Individual‐Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary: II. Alternative Baselines and Good versus Bad Years

We used a previously described individual‐based population model to further explore the population dynamics of Delta Smelt Hypomesus transpacificus in the upper San Francisco Estuary. We formulated four alternative baseline configurations of the model and used a factorial design to systematically isolate the effects of factors that determined a good versus bad year. The alternative baseline conditions were obtained by substituting different assumptions about growth, maturity, and mortality into the original baseline configuration. In the simulation experiment, we varied five factors by setting each value to its 1998 (best year) or 2001 (worst year) value: salinity, temperature, zooplankton densities, hydrodynamics, and eggs per age‐1 individual at spawning. Although some of the alternative baselines resulted in lower January abundances, estimated finite population growth rates were very similar for all versions. The simulation experiment showed that juvenile growth in the winter prior to spawning (i.e., eggs per age‐1 individual) was the most important single factor in making 2001 a bad year, although no single factor alone was sufficient to fully account for the poor conditions in 2001 relative to 1998. Temperature played an important secondary role, and hydrodynamics played a more minor role. The results of the simulation experiment were robust, as similar results were obtained under the four alternative baselines. We compare our results with previous modeling and statistical analyses of the long‐term monitoring data; we also discuss some implications of our results for Delta Smelt management and suggest future directions for analyses.