Alvin Plantinga lays out his famous and important argument that, contrary to what most people would think, naturalism (the belief that nature is all there is) is actually incompatible with evolution. Unfortunately, the argument may be a little hard to follow for philosophical novices, so here's a quick and doubtless inadequate summary:
If our cognitive faculties (our reason) are the product of evolution then they have arisen because they confer fitness upon us in the struggle for survival.
However, survival advantage is irrelevant to the pursuit of truth. To see this, imagine there's a genetic propensity in some people to believe that one's reward in the afterlife is directly proportional to the number of offspring one has. Such a belief would have very high selection value since those who held the belief would tend to produce more offspring than those who didn't, but the belief has nothing to do with the truth. Thus our cognitive faculties would over time tend to produce beliefs which promote survival but which have only a coincidental relation to the truth.
Thus we would have no good reason, given the evolution of our cognitive faculties, to think any of the beliefs produced by those faculties, particularly our metaphysical beliefs, to be true. But naturalism is a metaphysical belief produced by our cognitive faculties. Therefore, if evolution is true we have no good reason to believe that naturalism is true. They're mutually exclusive.
Indeed, Plantinga argues that the probability of naturalism being true is either low or unknowable (inscrutable) and therefore we lack epistemic justification for believing it.
Those intrepid enough to wade through the entire argument will find it, and a criticism of it, at the link.RLC