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 loci and also a complex case with two loci using epistatic effects. The epistatic effect will have a mutation on an SNP. This is required to confer advantage and another mutation on another SNP that adds up to the previous one (but does nothing on its own); this was inspired by the very real case of malaria resistance to the sulfadoxine/pyrimethamine drug, which always requires a mutation on the DHFR gene, which can be enhanced with a mutation on the DHPS gene; if you are interested in knowing more, refer to the Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum article from Vinayak et al on PLoS Pathogens at http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000830.

Getting ready

Read the previous recipe (Introducing forward-time simulations) as it will introduce the basic programming framework. If...