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

Jim THOMSON, Wim Kimmerer, Larry R. Brown, Ken B. Newman, Ralph MAC NALLY, William A. Bennett, Frederick Feyrer, Erica Fleishman

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    Abstract

    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 cor abiotic ovariates 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.
    Original languageEnglish
    Pages (from-to)1431-1448
    Number of pages18
    JournalEcological Applications
    Volume20
    Issue number5
    DOIs
    Publication statusPublished - 2010

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    THOMSON, J., Kimmerer, W., Brown, L. R., Newman, K. B., MAC NALLY, R., Bennett, W. A., ... Fleishman, E. (2010). Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications, 20(5), 1431-1448. https://doi.org/10.1890/09-0998.1
    THOMSON, Jim ; Kimmerer, Wim ; Brown, Larry R. ; Newman, Ken B. ; MAC NALLY, Ralph ; Bennett, William A. ; Feyrer, Frederick ; Fleishman, Erica. / Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. In: Ecological Applications. 2010 ; Vol. 20, No. 5. pp. 1431-1448.
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    title = "Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary",
    abstract = "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 cor abiotic ovariates 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.",
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    author = "Jim THOMSON and Wim Kimmerer and Brown, {Larry R.} and Newman, {Ken B.} and {MAC NALLY}, Ralph and Bennett, {William A.} and Frederick Feyrer and Erica Fleishman",
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    THOMSON, J, Kimmerer, W, Brown, LR, Newman, KB, MAC NALLY, R, Bennett, WA, Feyrer, F & Fleishman, E 2010, 'Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary', Ecological Applications, vol. 20, no. 5, pp. 1431-1448. https://doi.org/10.1890/09-0998.1

    Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. / THOMSON, Jim; Kimmerer, Wim; Brown, Larry R.; Newman, Ken B.; MAC NALLY, Ralph; Bennett, William A.; Feyrer, Frederick; Fleishman, Erica.

    In: Ecological Applications, Vol. 20, No. 5, 2010, p. 1431-1448.

    Research output: Contribution to journalArticle

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    AU - Kimmerer, Wim

    AU - Brown, Larry R.

    AU - Newman, Ken B.

    AU - MAC NALLY, Ralph

    AU - Bennett, William A.

    AU - Feyrer, Frederick

    AU - Fleishman, Erica

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    AB - 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 cor abiotic ovariates 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.

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    KW - USA

    KW - striped bass

    KW - threadfin shad

    KW - upper San Francisco Estuary

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    DO - 10.1890/09-0998.1

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