Fig 1.
Sampling locations of California Current Ecosystem biology included in the study analyses.
Abundance data for pelagic juvenile groundfishes and invertebrates are collected on the Rockfish Recruitment and Ecosystem Assessment Survey (RREAS). Ichthyoplankton data are collected on the California Cooperative Oceanic Fisheries Investigations (CalCOFI) survey. Seabird reproductive success and California sea lion (Zalophus californianus) pup time series are collected on Southeast Farallon Island and San Miguel Island, respectively. See S1 Table and S1 Fig for detailed information on the individual time series. The base map layer was sourced from NOAA National Geophysical Data Center (2009) ETOPO1 1 Arc-Minute Global Relief Model. NOAA National Centers for Environmental Information (accessed: 19 April 2013, [49]).
Fig 2.
Shared trend with 95% credible intervals of climate variability in the southern and central California Current ecosystem (1981–2017).
Fig 3.
Posterior distributions for loadings on all of the individual time series associated with the climate trend (Fig 2).
Loadings with darker shading indicate time series loading most strongly on the climate trend. SST, sea surface temperature; SSH, sea surface height; ILD, isothermal layer depth; BV, Brunt-Väisälä frequency (stratification); CUTI, Coastal Upwelling Transport Index; BEUTI, Biologically Effective Upwelling Transport Index. See S1 Table and S1 Fig for climate times series details.
Table 1.
Summary information for climate and biology Bayesian DFA models, including whether process error was estimated, observation error variances (unequal or equal among time series, or unique to each survey), the number of model trends, expected log pointwise predictive densities (ELPD), and standard error of ELPD.
Fig 4.
Results of Hidden Markov Models (HMM) showing state probability for latent trends in the climate data set.
The best model invoked two states, and the median probability (and 95% credible intervals) of being in one state versus the other is shown. The figure reflects the probability of being in the state associated with warmer conditions versus one with cold conditions.
Fig 5.
Shared trend with 95% credible intervals of community variability in the southern and central California Current ecosystem (1951–2018: Marine heatwave occurred 2014–2016).
Fig 6.
Posterior distributions for loadings on individual time series associated with the biology trend (Fig 5).
Only time series with ≥ 90% of the loading distributions above or below zero are shown). Loadings with darker shading indicate time series loading most strongly on the biology trend. Cal. = California, Juv. = juvenile fish stage, Juv./adult = juvenile and adult fish stages combined, all other fish are larval fish. See S1 Table and S1 Fig for times series details.
Fig 7.
Results of Hidden Markov Models (HMM) showing state probability for latent trends in the biology data set.
The best model invoked two states, and the median probability (and 95% credible intervals) of being in one state versus the other is shown. The figure indicates that ecosystem did not shift into a new state following the marine heatwave.
Fig 8.
A summary of the effect of the Biologically Effective Upwelling Transport Index (BEUTI), a measure of nitrate flux through the base of the mixed layer, on the single species parameters.
Cal. = California, Juv. = juvenile fish stage, Juv./adult = juvenile and adult fish stages combined, all other fish are larval fish. Blue error bars reflect 95% credible intervals. S5–S7 Figs show effects of other environment covariates on the biological variables.
Table 2.
Summary information for the top biology-covariate Bayesian DFA models for each covariate and the top two biology only models (years 1981–2017).
Fig 9.
Community variability and forecast of the community state in the southern California Current.
The shared biology trend (blue line, with 95% credible intervals) derived from biology-BEUTI model fit to subset of data (1981–2018) is shown along with the trend forecast for 2018 (circle, with 95% credible intervals). See S8 Fig for model loadings.
Fig 10.
Forecasts and model estimates of the ‘true’ community state in the southern and central California Current in years 2008–2018 (circle, with 95% credible intervals).