Getting extant mutation ages on treesequences

[Daniel Pelletier]

Hi, I'm simulating treesequences with slim, then adding mutations with msprime (example code below). For a sample of chromosomes, I'd like to get the ages of extant mutations, but I'm not sure how to separate the extant mutations (most recent mutation at a site for a chromosome) from ancestral mutations that have been replaced. The mutations table includes all of these with no distinction.

Ex.:

#simulating a simple tree sequence with msprime, 1-locus chromosome, ending in 5 diploid individuals

ats=msprime.sim_ancestry(5, sequence_length=1)

#binary (0 or 1) mutations, with state-dependence so no silent mutations

mts=msprime.sim_mutations(ats, rate=0.5, model=msprime.BinaryMutationModel(state_independent=False))

This gives me a treesequence with 8 mutations. At present time (generation 0, or 'present'), some of those mutations have gone extinct (fully replaced by other mutations), and some exist on one or a few chromosomes. If I want to calculate the average age of mutations:
np.mean(mts.tables.mutations.time)

The ages of all mutations that have happened on the tree are included, rather than just those that are the most recent mutation for at least 1 sample chromosome.

I'd really appreciate advice on how to get the ages (or just mean age) of extant mutations! Hopefully I'm not just missing an obvious function.

Thanks,

Daniel

[Ben Haller]

Hi Daniel!  Someone on this list might know the answer (I don't), but it seems like a question for the tskit/msprime folks; as your example code shows, the question arises even for a purely msprime simulation, and it looks like you're not even using msprime.SLiMMutationModel.  So I'd recommend that you ask over there.  Good luck!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University

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SLiM forward genetic simulation: http://messerlab.org/slim/
Before posting, please read http://benhaller.com/slim/bugs_and_questions.html
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[Daniel Pelletier]

Ah yes you're right, I hadn't thought of that- I posted the question to the tskit github discussion page! Thanks!