Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary

Ecological Applications
By: , and 



We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, California, USA, over 40 years using Bayesian change point models. Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). We coupled Bayesian model selection with linear regression splines to identify biotic or abiotic covariates with the strongest associations with abundances of each species. We then refitted change point models conditional on the selected covariates to explore whether those covariates could explain statistical trends or change points in species abundances. We also fitted a multispecies change point model that identified change points common to all species. All models included hierarchical structures to model data uncertainties, including observation errors and missing covariate values. There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2‰ isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species' abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.
Publication type Article
Publication Subtype Journal Article
Title Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary
Series title Ecological Applications
DOI 10.1890/09-0998.1
Volume 20
Year Published 2010
Language English
Publisher Ecological Society of America
Publisher location Ithaca, NY
Contributing office(s) California Water Science Center
Description 18 p.
Larger Work Type Article
Larger Work Subtype Journal Article
Larger Work Title Ecological Applications
First page 1431
Last page 1448
Country United States
State California
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