Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR

Ralph MAC NALLY, Jim THOMSON, Wim Kimmerer, Frederick Feyrer, Ken B. Newman, Andy Sih, William A. Bennett, Larry R. Brown, Erica Fleishman, Steven Culberson, Gonzalo Castillo

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    Abstract

    Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2%o isohaline (a measure of the physical response of the estuary to freshwaterf low) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock-recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state-space models that describe more fully the life-history dynamics of the declining species.
    Original languageEnglish
    Pages (from-to)1417-1430
    Number of pages14
    JournalEcological Applications
    Volume20
    Issue number5
    DOIs
    Publication statusPublished - 2010

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    pelagic fish
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    invasive species
    zooplankton
    life history
    phytoplankton
    analysis
    biomass
    water

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    MAC NALLY, Ralph ; THOMSON, Jim ; Kimmerer, Wim ; Feyrer, Frederick ; Newman, Ken B. ; Sih, Andy ; Bennett, William A. ; Brown, Larry R. ; Fleishman, Erica ; Culberson, Steven ; Castillo, Gonzalo. / Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR. In: Ecological Applications. 2010 ; Vol. 20, No. 5. pp. 1417-1430.
    @article{e37367ee787d405a8f9925872fb2ea54,
    title = "Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR",
    abstract = "Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2{\%}o isohaline (a measure of the physical response of the estuary to freshwaterf low) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock-recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state-space models that describe more fully the life-history dynamics of the declining species.",
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    year = "2010",
    doi = "10.1890/09-1724.1",
    language = "English",
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    MAC NALLY, R, THOMSON, J, Kimmerer, W, Feyrer, F, Newman, KB, Sih, A, Bennett, WA, Brown, LR, Fleishman, E, Culberson, S & Castillo, G 2010, 'Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR', Ecological Applications, vol. 20, no. 5, pp. 1417-1430. https://doi.org/10.1890/09-1724.1

    Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (MAR. / MAC NALLY, Ralph; THOMSON, Jim; Kimmerer, Wim; Feyrer, Frederick; Newman, Ken B.; Sih, Andy; Bennett, William A.; Brown, Larry R.; Fleishman, Erica; Culberson, Steven; Castillo, Gonzalo.

    In: Ecological Applications, Vol. 20, No. 5, 2010, p. 1417-1430.

    Research output: Contribution to journalArticle

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    AU - MAC NALLY, Ralph

    AU - THOMSON, Jim

    AU - Kimmerer, Wim

    AU - Feyrer, Frederick

    AU - Newman, Ken B.

    AU - Sih, Andy

    AU - Bennett, William A.

    AU - Brown, Larry R.

    AU - Fleishman, Erica

    AU - Culberson, Steven

    AU - Castillo, Gonzalo

    PY - 2010

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    N2 - Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2%o isohaline (a measure of the physical response of the estuary to freshwaterf low) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock-recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state-space models that describe more fully the life-history dynamics of the declining species.

    AB - Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). The estuary has been monitored since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. We used multivariate autoregressive (MAR) modeling to discern the main factors responsible for the declines. An expert-elicited model was built to describe the system. Fifty-four relationships were built into the model, only one of which was of uncertain direction a priori. Twenty-eight of the proposed relationships were strongly supported by or consistent with the data, while 26 were close to zero (not supported by the data but not contrary to expectations). The position of the 2%o isohaline (a measure of the physical response of the estuary to freshwaterf low) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa (including fishes and the fishes' main zooplankton prey). Our results were relatively robust with respect to the form of stock-recruitment model used and to inclusion of subsidiary covariates but may be enhanced by using detailed state-space models that describe more fully the life-history dynamics of the declining species.

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    KW - expert models

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    KW - Sacramento River

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    KW - striped bass

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    KW - threatened species

    KW - water management.

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