Consider what will happen to eye color over time in such a fruit fly population. If white eyes start out rare, females will mate preferentially with males with white eyes, so white-eyed males reproduce most and white eyes will become common. Now red eyes have higher fitness and red eyes become common again. A second example of negative frequency dependent selection occurs in host populations that are subject to diseases. Since virtually all species get diseases, this is likely to be a very widespread example of negative frequency dependent selection.
Pathogenic organisms are typically much smaller than their host and have a much shorter life cycle.
Because of their shorter generations, pathogens evolve much faster than do their hosts. Pathogens will have high fitness if they can successfully attack their hosts, and evade their hosts' immune system defenses. We would expect pathogens to evolve through natural selection to be able to attack whatever the most common immune defense in the population is, since this is the environment in which they will most commonly be occurring. Again, consider what happens over time. A rare form of the immune system that can avoid being attacked by some disease will have high fitness and as a result will become common over time, while the common forms, having lower fitness because they are more susceptible to disease, will become rare.