Individual‐Based Modeling of Delta Smelt Population Dynamics in the Upper San Francisco Estuary III. Effects of Entrainment Mortality and Changes in Prey

Abstract

We used an individual‐based model, developed previously for the endangered, endemic Delta Smelt Hypomesus transpacificus, to investigate two factors widely believed to affect its abundance in the San Francisco Estuary: entrainment in large water diversion facilities and declines and species shifts in their zooplankton prey. Previous analyses suggested that these factors had substantial effects on the Delta Smelt population, although evidence is accumulating that other factors, such as contaminants and predation, are also having effects. Simulations were performed for 1995–2005 with either entrainment mortality set to zero or zooplankton biomasses replaced with values sampled from pre‐decline years. The detailed individual‐based and spatial model output was summarized as the annual finite population growth rate (λ). Eliminating entrainment mortality increased the geometric mean λ by 39% through increased survival of larvae and adults. Substituting historical food for present‐day food resulted in variable annual λ values with a geometric mean that was 41% greater than the baseline value (14–81% across 10 alternative food scenarios). Historical food caused higher juvenile consumption and growth rates, leading to larger recruits, earlier maturity, and higher individual fecundity. These results were robust to four sets of simulations using alternative formulations for density dependence, mortality, maturity, and larval growth.

Zooplankton Dynamics in the Cache Slough Complex of the Upper San Francisco Estuary

“…Interest in the restoration of tidal wetlands in the California Delta has arisen because of their potential to enhance food supply for declining species of pelagic fish, notably Delta Smelt (Hypomesus transpacificus) (Herbold et al 2014). Delta Smelt, and probably other fishes in the estuary, are food limited, meaning that a greater abundance of their zooplankton prey would increase smelt population size through faster growth and higher reproductive rate (Kimmerer and Rose 2018). Food limitation of Delta Smelt is suggested by analyses of gut fullness (Nobriga 2002;Slater and Baxter 2014), glycogen depletion (Bennett 2005;Hammock et al 2015), reduced size at age (Bennett 2005), statistical relationships of food to survival indices (Kimmerer 2008), and functional responses measured in the laboratory that show low feeding rates at current levels of prey abundance (Sullivan et al 2016).…”

Role of freshwater floodplain-tidal slough complex in the persistence of the endangered delta smelt

“…Calanoid copepods, including Pseudodiaptomus forbesi are the preferred prey for Delta Smelt [34], and dominated the diet composition of fish in our study. Higher availability in prey abundance has been shown to improve the growth and survival of Delta Smelt [59,60,61]. Second, Secchi depth values in the Yolo Bypass were typically within the optimal range for Delta Smelt (0.1–0.3 meters) year-round [39,40].…”

Did a Shifting Ecological Baseline Mask the Predatory Effect of Striped Bass on Delta Smelt?

“…This scenario has the implicit assumptions that the Delta Smelt population was stable before its decline in the early 1980s, and the decline was driven by an ecosystem shift associated with this time-period. The numerous quantitative models that have been developed in the last decade to evaluate drivers of Delta Smelt population dynamics have focused on concurrent potential drivers (Mac Nally et al 2010;Thomson et al 2010;Maunder and Deriso 2011;Miller et al 2012;Rose et al 2013;Hamilton and Murphy 2018;Kimmerer and Rose 2018). However, an alternative assumption is that the Delta Smelt decline had already occurred when the first fish monitoring program began in 1959 ( Figure 2).…”