The first two sections of the chapter contain background information on evolutionary biology, with an emphasis on the accumulation of mutations in species, and a description of abstract mathematical models of mutation accumulation.
The main body of the chapter is on how the abstract models are implemented in a computer program. For the most part this simulator is an ``ab initio'' simulation, i.e. it simulates basic events in the underlying biological processes with little or no mathematical abstraction. The three crucial optimizations that allow the system to simulate larger populations (up to several hundred individuals) are described in this section; each of them takes advantage of properties of the underlying mathematical models.
Several course projects of varying sizes can be based on of this chapter. At various points in the text there are exercises and descriptions of computational projects, including: