I'm not a programmer, but I want to mention the fact that all discussion here is entirely focused on the influences of natural selection and mutation, which are only parts of the whole system of evolution (especially with the small population sizes present at the start of the microbe stage)-- one of the most important being genetic drift. This is something very important in small populations, but would require a very complex gene model to implement naturally, which is really unnecessary. Fortunately, plenty of mathematical formulas exist that can efficiently calculate the effects of genetic drift. As population sizes become larger, the effect becomes basically negligible and can be ignored in calculations.
Gene flow isn't really something important for now at least, so it can probably be ignored.
A huge thing to consider is horizontal gene transfer in bacteria. Most of you probably know about this already, and it has a very significant impact on bacterial population genetics. Horizontal gene transfer does occur in other organisms, but not to an extent that I think it would really need to be modeled.
With genetic drift, the one requirement is sexual reproduction, which isn't in the game yet. Is this feature planned to be developed soon? It's obviously an important mechanic for evolution and of course necessary for the majority of multi-cellular organisms.