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Genetic Management of the Delta Smelt Refuge Population

The Delta Smelt (Hypomesus transpacificus) is a threatened species endemic to the Sacramento-San Joaquin Delta. A refuge population was initiated in response to their rapid decline in the wild.

Genetic Management of the Delta Smelt Refuge Population

A 2-year-old delta smelt implanted with an elastomere tag                

For more information contact Dr. Mandi Finger:

Background and Significance of Study

The Delta Smelt (Hypomesus transpacificus) is a threatened species endemic to the Sacramento-San Joaquin Delta. In 2008, in response to the rapid decline of Delta Smelt in the wild, a refuge population was initiated at the UC Davis Fish Conservation and Culture Laboratory.  The underlying motivation for the creation of the refuge population is to provide an “insurance policy” in the event of species extinction in the wild. The broodstock for the captive population is kept at the FCCL, with an additional, smaller backup population maintained at the Livingston Stone National Fish Hatchery. Dr. Mandi Finger is the PI for the genetic monitoring and management portion of the FCCL population. The goal of genetic management is to maintain a captive population that is genetically (and therefore phenotypically) similar to the wild population. This way, in the event of the need to reintroduce Delta Smelt, the hatchery population will be best-poised to survive and thrive. This goal is achieved through making single pair crosses (one male x one female) each year that 1. minimize of inbreeding, 2. incorporate wild fish into the broodstock, and 3. maximize overall population genetic diversity using the aquaculture facilities at FCCL.

Future Work

We hope to use archived fin clips and DNA to investigate the genetic consequences of domestication at the FCCL. We have noticed that we do not recover as many offspring from fish with wild parents as those with two cultured parents. This indicates that fish from two cultured parents have better survival to adulthood rates. We will use recovery as a phenotype measure to examine the genetic architecture of this phenomenon.

Resulting Publication

Finger, A.J., Mahardja, B.M., Benjamin, A., Lindberg, J., Ellison, L., Fisch, K., Hung, T-C., May, B.P. (2018) Evidence of domestication selection in a conservation hatchery for Delta Smelt. Journal of Heredity, 109(6):689-699). (pdf)


Fish Culture and Conservation Laboratory


Delta Smelt remains on the edge of extinction (1/2017)

California drought: Delta Smelt survey finds single fish, heightening debate over water supply

“Refuge” for the endangered Delta Smelt – newly funded

UC Davis reels in $10M to save Delta Smelt from extinction

Feds fund captive breeding program for Delta Smelt

Swimming upstream to save a victim of the state’s water crisis

Delta smelt almost gone, except in hatchery

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