Geochemical Tools Identify the Origins of Chinook Salmon Returning to a Restored Creek

Abstract

Populations of Chinook Salmon Oncorhynchus tshawytscha in California are in decline due to the combined effects of habitat degradation, water diversions, and climate change. Reduced life history diversity within these populations inhibits their ability to respond to these stressors. Putah Creek, a small creek in California’s Central Valley that once supported Chinook Salmon, is undergoing restoration to provide spawning habitats for this imperiled species. Beginning in 2014, increasing numbers of Chinook Salmon spawned throughout the creek, and emigrating juveniles were observed in the following months. Here we used otolith annual growth bands and microchemistry to investigate the age structure and natal origins of the adult spawners. Most individuals were 2 or 3 years old, and they originated from at least seven different natal sources, overwhelmingly from Central Valley hatcheries (~88%). These findings highlight that straying fall‐run Central Valley Chinook Salmon can rapidly utilize restored habitats, potentially establishing new populations. However, to facilitate local adaptations, straying rates and gene flow will have to be managed over time. Reconnecting migratory pathways and restoring many small and diverse streams, like Putah Creek, provides an opportunity to increase life history diversity, strengthening the recovery and resilience of Chinook Salmon.

Ancient DNA analysis of archaeological specimens extends Chinook salmon’s known historic range to San Francisco Bay’s tributaries and southernmost watershed

“…Lastly, our study does not verify whether today’s Chinook population is self-sustaining with local smolts returning as successfully spawning adults. This should be further investigated via isotopic analysis of contemporary adult salmon carcass otoliths, as they possess the same elemental composition as when the otoliths formed in early life, and are thus natal stream specific [ 10 ].…”

“…The salmon runs approached 1,000 adult fish in the late 1990s but were nearly extirpated in the early 2000s when the Army Corps of Engineers and Santa Clara Valley Water District completed major anthropogenic alterations to the river mainstem to mitigate flooding. Contemporary San Francisco Bay watershed salmon runs have been attributed to hatchery strays, with very high rates of straying in recent drought years when hatchery-produced juvenile salmon were trucked downstream to the San Francisco Bay estuary to improve smolt survival [ 10 ]. Without a natal stream to home to as returning adults, these fish colonize new habitat for spawning.…”

Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

“…The salmon runs approached 1,000 adult fish in the late 1990s but were nearly extirpated in the early 2000s when the Army Corps of Engineers and Santa Clara Valley Water District constructed major anthropomorphic alterations to the river mainstem to mitigate flooding. San Francisco Bay watershed salmon runs have been attributed to hatchery strays, with very high rates of straying in recent drought years when hatchery-produced juvenile salmon were trucked downstream to the San Francisco Bay estuary to improve smolt survival [9]. Without a natal stream to home to as adults, these fish return and colonize new habitat for spawning.…”

“…Lastly, our study does not verify whether today's Chinook population is self-sustaining, that is whether local smolts eventually return as successfully spawning adults. This should be further investigated via isotopic analysis of contemporary adult salmon carcass otoliths, as they possess the same elemental composition as when the otoliths formed in early life, and are thus natal stream specific [9].…”

Otolith 87Sr/86Sr identifies natal origin, movement and life history of Burbot Lota lota in the Kootenai River following 45 years of impoundment

“…Solid lines are homogenous segments of otolith 87 Sr/ 86 Sr determined by regression tree analysis.Random forest (RF) classification was used to assign the archived Burbot otolith samples to their presumptive origins in the Kootenai River mainstem or the Palaeozoic and Proterozoic geologic formations. Random forest is a machine-learning method based on classification trees that have been used for provenance studies of fish involving both multi-(Tournois et al, 2017) and single-variate(Willmes et al, 2021) otolith markers. An important feature of RF is that it does not require the assumption of normal distribution for the data, and it has been shown to provide higher assignment accuracy compared to other classification methods(Mercier et al, 2011).…”