An empirical global core-top calibration that relates the alkenone unsaturation index U 37 K ′ to mean annual SST (maSST) is statistically the same as that defined for a subarctic Pacific strain of Emiliania huxleyi (CCMP1742) grown exponentially in batch culture under isothermal conditions. Although both equations have been applied widely for paleoSST reconstruction, uncertainty still stems from two key ecological factors: variability in the details of biosynthesis among genetically distinct alkenone-producing strains, and impacts of non-thermal physiological growth factors on U 37 K ′ . New batch culture experiments with CCMP1742 here reveal that U 37 K ′ diverge systematically from the core-top calibration in response to nutrient depletion and light deprivation, two physiological stresses experienced by phytoplankton populations in the real ocean. Other aspects of alkenone/alkenoate composition also respond to these stresses and may serve as signatures of such effects, providing an opportunity to detect, understand, and potentially correct for such impacts on the geologic record. A test case documents that sediments from the Southeast Pacific display the alkenone/alkenoate compositional signature characteristic of cells physiologically stressed by light deprivation. Such an observation could be explained if marine snow provided a major vector of sedimentation for these biomarkers. Late Pleistocene U 37 K ′ records in the Southeast Pacific yield plausible paleotemperature histories of ice-age cooling, but ice-age alkenone/alkenoate signatures fall outside the range of modern calibration samples of similar U 37 K ′ . They better match core-top samples deposited beneath waters characterized by much cooler maSST, suggesting key features of ice-age ecology for alkenone-producing haptophytes were different from today, and that the U 37 K ′ index taken alone may misgauge the total range of ice-age cooling at these locations. Analysis of the full spectrum of alkenone/alkenoate compositions preserved in sediments opens up a new opportunity that may improve the accuracy of paleotemperature estimates based on simple U 37 K ′ analysis and help resolve longstanding disagreements between various paleotemperature reconstruction methods.