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Parentage-Based Tagging of Chinook Salmon in Putah Creek.

Parentage-Based Tagging of Chinook Salmon in Putah Creek.

Background and Significance

Putah Creek is a tributary of the Sacramento River that runs through Yolo and Solano Counties in California. Dams constructed on Putah Creek in the 1950’s greatly reduced flows which caused native fishes such as Chinook salmon to decline. In the 1980s, prolonged drought caused Putah Creek to desiccate, and a resulting lawsuit against water managers led to a legal agreement which established a more natural flow regime in the creek. Slowly native fish populations started to rebound. In 2015, around 200 adult Chinook salmon returned to spawn in Putah Creek and they have been documented spawning there nearly every year since.

Chinook salmon exhibit natal philopatry, which means they almost always return to the location they were born to reproduce. But sometimes Chinook born in hatcheries get lost, or “stray,” on

their way back to the hatchery. Currently we aren’t sure whether salmon spawning in Putah Creek were born there or if they are strays from Sacramento River hatcheries. We can answer this question by collecting genetic data on spawning adults over a period of many years and performing parentage analysis to identify their offspring returning to spawn. In the Central Valley, Chinook salmon spend 2-3 years in the ocean before returning to spawn, so we can perform parentage analysis on spawning adults three years apart to find parent-offspring pairs. This analysis, called parentage-based tagging, allows us to study the salmon’s spawning behavior without physically tagging baby salmon to document their return.

Each year, tissue will be collected from as many Chinook salmon returning to spawn in Putah Creek as possible. Data will be collected at SNP loci throughout the genome of each individual and parentage analysis will be performed on spawning runs 2-3 years apart. The presence of parent-offspring pairs would confirm the development of a unique Putah Creek Chinook spawning run. These data can also be used to address other behavioral and ecological questions about the Putah Creek Chinook population.


This work is part of a larger project to monitor biodiversity and study the ecology of native fishes in Putah Creek, led by Dr. Andrew Rypel and Dr. Nann Fangue, and funded by the Solano County Water Agency. From the GVL, Dr. Mac Campbell and Dr. Andrea Schreier are leading bioinformatics and parentage analysis.

See the below paper for additional information about PBT: 

Steele, C. A., Hess, M., Narum, S., & Campbell, M. (2019). Parentage‐based tagging: reviewing the implementation of a new tool for an old problem. Fisheries, 44(9), 412-422. 

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