Bioinformatics with Python Cookbook - Second Edition

Simulating selection

We will now perform an example of simulating selection with simuPOP. We will perform a simple case with dominant mutation on a single locus, along with a complex case with two loci using epistatic effects. The epistatic effect will have a required mutation on a main SNP. While this mutation is required to confer advantage, another mutation on another SNP adds up to the previous one (but does nothing on its own); this was inspired by the very real case of malarial resistance to the Sulfadoxine/Pyrimethamine drug, which always requires a mutation on the Dihydrofolate Reductase (DHFR) gene, which can be enhanced with a mutation on the Deoxyhypusine Synthase (DHPS) gene. If you are interested in finding out more, refer to ...