Coral reef ecosystems are particularly sensitive to climate change. Since the 1980s, coral reef bleaching, caused by unusually high sea temperatures, has had devastating and widespread effects worldwide (Baker et al. 2008 and references therein). Environmental extremes, such as high or low temperatures or high irradiance, trigger a cacade of physiological and biochemical changes that lead to eventual cellular damage in the dinoflagellate symbionts and/or their coral hosts, and can lead to the expulsion of symbionts and the eventual breakdown of the symbiosis (Lesser 2004, 2006; Baker et al. 2008 and references therein). The loss of zooxanthellae (and/or a reduction in their pigment concentrations) as a result of this process is known as “bleaching”. In extreme cases, bleaching leads to the visible paling of the host organism, as the yellow-brown pigmentation of the symbionts is lost (Baker et al. 2008).

These episodes of mass coral bleaching and mortality have raised concerns about the long-term survival of coral reef ecosystems. There is increasing evidence that under "normal" conditions dinoflagellate communities in coral reefs are in flux, with species densities and species composition shifting in response to numerous factors including changes in environmental conditions, such as warming of the seas. Some researchers are hopeful that mass bleaching events, which involve large-scale losses of endosymbiotic zooxanthellae, are simply an extreme example of a "normal" transition in the dinoflagellate community composition and that given time some reef recovery is possible (Baker 2003 and references therein). (Some researchers have even argued that bleaching is an adaptive response to extreme environmental changes that allows corals to rapidly change their dinoflagellate associates to species better suited to the new environmental conditions.) Most ecological communities are quite resilient, but as is is often the case with extreme environmental perturbations, the question of whether long-term persistence of coral reefs is possible turns largely on questions of scale: Is the change too rapid for corals and their dinoflagellate associates to adapt? Might persistence be possible on a large geographic scale even if local extinctions are inevitable? If recovery is possible, how long might it take and how similar would the recovered reef systems be to those that preceded them?