence remains C (which remains fixed in p2). My question is whether position 123 will be included in the .output() of a sample of genomes from p1 even though it's not polymorphic in p1, simply because it differs from the ancestral sequence?

Thanks a ton!
Chase

Chase W. Nelson

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Nov 2, 2021, 1:44:56 PM11/2/21
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Further apologies for the clutter; I have answered my own question and the answer is 'yes'!

Chase
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