Seasonal floodplain-tidal slough complex supports size variation for juvenile Chinook salmon (Oncorhynchus tshawytscha)

Population diversity is a mechanism for resilience and has been identified as a critical issue for fisheries management, but restoration ecologists lack evidence for specific habitat features or processes that promote phenotypic diversity. Since habitat complexity may affect population diversity, it is important to understand how population diversity is partitioned across landscapes and among populations. In this study, we examined life history diversity based on size distributions of juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) within the Yolo Bypass, a remnant transitional habitat from floodplain to tidal sloughs in the upper San Francisco Estuary (SFE). We used a generalized least squares model with an autoregressive (AR1) correlation structure to describe the distribution of variation in fish size from 1998 to 2014, and tested the effect of two possible drivers of the observed variation: (i) environmental/seasonal drivers within the Yolo Bypass, and (ii) the juvenile Chinook source population within the Sacramento River and northern SFE. We found that the duration of floodplain inundation, water temperature variation, season, and sampling effort influenced the observed time-specific size distribution of juvenile Chinook salmon in the Yolo Bypass. Given the lack of seasonally inundated habitat and low thermal heterogeneity in the adjacent Sacramento River, these drivers of juvenile size diversification are primarily available to salmon utilizing the Yolo Bypass. Therefore, enhancement of river floodplain-tidal slough complexes and inundation regimes may support the resilience of imperiled Central Valley Chinook salmon.