Understanding imperfect detection in a San Francisco Estuary long‐term larval and juvenile fish monitoring programme

Mahardja, Brian; Young, Matthew J.; Schreier, Brian M.; Sommer, Ted

doi:10.1111/fme.12257

Cited by 20 publications

(29 citation statements)

References 65 publications

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“…, Mahardja et al. ). Contrary to the constant impact assumption, the completely catchable assumption is likely not able to be addressed through increased computational power alone.…”

Section: Discussionmentioning

confidence: 99%

“…While it is generally presumed that the efficiency of the 20-mm net at capturing delta smelt increases with fish size (Kimmerer 2008, Merz et al 2011, no published studies have explicitly quantified the efficiency of the net, either generally or as a function of size. Previous work suggests net efficiency increases with size up tõ 15 mm and then does not change with size for larger smelt (Merz et al 2011), although that conclusion is contingent upon the model used and it is possible that larger smelt may exhibit a decreased detection probability (Mahardja et al 2017). For the present analyses, we restricted our dataset to smelt that were at least 15 mm in length and made the assumption that smelt over 15 mm do not show a change in detection with size, allowing us to avoid the complexity associated with modeling the smelt size distribution alongside their population density.…”

Section: Data Preparation and Summarymentioning

confidence: 95%

“…), although that conclusion is contingent upon the model used and it is possible that larger smelt may exhibit a decreased detection probability (Mahardja et al. ). For the present analyses, we restricted our dataset to smelt that were at least 15 mm in length and made the assumption that smelt over 15 mm do not show a change in detection with size, allowing us to avoid the complexity associated with modeling the smelt size distribution alongside their population density.…”

Section: Datasetsmentioning

confidence: 99%

“…Starting with the onset of the California gold rush in the mid‐1800s, many hydrological and morphological alterations have converted the SFE from a contiguous marsh into a system of interconnected managed‐flow channels snaking around leveed islands (Conomos , Kimmerer , Mahardja et al. ). The Delta plays a central role in California's water infrastructure: 6–10 km 3 of freshwater (15–25% of the state's annual freshwater usage, Maupin et al.…”

Section: Introductionmentioning

confidence: 99%

“…1), the only inland delta in the world (Thomson et al 2010). Starting with the onset of the California gold rush in the mid-1800s, many hydrological and morphological alterations have converted the SFE from a contiguous marsh into a system of interconnected managed-flow channels snaking around leveed islands (Conomos 1979, Kimmerer 2004, Mahardja et al 2017. The Delta plays a central role in California's water infrastructure: 6-10 km 3 of freshwater (15-25% of the state's annual freshwater usage, Maupin et al 2014) are pumped south from the Delta each year into aqueducts that stretch across nearly half the state's length to supply drinking water for twothirds of the state's population and irrigation for a multi-billion-dollar agricultural industry that supplies half of the United States' produce (Healey et al 2008, Dettinger et al 2015; also see Fig.…”

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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“…, Mahardja et al. ). Contrary to the constant impact assumption, the completely catchable assumption is likely not able to be addressed through increased computational power alone.…”

Section: Discussionmentioning

confidence: 99%

Section: Data Preparation and Summarymentioning

confidence: 95%

Section: Datasetsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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Resistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary

Mahardja

Tobias

Khanna

et al. 2021

Ecological Applications

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Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoring data from the San Francisco Estuary, California, U.S.A, to evaluate the resistance and resilience of fish communities to disturbance from prolonged drought events. High resistance was defined by the lack of decline in species occurrence from a wet to a subsequent drought period, while high resilience was defined by the increase in species occurrence from a drought to a subsequent wet period. We found some unifying themes connecting the multiple drought events over the fifty-year period. Pelagic fishes consistently declined during droughts (low resistance), but exhibit a considerable amount of resiliency and often rebound in the subsequent wet years. However, full recovery does not occur in all wet years following droughts, leading to permanently lower baseline numbers for some pelagic fishes over time. In contrast, littoral fishes seem to be more resistant to drought and may even increase in occurrence during dry years. Based on the consistent detrimental effects of drought on pelagic fishes within the San Francisco Estuary and the inability of these fish populations to recover in some years, we conclude that freshwater flow remains a crucial but not sufficient management tool for the conservation of estuarine biodiversity.

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Space‐for‐time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay‐Delta

Duarte

Peterson

2021

Ecology and Evolution

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Occupancy models are often used to analyze long-term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non-detection data at a sample unit and many long-term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e.

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Understanding imperfect detection in a San Francisco Estuary long‐term larval and juvenile fish monitoring programme

Cited by 20 publications

References 65 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

Resistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary

Space‐for‐time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay‐Delta

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