This Part is heavy on broad concept and relatively light on useful technical details. I should probably move this to the end (after I decide what to do with the topics presently found in Part IV) even though that rather bruises the narrative.
I don't actually know much (well, relatively speaking) about computer models for entire populations - but that is certainly computational biology and should absolutely be included here.
The first chapter will explain the differences in sequence that allow organisms to thrive in different environments or on different chemical substrates.
The second chapter will discuss the relationship between the observed complexity of an organism and the complexity of that organisms genome.
The third chapter discusses how whole-genome analysis leads to the conclusion that there existed a single, common ancestor to all known life forms. There will be some discussion of how we come to that conclusion, what we think we known about this ancestral organism. If there's room, I may include a chapter on the Origins of Life on Earth.
Chapter four is self-explanatory.
Chapter five will discuss how whole genome analysis leads us to conclude that Chloroplasts and Mitochondria are descended from eubacterial endosymbionts.
Chapter six is essentially devoted to computational studies of genes related to development - pariticularly in comparison to their homologs found in single celled organisms such as Yeast.
Chapter seven discusses means of measuring effective population sizes - and what the effective population size means in terms of the real diversity of an organismal genome. If the population genetics textbook is ever finished I hope to life most of this from there.
Chapter eight extends the discussion in chapter seven to the special case when a population splits into multiple groups in limited genetic contact.