Effects of managed flows on Chinook Salmon (Oncorhynchus tshawytscha) in relation to run-timing, fertility, and fluctuations in water temperature and flow volume

We evaluated annual and seasonal patterns of run-timing in two genetically differentiated races of adult Chinook Salmon (Oncorhynchus tshawytscha) inhabiting the upper Trinity River, California. Our analysis provides evidence that highly managed flow regimes implemented since 2003 have 1) altered the pattern of run-timing in sympatric anadromous populations of spring-and fall-run Chinook Salmon, 2) resulted in significant differences among managed flow-types in relation to the taxon-specific "historical" post-dam baseline flow-type, 3) altered environmental measures of water temperature and flow volume, and 4) potentially affected hatchery-parental broodstock female average annual percent fertility associated with egg production. Additionally, counts of coded wire tagged spring-and fall-run adult Chinook Salmon were significantly correlated with total hatchery returns of all age classes of marked and unmarked fish, and all three groups of salmon exhibited a significant and negative decline in relative abundance since peaking in 2004. Trends in declining stocks of all Chinook Salmon coincided with establishment of the Trinity River Restoration Program in 2002 and subsequent highly managed flow releases including periodic pulsed augmentation flows beginning in 2003. Deviation away from the baseline flow pattern in run-timing occurred in spring-run fish by compression and movement of peak counts to earlier in the season; whereas in fall-run fish peak counts occurred earlier and later in the season relative to the baseline condition. Further, we show significant differences between the baseline flow pattern and managed flow hydrographs in both annual and seasonal measures of average daily water temperature, extremes in average daily water temperature, and average daily flow volume. Analyses of annual trends in hatchery records using generalized additive modeling also revealed a significant negative relationship between year and average annual percent fertility of hatchery raised parental broodstock associated with hatchery egg-take in both spring-and fall-run Chinook Salmon. Declining concordant trends in fertility suggest that these seasonally disjunct and genetically differentiated races of Chinook Salmon are tracking conditions in the upper Trinity River in parallel, which may in part be a function of the potentially negative consequences of altered flow on riverine ecosystem processes and the fisheries resources they support.