Using genetic tools to determine habitat use patterns of juvenile Chinook salmon in the Sacramento River

Background/Question/Methods

The Yolo Bypass is a flood structure that occupies the historic floodplain habitat of the lowermost Sacramento River. This seasonally flooded and highly managed habitat is important to a number of special status fishes, including threatened and endangered populations of Chinook salmon (Oncorhynchus tshawytscha). Juvenile fish found inside the Bypass have increased growth compared to juveniles found in the mainstem of the Sacramento River. Therefore, this area has been identified as a high restoration priority by the National Marine Fisheries Service, the National Academy of Sciences, and the Bay Delta Conservation Plan. Much of the restoration projects in the area have focused on providing rearing habitat for native fishes, such as juvenile Chinook salmon. However, very little is known about how the different populations of Chinook salmon use the habitat in the Yolo Bypass and how this compares to their habitat use in the mainstem of the Sacramento River. To address this uncertainty, we sampled juvenile Chinook found in the Yolo Bypass and the mainstem Sacramento River to evaluate if there is differential occupancy of the habitats across the different Chinook populations. We used our newly developed panel of single nucleotide polymorphisms (SNPs) to identify juvenile Chinook to their run of origin, as visual identification is not possible.

Results/Conclusions

Our newly developed panel of SNPs is highly effective at determining run of origin for juvenile Chinook salmon and will prove to be a very useful tool for conducting field studies. We found differences in the use of the floodplain habitat among the different runs. This has important implications for the management of the floodplain habitat in the Yolo bypass—in order to increase the habitat benefit provided by the floodplain habitat, the goal should be to ensure there is adequate flooding in the Bypass during the peak emigration timing. Additionally, performance criteria for restoration plans and activities should be developed in light of these results, considering which populations of Chinook juveniles are most likely to be affected by proposed actions.