Delta Smelt life history

Delta Smelt on the brink of extinction

California’s endemic Delta Smelt (Hypomesus transpacificus) is rapidly approaching extinction in the San Francisco Estuary, placing it in the crossfire between human and environmental uses of limited freshwater resources. Though managed as an anadromous species, recent studies have challenged this simple life-cycle model for Delta Smelt, suggesting the species is estuarine resident with several localized “hot-spots” of abundance.

Reconstructing life histories from otoliths

Otoliths (ear bones) provide a life-long archive of physiological (growth) and environmental conditions (chemistry) that a fish has experienced and thus can be used to reconstruct complex life history patterns. Using laser-ablation otolith strontium isotope microchemistry, we discovered three distinct life history phenotypes: freshwater resident (FWR), brackish water resident (BWR), and semi-anadromous (SA) fish. We further refined life history phenotypes using a novel unsupervised algorithm and hierarchical clustering and found that in the last resilient year-class, the FWR (12%) and BWR (7%) comprised a small portion of the population, while the majority of fish were SA (81%). Furthermore, the SA fish could be clustered into four additional life history phenotypes that varied by natal origin, dispersal age and adult salinity history.

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Future conservation efforts should explicitly account for these diverse life history strategies in management actions to avoid Delta Smelt extinction in the wild.

Further reading

Hobbs, J.A., Lewis, L.S., Willmes, M., Denney, C., and Bush, E. 2019. Complex life histories discovered in a critically endangered fish. Scientific Reports 9(1): 16772.

Aggie Chinooks: Salmon returning to the UC Davis watershed

Putah Creek is a small river running from Lake Berryessa through the town of Winters, along the UC Davis campus into the Yolo Bypass. Salmon were once abundant here but became extirpated due to habitat alteration and water diversions. Following on-going restoration efforts Chinook salmon have returned to Putah Creek for the third year in a row. Chinook salmon are well established in many rivers in the Central Valley and are supplemented with several large hatcheries. We conducted in-river surveys and collected otolith (fish ear stones) from carcasses to determine the origin of these pioneering salmon. Otoliths have daily growth increments and can provide a life-long archive of age, growth and environmental signatures. Strontium isotopes measured in otoliths enable us to reconstruct how fish move through habitats and to determine their origin. This project is being carried out in the OGFishlab at UC Davis in collaboration with Nann Fangue, Andrew Rypel, Eric Chapman and Emily Jacinto.

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Chinook Salmon in the Feather River, California

Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento-San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of wild salmon populations. Here, we reconstructed the proportion of hatchery fish on natural spawning grounds in the Feather River, a major tributary to the Sacramento River, using strontium isotope (87Sr/86Sr) ratios of otoliths collected during carcass surveys from 2002-2010. Our results show that prior to the 2007-2008 salmon stock collapse 55-67% of in-river spawners were of hatchery origin; however, hatchery contributions increased drastically (89%) in 2010 following the collapse. Data from a recent hatchery marking program corroborate our results, showing that hatchery fish continued to dominate (~90%) in 2011-2012. Though the rebound in abundance of salmon in the Feather River suggests recovery of the stock post-collapse, our otolith chemistry data document a persistent decline of wild spawners, likely leading to the erosion of locally-adapted Feather River salmon populations.

Download the Paper (Open Access)

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