Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary

Brock Huntsman,Samuel Bashevkin,Brian Mahardja

doi:10.15447/sfews.2022v20iss20art3

Abstract

Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.

Highlights

The status and trends of fish populations help shape environmental regulations in the San Francisco Estuary and can often drive substantial changes to water operations
The number of individual tows analyzed for this study was highest from the Bay Study (BSOT = 19,075 and Bay Study Midwater Trawl (BSMT) = 16,782), followed by the Fall Midwater Trawl (FMWT) (16,782); the fewest tows were from the Suisun Marsh Otter Trawl (SMOT) (9,134)
We used only three of the many surveys that collect information on fishes in the estuary (Stompe et al 2020) and expanding the data set to include more surveys would likely improve predictive performance and provide insight into the relative efficiency of different gears at capturing targeted fish species. Expanding these analyses could help identify which gears and methods are most compatible for each species in terms of catchability, limiting the amount of catchability bias that would affect inferences about fish population and community dynamics that were drawn from analyzing multiple data sets

Summary

Introduction

The status and trends of fish populations help shape environmental regulations in the San Francisco Estuary (estuary) and can often drive substantial changes to water operations. The sampling equipment used by the long-term fish surveys in the estuary can only sample a fraction of the water present in the system. At a given sampling location, the number of fish caught by sampling equipment may not reflect their true density, and a species may go undetected even if it is truly present (i.e., false negative/type II error). Species, fish size, gear, and environmental conditions can all affect components of catchability, and should be incorporated into estimates of abundance or distribution, or both. A substantial amount of work has been done to account for observation error from differences in catchability and to provide measures of uncertainty (Walsh 1997; Royle 2004; MacKenzie and Royle 2005; Kéry and Royle 2016). Work to estimate catchability in the estuary to date has either included a select few species (Perry et al 2016; Mitchell et al 2017; Mitchell et al 2019; Huntsman et al 2021a, 2021b) or focused on occupancy rather than abundance (Mahardja et al 2017; Peterson and Barajas 2018)

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