Added marker mutations are MULTIALLELIC and introgressed mutations have different MID

[Aubrey Baolong Pham]

Hi Ben,

I am trying to simulate Human and Archaic introgression, and using neutral marker mutations to detect the archaic introgression. The intention here is to be able to find what part of the human genome came from archaic ancestry and what came from human ancestry. 

I noticed in the SLiM output, that the mutations I'm manually added are 'MULTIALLELIC' and have different MID's. I'm not sure if this is the expected behavior or if there is a way to prevent this? I want to be able to add neutral mutations that are not 'MULTIALLEIC.'

Another strange behavior I have encountered is the marker mutations that introgressed into the Human population have different MID's compared to the Archaic individual I sampled from my population. For example, a marker mutation I added has MID 949383459 and 973788339 in my Archaic individual and 915586701 in my human file. I was wondering what could be causing the MID's to not match?

Below are screenshots of the code I'm using to add neutral mutations and an example of what I'm talking about. Also let me know if further details are needed.

Thanks,

Aubrey

[Ben Haller]

Hi Aubrey,

Sorry for the slow reply; I've been rather swamped lately.  :-O

My initial guess is that you're being bitten by the fact that SLiM tracks mutational lineages (identity by descent) not mutational states (identity by state).  Because of this, if you do something like:

haplosome1.addNewMutation(m1, 0.0, 1468);
haplosome2.addNewMutation(m1, 0.0, 1468);
haplosome3.addNewMutation(m1, 0.0, 1468);

to add a mutation at position 1468 in three different haplosomes, you will NOT get the same mutation in all three haplosomes; you will get three different mutation objects that will be considered different mutations – differebt "mutational lineages" – even though they are "identical by state" – identical mutation types, selection coefficients, and positions.  Position 1468 will therefore be multiallelic; it will have those three mutations all segregating at it (in addition to the "empty state" when haplosomes don't contain any of those three mutations).

If you want to get a single mutation object across all of those haplosomes, you need to be careful to add just one new mutation.  You might do that with a pattern like:

c(h1, h2, h3).addNewMutation(m1, 0.0, 1468);

to add the mutation to all of the target haplosomes at the some time, or:

mut = h1.addNewMutation(m1, 0.0, 1468);
h2.addMutations(mut);
h3.addMutations(mut);

to add the existing mutation object to h2 and h3 after you create it in h1.  The same kind of thing can happen if you load the same mutations from VCF files in multiple passes (archaic vs. modern humans being loaded separately, for example); a given mutation needs to be loaded from a single VCF file that describes all of the places where it occurs.

For further discussion of these sorts of considerations, please see section 1.5 of the SLiM manual, especially 1.5.2 and 1.5.3.

If this is not the problem you're encountering, please post again with a complete but minimal example that demonstrates the problem you're encountering.  That minimal example should run in SLiMgui (i.e., with no command-line arguments needed), and any input files needed should be supplied.  Good luck, and happy modeling!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University

--
SLiM forward genetic simulation: http://messerlab.org/slim/
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