WESPEN Online Order Form print this page
US Fish & Wildlife Service FieldNotes
  STOCKTON FWO:  Modeling Pelagic Fish Declines in the Delta of the San Francisco Estuary
Region 8, September 28, 2010
Figure 1. Two of the declining native fish being investigated in the San Francisco Estuary:  Top: Delta Smelt (Hypomesus transpacificus). Source: B. M. Peterson, USFWS. Bottom: Longfin smelt (Spirinchus thaleichthys) . Source: Rene Reyes, USBR.
Figure 1. Two of the declining native fish being investigated in the San Francisco Estuary: Top: Delta Smelt (Hypomesus transpacificus). Source: B. M. Peterson, USFWS. Bottom: Longfin smelt (Spirinchus thaleichthys) . Source: Rene Reyes, USBR. - Photo Credit: n/a
Figure 2. Two of the declining non-native fish being investigated in the San Francisco Estuary. Top: Striped bass (Morone saxatilis). Source: www.fws.gov/digitalmedia. Bottom:Threadfin shad (Dorosoma petenense). Source: Rene Reyes, USBR.
Figure 2. Two of the declining non-native fish being investigated in the San Francisco Estuary. Top: Striped bass (Morone saxatilis). Source: www.fws.gov/digitalmedia. Bottom:Threadfin shad (Dorosoma petenense). Source: Rene Reyes, USBR. - Photo Credit: n/a

As part of an interdisciplinary multiagency study, Stockton USFWS employees Ken Newman and Gonzalo Castillo collaborated in a modeling study (McNally et al. 2010) to investigate the changes in abundance of pelagic fishes in the upper San Francisco Estuary (Delta).  The study involved cooperation between the National Center for Ecological Analysis and Synthesis (NCEAS) and the Interagency Ecological Program of the Sacramento-San Joaquin Estuary (IEP). Four species of pelagic fish of in the Delta have declined precipitously since the early 2000s. These include two native species: delta smelt (Hypomesus transpacificus) and longfin smelt (Spirinchus thaleichthys), (Figure 1), and two introduced species: striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense).

The estuary has been monitored by the IEP since the late 1960s with extensive collection of data on the fishes, their pelagic prey, phytoplankton biomass, invasive species, and physical factors. To discern the main factors responsible for these declines, the researchers used multivariate autoregressive (MAR) modeling. An expert-elicited model was built to describe the system. Fifty-four relations were built into the model, only one of which was of uncertain direction a priori. Results showed that 28 of the proposed relations 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 X2 (the distance in kilometers from the Golden Gate to the 2 ppt salinity line) and increased water clarity over the period of analyses were two factors affecting multiple declining taxa, including fishes and the fishes' main zooplankton prey. The model 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.

Stockton FWS mathematical statistician Ken Newman further collaborated in a concurrent NCEAS-IEP study involving Bayesian change point models. These models were used to examine trends in abundance of the four pelagic fish species mentioned earlier over 40 years of record (Thomson et al 2010). Change point models identify times of abrupt or unusual changes in absolute abundance (step changes) or in rates of change in abundance (trend changes). The models were fitted on selected biotic or abiotic covariates to explore whether those covariates could explain statistical trends or change points in species abundances. They also fitted a multispecies change point model that identified change points common to all species. Results showed 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 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.  Additional studies involving Stockton FWS collaboration with IEP and NCEAS are being considered.

References:

Mac Nally, R., J.R. Thomson, W.J. Kimmerer, F. Feyrer, K.B. Newman, A. Sih, W.A. Bennett, L. Brown, E. Fleishman, S.D. Culberson, and G. Castillo. 2010. Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modelling (MAR). Ecological Applications 20:1417–1430.

Thomson, J. R., W.J. Kimmerer, L.R. Brown, K.B. Newman, R. Mac Nally, W.A. Bennett, F. Feyrer, and E. Fleishman. 2010. Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary.  Ecological Applications 20:1431–1448.

Contact Info: Gonzalo Castillo, 209-334-2968x323, gonzalo_castillo@fws.gov