I’m sure you’ ve heard, but in case not: Not one, not two, not even three, but TEN new genomes were just released, bringing the total for fruit fly genomes to twelve species.
These fruit flies diverged several tens of millions of years ago, which in the large picture, is kinda recent. This will allow a useful meso-time scale comparative study across diverging genomes trapped in somewhat less divergent phenotypes.
We are now starting to see patterning in the fundamental nature of selection For instance, it is now possible to begin to estimate the relative rate of genetic change at the base-pair level that is accounted for by different kinds of selective forces, such as sexual selection, selection on the immune system, and so on, and to place this in the broader context of neutral process.
A good place to start reading about this is here, at Nature News.