Phylogenetic comparative methods are extremely commonly used in evolutionary biology. In this paper, I highlight some of the problems that are frequently encountered in comparative analyses and review how they can be fixed. In broad terms, the problems boil down to a lack of appreciation of the underlying assumptions of comparative methods, as well as problems with implementing methods in a manner akin to more familiar statistical approaches. I highlight that the advent of more flexible computing environments should improve matters and allow researchers greater scope to explore methods and data.
