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How Can I Simulate A Shrinking Population With A Selective Sweep?

I need to simulate a genomic region with a shrinking effective population size from 100 (past) to 30 (present). The region must include a selective sweep undergoing positive selection. any idea?

genetics simulation
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updated by Adam Adam • written by user • user

2 answers

I don't know of any tool that simulates this, so I guess you will have to implement a Monte Carlo simulation algorithm which includes the features that are believed to result from what you describe:

  • shrinking Ne -> incrinsing genetic drift -> higher rate of random fixation
  • strong positive selection -> higher dN/dS (>1)

Maybe you can use a sequence simulation software for the sequence evolution part (I developed alfacinha if you want to try it out), but you will definitely have to write a part of the implementation yourself.

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written by Leonor Palmeira Leonor Palmeira

SFS_CODE should be able to do this I think.

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written by Adam Adam

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