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SHERLOCK Assays for Invasive Species in the San Francisco Bay-Delta

SHERLOCK Assays for Invasive Species in the San Francisco Bay-Delta

Background and Significance

Invasive species can be very destructive to ecosystems, as they can compete with or eat native species and alter habitat structure or nutrient cycling. It is very difficult to eradicate invasive species once they become established in an ecosystem making early detection imperative. In the San Francisco Bay-Delta system, invasive species of significant concern include Dreissenid mussels and nutria.

Why are Dreissenid Mussels and Nutria a Problem? 

The Dreissenid mussels, zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussels, native to Eurasia, have significantly damaged the North American aquatic ecosystems. They have invaded by altering native food webs and changing water chemistry and clarity. These mussels can infiltrate and clog water infrastructure, which is a significant threat to California’s water delivery system. Though zebra and quagga mussels have invaded a few isolated water bodies in central and northern California, they have not yet entered the Bay-Delta. 

The nutria (Myocastor coypus), on the other hand, is a semi-aquatic rodent native to South America that has already been detected in the Bay-Delta. Nutria burrow into levies, degrading flood protection infrastructure, and destroy important wetland habitats.


Zebra and quagga mussels are small and difficult to detect in low numbers and nutria are elusive, despite their relatively large size, and difficult to trap. Sensitive genetic identification methods like SHERLOCK can be used to detect DNA and RNA shed by these organisms into the water. Environmental DNA, or eDNA, remains in water longer than environmental RNA, or eRNA, so the former should allow for the most sensitive detection of invasive mussels or nutria. However, DNA can be shed by living or dead organisms, while RNA is produced only by living organisms. The detection of both eDNA and eRNA at a location would provide strong evidence

of recent occupation of that area by a live, target organism. Our eDNA and eRNA SHERLOCK assays for the Dreissenid mussels and nutria will provide initial evidence that these organisms have entered an area, flagging those areas for more intensive monitoring.

We will extract DNA and RNA from tissue samples from zebra and quagga mussels and nutria. SHERLOCK assays will be designed and tested against samples of related mussels and rodents, shared by colleagues at UC Davis and museums across North America, to make sure the assays detect only their intended targets. We will use EQO’s Osprey eDNA/eRNA sampler to filter large volumes of water from systems known to be inhabited by these invasive species as well as

those known to be free of them. We will determine whether the SHERLOCK assays can detect eDNA and eRNA of target species when they are present without give false positives when they

are absent.


This work is being led by Dr. Emily Funk with assistance from undergraduate researcher Alexis Samaniego, in collaboration with biologists at the California Department of Water Resources

and the California Department of Fish and Wildlife and the biotech company EQO. Initial assay design for Dreissenid mussels was performed by Alisha Goodbla. This project is funded by the California Department of Water Resources.

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