The results presented in this chapter give an overview of the features of the simulation while illustrating its operation. Starting with two very simple examples, the simulation of species and subsequent reconstruction from fossils and character information is shown. Next, with migration included, an example is given showing tracing of ancestry, and the three-dimensional display of intercontinental migrations. This example is also used to illustrate the automatic clade generation algorithm. The more advanced features of including non-linear mutation rates, non-hereditary characters and interbreeding are shown in the chapter's final examples.

In the discussion of the simulation results below and in subsequent chapters, the following abbreviations are employed:

CA, true most recent common ancestor;

WCA, most recent common ancestor according to the Wagner reconstruction;

FCA, most recent fossil common ancestor;

RCA, most recent fossil common ancestor according to the fossil reconstruction.

Note that ‘most recent’ is always implied by the abbreviation, although ‘MR’ is not added in each case.

A simple example

The two examples displayed in this section have been kept simple deliberately, in order to illustrate more clearly the fundamental aspects of the simulation, without the complicating effects of the many more advanced features available. Both simulations were run with the same parameters, so they also serve to emphasise the fact that the degree of variation between any two runs can be quite substantial.