This abundance and diversity data was obtained from several ~8 hour small-boat cruises done about every other week from August to October. Vertical tow samples were taken from the mid-bay of the Chesapeake from several stations in a transect, corresponding to the mid-line transect sampled by the two week-long cruises (stations M1-M3, cruises 1301/1302). More stations along the same transect were included in the collection of this data set.

The plankton nets used for sampling were 0.5m in diameter and made of either 200µm or 64µm mesh. These were equipped to close with a mechanical messenger trigger and were deployed from the winch arm of the R/V Parker.

A CTD cast was done at each station prior to sampling with the plankton net. Sampling depths were determined based on the location of the pycnocline; the aim was to capture zooplankton below and above the pycnocline. For sampling below the pycnocline, the net was deployed below the pycnocline, towed up to the pycnocline, triggered to close, and returned to the surface. Sampling above the pycnocline was done by standard vertical tow: deploy net to desired depth and winch to the surface.

Once brought on board, the nets were rinsed down with to seawater to collect plankton in the codend. Codends were filtered onto 64µm sieves, then the samples were transferred to glass jars labeled on the lid with the date, time, station, and depth sampled. Sieves with 64µm mesh were selected to catch all life stages of the copepod Acartia tonsa since Acartia tonsa eggs are about 75µm in diameter and all subsequent life stages are larger. Buffered formalin was added to each jar to preserve the sample in a 4% solution.

After returning from the cruises, samples were stored indoors in climate-controlled laboratory space. To process the samples, the contents of the jars were filtered onto 25µm mesh (to avoid loss of organisms), resuspended, and a subsample taken with a stemple pipette was transferred to a counting wheel where it was checked for density and diluted if necessary, the goal being at least 200 individuals of Acartia tonsa present but less than 300.

The sample was then examined for species composition under dissecting microscope with darkfield illumination. All organisms were identified to lowest possible taxonomic level. When species composition analysis was complete, the sample was returned to the original glass jar and returned to storage.

Abundance data were entered into Excel spreadsheets and checked for transcription errors, then imported into MatLab for data analysis.

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