Genomics for chum salmon stock identification

Chum salmon in western Alaska are a vital resource and have recently undergone extreme population declines that have caused community hardship throughout this vast and remote region. Chum salmon from western Alaska are intercepted in mixed-stock fisheries near the Alaska Peninsula and as bycatch in the Bering Sea pollock fishery. Rigorous identification of chum salmon stocks in these targeted and non-targeted fisheries would provide critical new tools for sustainably managing these imperiled stocks. In particular, improving the resolution of stock identification would allow managers to estimate stock-specific impacts of these fisheries. Genetic analysis is the most powerful tool for stock discrimination, but unfortunately, most populations of chum salmon in western Alaska are impossible to differentiate using current genetic methods. Previous efforts to improve stock identification have focused on genotyping thousands of markers on a subset of individuals then selecting panels of a few hundred markers to run on many fish. Here, we propose a different genetic approach, whole genome sequencing. This approach would be used to create a baseline of genetic diversity by genotyping millions of markers in approximately 80 populations across western Alaska (most tissue samples already available from ADFG archives) then using that high-resolution baseline to assign unknown individuals back to their population of origin. We propose that this work be guided by local and Indigenous knowledge in the region. Knowledge holders can help identify populations that can be distinguished by outward characteristics, interpret the geographic patterns in genetic structure, and highlight ways in which this information could eventually be used in management. This novel approach represents our best chance to use genetics to solve the longstanding challenge of stock identification for western Alaska chum salmon.

We anticipate that this project will increase the number of identifiable stocks, although it still may be impossible to tell apart some of the most genetically similar populations. Successful development of whole genome genetic stock identification could eventually help managers estimate stock-specific impacts of these fisheries. It would also provide critical baseline data to help conserve Alaska salmon biodiversity over the long-term.