Decoupling Abundance and Timing of Presence to Characterize Distributional Patterns of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary

Coincident changes in abundance and phenology pose a challenge for interpreting abundance indices derived from monitoring programs. In the San Francisco Estuary, long-term monitoring programs have documented changes in overall longfin smelt (Spirinchus thaleichthys) abundance as well as regional differences in presence over time. Seasonal patterns in regional presence of longfin smelt through its life cycle were developed using monitoring data and generalized additive modelling. We investigated the year-to-year variability in seasonal patterns of presence using functional data analysis to separate variability due to population size from variability due to changing timing of presence. We found that longfin smelt have consistent seasonal distribution and that two trawl types were needed to accurately describe those patterns. After accounting for variability due to population abundance, shifts in the timing of presence were evident in three regions. These shifts were interpreted as changes in migration timing. The most variable period for the upstream regions was for age-0 fish in summer and for the downstream region was for age-0 fish in late fall. This study highlights that identifying portions of the life cycle with the most and least variability in distribution can help inform the types of management strategies that will be most effective. It also illustrates an analytical method that can be used to address the problem of confounded effects of abundance and phenology on patterns in monitoring data.