Assigning Grandparents To Wild Caught Delta Smelt

Grandparentage analysis for Delta Smelt: can hatchery-born fish spawn successfully in the wild?

Background

In 2021 a multi-agency effort began to reintroduce Delta Smelt into their native range in the San Francisco Estuary. For the first few years, this effort was considered experimental, while biologists learned details about where, how, and when to release fish to maximize their survival. Releases typically involve tens of thousands of fish released several times during a season at different locations. In 2024 the program evolved into the Delta Smelt supplementation program to focus on increasing the number of fish released, though experiments are ongoing to improve all aspects and learn from mistakes.

Since its inception and by necessity, all released fish were from genetically managed crosses selected by the GVL; any adult fish caught in the “wild” (i.e. a wild-caught fish) can be analyzed to determine if they were born in the hatchery, and who their parents are.

Since the supplementation program began, the GVL conducted parentage analysis on all wild caught adult fish as part of its hatchery workflow.  Though very few fish are caught (typically <100 per year), most of these fish assign to FCCL parents, indicating that 1) released delta smelt can survive for days to months and 2) very few if any truly “wild” (i.e., no genetic influence from the hatchery) exist.

However, some wild-caught fish do not “assign” to parents, indicating either that parentage failed, which is unusual, or that an adult fish does not have hatchery parents. We wanted to understand if any of the unassigned fish could be from released fish that spawned in the wild, producing offspring that matured into adulthood – in other words we wanted to know if a wild caught fish had hatchery grandparents.

While parentage is relatively easy to assess genetically, it is harder to determine if a fish is the offspring of two hatchery-derived fish from the previous year (i.e., they have hatchery grandparents, but wild-born parents with hatchery ancestry). This analysis is called “grandparentage” analysis.

To develop a protocol to assign a fish to its grandparents, we are developing a microhaplotype/SNP panel to assign “grand-offspring” to their hatchery grandparent crosses.  Our collaborators include the FCCL, US Fish and Wildlife Service, US Bureau of Reclamation, GTseek, and the UC Davis Genome Center.

Project Significance:

Over 100,000 fish are now produced annually at the FCCL and released in a labor-intensive multi-agency effort. If the goal is to eventually have a self-sustaining Delta Smelt population in the Estuary, it is important to know if released fish are surviving and reproducing. This is an important step in evaluating this goal.