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Estimating juvenile Chinook salmon (Oncorhynchus tshawytscha) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California

Open-File Report 2016-1099
Prepared in cooperation with the Bureau of Reclamation
By: , , and 
https://doi.org/10.3133/ofr20161099

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Abstract

Resource managers rely on abundance or density metrics derived from beach seine surveys to make vital decisions that affect fish population dynamics and assemblage structure. However, abundance and density metrics may be biased by imperfect capture and lack of geographic closure during sampling. Currently, there is considerable uncertainty about the capture efficiency of juvenile Chinook salmon (Oncorhynchus tshawytscha) by beach seines. Heterogeneity in capture can occur through unrealistic assumptions of closure and from variation in the probability of capture caused by environmental conditions. We evaluated the assumptions of closure and the influence of environmental conditions on capture efficiency and abundance estimates of Chinook salmon from beach seining within the Sacramento–San Joaquin Delta and the San Francisco Bay. Beach seine capture efficiency was measured using a stratified random sampling design combined with open and closed replicate depletion sampling. A total of 56 samples were collected during the spring of 2014. To assess variability in capture probability and the absolute abundance of juvenile Chinook salmon, beach seine capture efficiency data were fitted to the paired depletion design using modified N-mixture models. These models allowed us to explicitly test the closure assumption and estimate environmental effects on the probability of capture. We determined that our updated method allowing for lack of closure between depletion samples drastically outperformed traditional data analysis that assumes closure among replicate samples. The best-fit model (lowest-valued Akaike Information Criterion model) included the probability of fish being available for capture (relaxed closure assumption), capture probability modeled as a function of water velocity and percent coverage of fine sediment, and abundance modeled as a function of sample area, temperature, and water velocity. Given that beach seining is a ubiquitous sampling technique for many species, our improved sampling design and analysis could provide significant improvements in density and abundance estimation.

Suggested Citation

Perry, R.W., Kirsch, J.E., and Hendrix, A.N., 2016, Estimating juvenile Chinook salmon (Oncorhynchus tshawytscha) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California: U.S. Geological Survey Open-File Report 2016–1099, 21 p., http://dx.doi.org/10.3133/ofr20161099.

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Abstract
  • Introduction
  • Methods
  • Results
  • Discussion
  • Acknowledgments
  • References Cited
Publication type Report
Publication Subtype USGS Numbered Series
Title Estimating juvenile Chinook salmon (Oncorhynchus tshawytscha) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California
Series title Open-File Report
Series number 2016-1099
DOI 10.3133/ofr20161099
Year Published 2016
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) San Francisco Bay-Delta, Western Fisheries Research Center
Description iv, 21 p.
Country United States
State California
Other Geospatial Sacramento-San Joaquin Delta, San Francisco Bay
Online Only (Y/N) Y
Additional Online Files (Y/N) N
Google Analytic Metrics Metrics page
Additional publication details