Climate change is now the leading cause of coral-reef degradation and is altering the adaptive landscape of coral populations 1,2 . Increasing sea temperatures and declining carbonate saturation states are inhibiting short-term rates of coral calcification, carbonate precipitation and submarine cementation [3][4][5] . A critical challenge to coral-reef conservation is understanding the mechanisms by which environmental perturbations scale up to influence long-term rates of reef-framework construction and ecosystem function 6,7 . Here we reconstruct climatic and oceanographic variability using corals sampled from a 6,750-year core from Pacific Panamá. Simultaneous reconstructions of coral palaeophysiology and reef accretion allowed us to identify the climatic and biotic thresholds associated with a 2,500-year hiatus in vertical accretion beginning ∼4,100 years ago 8 . Stronger upwelling, cooler sea temperatures and greater precipitation-indicators of La Niña-like conditions-were closely associated with abrupt reef shutdown. The physiological condition of the corals deteriorated at the onset of the hiatus, corroborating theoretical predictions that the tipping points of radical ecosystem transitions should be manifested sublethally in the biotic constituents 9 . Future climate change could cause similar threshold behaviours, leading to another shutdown in reef development in the tropical eastern Pacific.Climatic and oceanographic variability have played a dominant role in the development of reefs throughout the Phanerozoic eon 10 , and the recent past is no exception. In Panamá and several other locations in the Pacific, coral reefs stopped accreting vertically for 2,500 years, beginning ∼4,100 cal yr BP (ref. 8; calibrated 14 C calendar years before 1950; Fig. 1a). Correlations with regional palaeoclimate proxies suggest that enhanced variability of the El Niño/Southern Oscillation (ENSO) was the ultimate cause of reef shutdown in the tropical eastern Pacific 8 (TEP). Climatic shifts at that time led to environmental and cultural impacts on a global scale 11,12 .In this study we investigated the long-term impacts of environmental variability on coral physiology and reef development in the TEP to ascertain the climatic, oceanographic and biotic controls on ecosystem state in the past. We quantified the range of environmental conditions that corals experienced during the past ∼6,750 years to determine whether significant changes in climate or oceanography were associated with changes in coral physiology or reef accretion. We then evaluated the environmental and physiological thresholds that characterized the catastrophic phase shift to the hiatus.In Pacific Panamá, El Niño-like periods are characterized by a warm, dry climate and a reduction in seasonal upwelling. Those conditions are reversed during La Niña-like periods (Supplementary Discussion and Supplementary Fig. 1). Contemporary environmental variability is high at Contadora Island, a site in Pacific Panamá that is exposed to intense seasonal upwelling and ...