Resource managers rely on long-term monitoring surveys conducted in the San Francisco Estuary to evaluate the status and trends of resident fish populations in this important region. These surveys are potentially confounded because of the incomplete detection of individuals and species, the magnitude of which is often related to the same factors that affect fish populations. We used multistate occupancy estimators to evaluate the distribution, abundance, and detection probability of four fish species collected during 1995–2015 with three long-term surveys. Detection probabilities varied positively with fish abundance and negatively with Secchi depth. Detection varied among species and was greatest for the 20-mm Survey and least for the midwater trawl used for the midwater trawl used in the San Francisco Bay Study. Incomplete detection resulted in underestimates of occupancy and abundance across species and surveys and were greatest for the Bay Study. However, trends in occupancy and abundance of the study period appeared to be unbiased. Fish occupancy and abundance were generally related to salinity or specific conductance, day-of-the year, and water temperature, but the nature of the relations varied among surveys and species. There also was strong spatial and temporal dependence in species-specific occupancy and abundance that changed through time and were unrelated to the covariates considered. Our results suggest that managers consider incorporating methods for estimating detection and adjusting data to ensure data quality. Additionally, the strong spatio-temporal patterns in the monitoring data suggest that existing protocols may need to be modified to ensure that data and inferences reflect system-wide changes rather than changes at a specific set of non-randomly selected locations.

Beginning in the 1980s, return rates of Atlantic salmon to the Penobscot River, Maine U.S.A. declined and have persisted at low levels. This downturn coincided with similar declines in North American and European Atlantic salmon stocks and with changes in the Northwest Atlantic ecosystem. Previous studies investigated whether early marine growth explained the declines, but results varied, with decreased growth associated with declines in European stocks but not North American stocks. In this study, we evaluate whether growth over the entire marine stage is related to Atlantic salmon marine survival. We constructed a growth time series from scales of returned Penobscot River Atlantic salmon spanning periods of varying marine survival. We used ANOVA and post-hoc tests to quantify seasonal growth increment differences and principal component analysis to characterize variability among the suite of growth increments. We observed reduced growth during the second winter and second marine year starting in the 1990s, with compensatory seasonal growth relationships. These results indicate that diminished growth during late marine stages is associated with low return rates in this population.

Failure to account for the impacts of climate and ecosystem change on stock dynamics can introduce uncertainty to stock assessments that can make meeting the objective of sustainable fisheries management challenging. The increased prevalence and magnitude of uncertainty in New England groundfish stock assessments (i.e. retrospective patterns) in recent years suggest that there may be common drivers impacting these stocks that are currently unaccounted for in the stock assessment. We examined the coherence in retrospective patterns across groundfish stock assessments and evaluated candidate drivers of retrospective patterns, including large-scale climate and ecosystem change, as well as significant management and monitoring changes. We found high coherence in moving window Mohn's rho time series for groundfish within the Gulf of Maine and Georges Bank areas. Fluctuations in Gulf of Maine groundfish Mohn's rho values were most strongly related to lagged bottom temperature and spiny dogfish biomass time series, whereas fluctuations in Georges Bank groundfish Mohn's rho values were strongly related to lagged time series of warm core rings formation from the Gulf Stream. Our identification of coherence in retrospective patterns across groundfish stocks by region supports the idea of common regional drivers with climate and ecosystem changes emerging as the leading contributing factors.