Methods for Lake Erie zooplankton Diel Zooplankton Tows: Diel samples of zooplankton were pumped through a 64 µm mesh net. The diel samples were collected every four hours over a 24 hour period using a Sandpiper, Warren Rupp diaphragm pump at a flow rate of 2.0 liters per second. Water was pumped to 1-m above the bottom. The water column was divided into epilimnion, metalimnion and hypolimnion based on the CTD profiles of water temperature and DO concentration. If the epilimnion was very deep, it was divided into an upper and lower epilimnion during certain times of the year. A fully mixed water column was divided in half. Water was pumped at 1-m intervals in each zone for a period of time to fully sample the zone and equal approximately one cubic meter of water. Detailed methods are described in Vanderploeg et al. (2009b). Transect Zooplankton Tows: Zooplankton were collected with a 0.5 meter diameter, 64 µm mesh net. The net was vertically towed through the water column at a speed of 0.5 m s-1 from 1 to 2 meters above the bottom to the surface. The nets were washed thoroughly, but gently and the contents were carefully transferred to a sample bottle, narcotized with Alka-Seltzer, and preserved with the addition of sugar formaldehyde to form a 2% solution (Haney & Hall, 1973). Preparation for counting and identifying zooplankton required measurement of the sample volume, gentle mixing of the sample, and removal of an aliquot with a Hensen-Stempel pipette. The aliquot was held in a 100 µm meshed bottom cup and rinsed with tap water to remove the preservative and finally it was poured into a circular counting dish. A minimum 550 zooplankton were identified for each sample. To count large predatory cladocerans, such as Bythotrephes, the whole sample was rinsed through a 600 µm mesh sieve, and all individuals were counted. Taxonomic groups were identified and categorized in the following manner. For copepods, both cyclopoid and calanoid nauplii were combined, copepodites were identified to genus and adult copepods were identified to species. The cladocerans, both herbivorous and predatory, were identified to species. To determine zooplankton biomasses, length measurements were made on a subsample of taxa (10 adult copepods and 25 copepodites or cladocerans) that were over 10% of the total density using Image Pro Plus, image analysis software (Media Cybernetics, Silver Spring, MD). In the case of large predatory cladocerans, all individuals were measured or up to 100 individuals if more than that were present. Biomasses were determined using published length-weight regressions (Culver et al. 1985, Makarewicz and Jones 1990). For zooplankton taxa that comprised less than 10% of the total density, a default weight from the literature was used to determine biomass for all taxa except Bythotrephes (Hawkins and Evans 1979).