Understanding the links between long-term biological evolution, the ocean-atmosphere system and plate tectonics is a central goal of Earth science. Although environmental perturbations of many different kinds are known to have affected long-term biological evolution, particularly during major mass extinction events, the relative importance of physical environmental factors versus biological interactions in governing rates of extinction and origination through geological time remains unknown. Here we use macrostratigraphic data from the Atlantic Ocean basin to show that changes in global species diversity and rates of extinction among planktonic foraminifera have been linked to tectonically and climatically forced changes in ocean circulation and chemistry from the Jurassic period to the present. Transient environmental perturbations, such as those that occurred after the asteroid impact at the end of the Cretaceous period approximately 66 million years ago, and the Eocene/Oligocene greenhouse-icehouse transition approximately 34 million years ago, are superimposed on this general long-term relationship. Rates of species origination, by contrast, are not correlated with corresponding macrostratigraphic quantities, indicating that physiochemical changes in the ocean-atmosphere system affect evolution principally by driving the synchronous extinction of lineages that originated owing to more protracted and complex interactions between biological and environmental factors.