Ancient Adaptations and Constraints

This chapter focuses on how to study ancient adaptations that occurred hundreds, even billions, of years ago. This might seem impossible given that the organisms are extinct (even if their descendants are alive) and their habitats destroyed (or at the very least grossly modified). Yet it can and has been done. Molecular phylogenetics is used not only to infer historical relationships but also to infer the sequences of common ancestors. The ancestral genes can be “resurrected,” the ancestral protein phenotypes studied, and the impact of ancient mutations on their functions quantified. Knowledge of structure and function allow alternative phenotypes to be engineered to reveal the selective forces that have constrained evolution, sometimes across billions of years of evolution. Of the many studies done, we focus on two: the evolution of spectral tuning in animal visual pigments and the evolution of coenzyme use in a family of enzymes.