Ancestral tracts

[yang lu]

Dear Ben and team,
I am new to SLiM and have recently completed the first five sections of the SLiM manual. My interest lies in calculating ancestral tract lengths under various adaptive introgression scenarios. I am aware that these models are thoroughly explained in the manual, and I will delve into them soon. But now, I wonder if there are any methods available to ascertain information regarding breakpoints during gene conversion, specifically those points that mark the transition in ancestry source, in other words, the end points of ancestral tracts. If there is relevant code available, where can I find it in the manual? It is crucial for me to know if SLiM can track this ancestral information, and I am deeply grateful to anyone who can offer assistance.
Cheers.

[Ben Haller]

Hi!  I think gene conversion tracts are recorded as part of tree-sequence recording, yes.  You might be the first person to try to use that in a real project, so of course please report if you find problems.  If they are indeed recorded, as I think, then the tree sequence file would have the ancestry information you need, and you'd access it in Python as described in the SLiM manual to some extent, but mostly in the pyslim and tskit manuals since those are the Python packages you'd be using.

Also, I'd recommend that you learn SLiM first by doing the SLiM Workshop, which is available online for free.  Reading the manual is also fine, but... it's pretty long.  :->  Most people find the workshop easier, and then use the manual for reference, and read the specific sections that interest them, I think.

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


yang lu wrote on 3/16/24 10:30 PM:

Dear Ben and team,
I am new to SLiM and have recently completed the first five sections of the SLiM manual. My interest lies in calculating ancestral tract lengths under various adaptive introgression scenarios. I am aware that these models are thoroughly explained in the manual, and I will delve into them soon. But now, I wonder if there are any methods available to ascertain information regarding breakpoints during gene conversion, specifically those points that mark the transition in ancestry source, in other words, the end points of ancestral tracts. If there is relevant code available, where can I find it in the manual? It is crucial for me to know if SLiM can track this ancestral information, and I am deeply grateful to anyone who can offer assistance.
Cheers.

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