We just had a paper published in PLoS Biology on evolution and genetic diversity in avian influenza viruses. Benjamin Roche put in a lot of work for this, on both the sequence analysis side as well as the epidemiological modeling. I only really advised a bit on how to do the evolutionary analyses.
The basic result is rather interesting. If you take hemagglutinin (HA) proteins from different avian influenza viruses you observe that some subtypes are more 'durable' than other subtypes. Basically, they survive longer sitting out on a lab bench. Some average just a few days, and others more than 20. We find more durable subtypes show greater genetic diversity across bird populations than the more fragile subtypes. The rest of the paper is investigating an epidemiological model to see if environmental persistence (on the scale of a few weeks) could result in the observed correlation between diversity and durability.