Prey availability, environmental constraints, and aggregation dictate population distribution of an imperiled fish

Abstract

Accelerated global loss of fish species underscores an urgent need to elucidate constraints on spatial and temporal population patterns and to mitigate human‐mediated impacts accordingly. We analyzed 20 yr of trawl data using a spatiotemporally explicit, hierarchically Bayesian model to define density distributions of an imperiled anadromous fish—the delta smelt, Hypomesus transpacificus—in the heavily modified and highly used San Francisco Estuary. To reduce management reliance on an estuary‐wide annual population index that minimizes data resolution and ignores uncertainty, our model took a spatiotemporal approach and explicitly accounted for sampling and observation variation through both stochastic and deterministic elements. Our model demonstrated that juvenile smelt density has decreased over annual time and displays a distinct seasonal pattern (the combination of growth into the sampled size class, mortality, and movement into and out of the sampling frame) of increases in March–June followed by decreases in June–August. Smelt density was highly spatiotemporally autocorrelated and strongly tracked prey availability yet was also constrained by local hydrological factors (salinity, turbidity, velocity). Specifically, juvenile smelt preferred slightly saline, turbid, generally slow‐moving water with ample copepod prey. However, poor swimming capabilities reduced the capacity of juvenile smelt to mix throughout the estuary and find optimal habitat, emphasizing the importance of accounting for spatiotemporal autocorrelation in species distribution models. Further, whole‐estuary outflow appeared to influence the spatial distribution of covariates and juvenile smelt, such that smelt densities tended to peak closer to the marine zone at a lower maximal value when outflow was high. The predictions of our model accurately matched observed patterns of juvenile delta smelt catch while embracing uncertainty (although the predictions tended to exaggerate the total smelt catch variation via over‐predicted tail values). These results highlight that data‐driven improvements can be made to the analytical methods currently used to guide delta smelt management and lay the groundwork for mitigating the impacts of water use, flow regimes, habitat alteration, and climate change on an endangered species in a highly impacted and economically consequential habitat.

Identifying Environmental Factors Limiting Recovery of an Imperiled Estuarine Fish

“…Prey density was not considered. Simonis and Merz (2019) analyzed data from April through July, concluding that juvenile delta smelt are associated with slightly saline, turbid, generally slow-moving water with ample prey. Occupancy was strongly spatiotemporally autocorrelated (indicating that juveniles tend to be geographically anchored).…”

“…While salinity may influence occupancy year-round, our results indicate that salinity of water where delta smelt reside has little influence on performance except in November and December when the fish may be responding to a dispersal cue for spawning, rather than another physiological response. The only occupancy study to consider prey, that by Simonis and Merz (2019), concluded that juvenile delta smelt strongly track prey availability. While a continual supply of sufficient food might be an obvious factor influencing occupancy, our results indicate that the prey limits delta smelt abundance particularly in April, and then from July through October.…”

A Bayesian hierarchical model of postlarval delta smelt entrainment: integrating transport, length composition, and sampling efficiency in estimates of loss

“…Using a time series approach and more highly resolved transport information, a spatially explicit model (a special case of the first spatial structure setting mentioned above) could estimate spatially stratified abundance for the entire population, then apply strata-specific transport rates to sampling locations. The drawback to a spatially explicit approach is that starting population distributions may be highly uncertain (Heimbuch et al 2007;Huret et al 2007;Simonis and Merz 2019). Further, any biases in the transport model (e.g., unaccounted fish behavior) compound over both time and space, because fish transport over longer distances must be modeled.…”

Community dynamics of estuarine forage fishes are associated with a latitudinal basal resource regime

“…Forage fish populations can be influenced by spatiotemporal variability in habitat and climatic conditions, which can affect community structure and dynamics (Burghart et al, 2013; Chacin et al, 2016; Faletti et al, 2019; Lubbers et al, 1990; Simonis & Merz, 2019). For example, latitudinal gradients in community composition and species diversity are quite common in marine and estuarine environments (Hillebrand, 2004; Pease, 1999).…”