SUMMARYTo understand the effects of global climate change on reef-building corals, a thorough investigation of their physiological mechanisms of acclimatization is warranted. However, static temperature manipulations may underestimate the thermal complexity of the reefs in which many corals live. For instance, corals of Houbihu, Taiwan, experience changes in temperature of up to 10°C over the course of a day during spring-tide upwelling events. To better understand the phenotypic plasticity of these corals, a laboratory-based experiment was conducted whereby specimens of Seriatopora hystrix from an upwelling reef (Houbihu) and conspecifics from a non-upwelling reef (Houwan) were exposed to both a stable seawater temperature (26°C) regime and a regime characterized by a 6°C fluctuation (23-29°C) over a 12h period for 7days. A suite of physiological and molecular parameters was measured in samples of both treatments, as well as in experimental controls, to determine site of origin (SO) and temperature treatment (TT) responses. Only chlorophyll a (chl a) concentration and growth demonstrated the hypothesized trend of higher levels when exposed to a TT that mimicked SO conditions. In contrast, chl a, maximum dark-adapted quantum yield of photosystem II (F v /F m ), and Symbiodinium ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), photosystem I (psI, subunit III) and phosphoglycolate phosphatase (pgpase) mRNA expression demonstrated significant TT effects. Specifically, levels of these response variables were higher in samples exposed to a variable temperature regime, suggesting that S. hystrix may acclimate to fluctuating temperatures by increasing its capacity for photosynthesis.Supplementary material available online at http://jeb.biologists.org/cgi/content/full/215/23/4183/DC1 Key words: acclimation, coral reef, endosymbiosis, gene expression, photosynthesis, Symbiodinium. susceptible to impact by unexpected environmental variability, and results must always be interpreted conservatively.With this in mind, by conducting a laboratory-based reciprocal transplant (LBRT) study, we took advantage of the thermally unique and dynamic environments of southern Taiwan in order to gain insight into how a common reef-building scleractinian, Seriatopora hystrix Dana 1846, acclimates to changes in seawater temperature. Coral colonies were collected from both Houbihu, a reef within Nanwan Bay that experiences episodic summer upwelling (Putnam et al., 2010), and Houwan, a reef on the western side of the Hengchun Peninsula that does not experience this phenomenon, and specimens from each site were incubated at either stable (26°C) or variable (23-29°C over a 12h period) temperature for 7days. This laboratory-based approach was also utilized in place of a reciprocal transplant in situ because of the multitude of other abiotic parameters (e.g. nutrient and dissolved oxygen levels) that are affected by upwelling events in Taiwan (Chen et al., 2004); while the physiological response to upwelling is indeed a worthy avenue ...