In my work on flu I've been trying to build joint evolutionary and epidemiological models, where natural selection emerges dynamically from influenza strains competing for susceptible hosts. In speaking on this, I found it useful to broaden the context a bit. Here, you can think very generally of genetic / ecological variants competing with one another in some sort of ecological space. Variants that are close together in this space strongly compete, while more distant variants exist more-or-less independently.
This is exactly the model that Darwin used to illustrate the Origin of Species. Here, I've described this idea in a bit more detail and built a visualization of the model.