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Resource-based physiology of the eight important planktonic diatom species in the large lakes of the Yellowstone region can be used to explain their relative abundances and seasonal changes. The diatoms are ranked along resource ratio gradients according to their relative abilities to grow under limitation by Si, N, P, and light. Hypotheses based on resource physiology can be integrated with observations on seasonal changes in diatom assemblages to explain the present distributions of diatoms and to test the causal factors proposed to explain diatom distributions over the Holocene. Knowledge of the limnology of these lakes and process-oriented physiology provide the basis for a more detailed interpretation of the paleorecord and a firmer basis for landscape-level transfer functions for fine-scale climate reconstruction.