Phytoplankton biomass was estimated using chlorophyll a by collecting ~125 ml of lake water in West Thumb of Yellowstone Lake (fig. S1) from 5-m depth in 2004, 1.2 liters of water from 5-, 10-, and 15-m depths in 2005 (18), and 1.2 liters of water from 5- and 15-m depths during 2016–2017. Chlorophyll a was collected on 7 dates (n = 56), 3 dates (n = 36), 11 dates (n = 88), and 9 dates (n = 72) in 2004, 2005, 2016, and 2017, respectively. To concentrate phytoplankton, water was filtered through 25-mm PALL type A/E glass fiber filters. Chlorophyll a was extracted by incubating filters in 90% ethanol buffered with MgCO3 overnight, and concentration was measured using the acid method with a pheopigment correction (58) on a fluorometer (Turner Designs 700, Sunnyvale, CA). A secondary solid standard was calibrated using a primary chlorophyll a commercial standard of Anacystis nidulans (Sigma-Aldrich). Chlorophyll a before lake trout invasion was measured to 20-m depth in West Thumb during 1972 by acetone extraction and a spectrophotometer (19). Differences in extraction methods were corrected for (58).

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