Spatiotemporal Models of an Estuarine Fish Species to Identify Patterns and Factors Impacting Their Distribution and Abundance

Polansky, Leo; Newman, Ken; Nobriga, Matthew L.; Mitchell, Lara

doi:10.1007/s12237-017-0277-3

Cited by 31 publications

(46 citation statements)

References 33 publications

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“…As has been noted previously (Polansky et al. ), there was considerable variation in the number of smelt caught among tows, even within the same visit to a station. Prior approaches to modeling smelt densities have typically ignored this variability by taking visit‐level averages of catch per unit effort (Kimmerer ) or further integrating density to a Delta‐wide average index value (Sweetnam and Stevens , Moyle et al.…”

Section: Discussionsupporting

confidence: 70%

“…), a necessary simplification because parameters would be non‐identifiable in the absence of prior information regarding the catchability of delta smelt (Data ; Royle and Dorazio , , Hooten and Hobbs , Polansky et al. ). While it is likely that this assumption does not hold, especially for smaller smelt (Kimmerer , Merz et al.…”

Section: Discussionmentioning

confidence: 99%

“…Following Polansky et al. (), given the confounding of density and detection and the lack of existing (prior) information regarding the detection rate, we assumed for the present manuscript that

ρ = 1

(but see also Data ). While it may be possible for

normalρ

to actually have been 1, it was likely lower, and so the estimated density of smelt should be considered a relative density, scaled by detection (Maunder et al.…”

Section: Statistical Population Modelmentioning

confidence: 99%

“…, Polansky et al. ). Indeed, the population ecology used to inform management decisions is primarily reliant on annual relative abundance index values (see Moyle et al.…”

Section: Introductionmentioning

confidence: 99%

“…“X2”) are used to guide water use management (USFWS ), the exact drivers of smelt movement and distribution remain unclear (Polansky et al. ).…”

Section: Introductionmentioning

confidence: 99%

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

Simonis¹,

Merz

2019

Ecosphere

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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.

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Section: Discussionsupporting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

ρ = 1

(but see also Data ). While it may be possible for

normalρ

to actually have been 1, it was likely lower, and so the estimated density of smelt should be considered a relative density, scaled by detection (Maunder et al.…”

Section: Statistical Population Modelmentioning

confidence: 99%

“…, Polansky et al. ). Indeed, the population ecology used to inform management decisions is primarily reliant on annual relative abundance index values (see Moyle et al.…”

Section: Introductionmentioning

confidence: 99%

“…“X2”) are used to guide water use management (USFWS ), the exact drivers of smelt movement and distribution remain unclear (Polansky et al. ).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Simonis¹,

Merz

2019

Ecosphere

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Salinity and diel timing affect group structure in Delta Smelt

Chase,

Tsai,

Croshaw

et al. 2023

Aquaculture Fish & Fisheries

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Delta Smelt are thought to be on the precipice of extinction. Studies that examine how this endangered species responds to environmental change are important to informing conservation efforts. In the wild, Delta Smelt are likely to encounter wide variation in the salinity of their environment that is influenced by both natural and anthropogenic factors. We examined how salinity affects the group structure of Delta Smelt across multiple diel cycles. We found that the interaction between salinity (0, 5, 10 and 15 ppt) and time period (Day 1, Night 1, Day 2 and Night 2) influenced their spatial distribution within a group. Specifically, Delta Smelt were less dispersed, more cohesive and more homogenously distributed in saline water than in freshwater, but only on the first day, and this difference was not statistically significant. We also found that Delta Smelt were significantly less dispersed, more cohesive and more homogenous during the day than at night. Thus, Delta Smelt appear to behaviourally adapt to the initial stress of acute salinity exposure, which may mirror their physiological ability to acclimate to such conditions. Additionally, Delta Smelt group structure appears to shift depending on the time of day, suggesting that diel timing may influence conspecific interactions and should be considered in the experimental design of future studies. These findings further our understanding of how Delta Smelt behaviourally respond to environmental and diel variation.

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Using Multistage Design‐Based Methods to Construct Abundance Indices and Uncertainty Measures for Delta Smelt

2019

Self Cite

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Population abundance indices and estimates of uncertainty are starting points for many scientific endeavors. However, if the indices are based on data collected by different monitoring programs with possibly different sampling procedures and efficiencies, applying consistent methodology for calculating them can be complicated. Ideally, the methodology will provide indices and associated measures of uncertainty that account for the sample design, the level of sampling effort (e.g., sample size), and the capture or detection probabilities. We develop and demonstrate consistent methodology for multiple monitoring programs that sample different life stages of Delta Smelt Hypomesus transpacificus, a critically endangered fish species endemic to the San Francisco Estuary, whose abundance indices have been at the center of much controversy given the regulatory consequences of their listed status. Current indices use different and incomparable methods, do not account for gear selectivity, and do not provide measures of uncertainty. Using recently available information on gear‐specific, length‐based conditional probabilities of capture given availability, we develop new abundance indices along with measures of uncertainty by means of a single methodological approach. These new indices are highly correlated with existing ones, but the approach taken here illuminates different sources of bias and quantifies between‐year variation using probabilistic statements where the previous indices cannot. Decomposition of uncertainty into its constituent sources reveals that early life stage uncertainty is dominated by gear inefficiency while later life stage uncertainty is dominated by sample size, thus providing guidance for improvements to existing surveys. An additional result of general methodological interest is a demonstration, via simulation intended to reflect realistic data properties, that a lognormal distribution is preferable to the normal distribution for making probabilistic statements about the indices. The work here facilitates the fitting of models attempting to identify factors associated with the dynamics and decline of the species.

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Spatiotemporal Models of an Estuarine Fish Species to Identify Patterns and Factors Impacting Their Distribution and Abundance

Cited by 31 publications

References 33 publications

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

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

Salinity and diel timing affect group structure in Delta Smelt

Using Multistage Design‐Based Methods to Construct Abundance Indices and Uncertainty Measures for Delta Smelt

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