Northwest Fisheries Science Center

Case examples: Endangered Salmon

Endangered salmon: Which population?

Water diversion screen Water diversion screen

Protected populations of salmon may share the same habitat with unprotected populations of the same species at certain stages of their lives. For instance, Upper Columbia River (UCR) spring-run Chinook are listed as endangered under the Endangered Species Act of 1973 (ESA), while the summer-run Chinook in the UCR are not protected. During certain times of the year, both populations can be found in the Methow River within the UCR basin.

The Methow Valley Irrigation District (MVID) diverts water from the Methow River into irrigation ditches throughout the spring and summer for farming in the Upper Columbia River Valley. The MVID is required to use water diversion screens to prevent salmon smolts from being pulled into irrigation ditches throughout the year. In the past, however, these screens were not 100 percent effective. In the fall when the MVID drew down the water for the winter, fish that had been diverted into the irrigation ditches were stranded once the water receded. Were fish from the protected spring-run population harmed?

Salmon smolts Salmon smolts

These salmon smolts were submitted as evidence that the MVID failed to protect ESA listed salmon. At this life history stage, carcasses can degrade quickly, making it difficult to positively identify species, and population or run time can only be determined by DNA testing as physical characters are not a reliable indicator.

Building a Genetic Baseline

In order to determine whether the smolts were the ESA-listed spring-run Chinook, or the non-protected summer-run, the Forensics Unit needed to find genetic markers diagnostic for the different groups. Drawing on the expertise of the Center’s comprehensive genetics program, the Unit’s forensic geneticist compiled a genetic baseline of Upper Columbia River spring and summer run Chinook for use in genetic stock identification (GSI). The map shows the locations of populations analyzed for the baseline.

Chinook baseline map

Upper Columbia Chinook Baseline

Each of these three graphs show how the spring-run and summer run Upper Columbia River Chinook differ significantly in three separate areas of their genomes. The genomes differ in the frequency of a specific allele or gene variant.

Cytochrome p450
allele A 0.035 0.926
allele B 0.965 0.074
allele A 0.021 0.919
allele B 0.979 0.081
haplotype A 0.932 0.592
haplotype B 0.068 0.408
Upper Columbia Chinook baseline graphs

This genetic database allowed the Forensics Unit to compare the relevant genes from the evidence against the baseline, and revealed that the some of the fish that were killed were indeed protected spring-run Chinook.


Schwenke, P. L., J. G. Rhydderch, M. J. Ford , A. R. Marshall, and L. K. Park. 2006. Forensic identification of endangered Chinook salmon (Oncorhynchus tshawytscha) using a multilocus SNP assay. Conservation Genetics The next link/button will exit from NWFSC web site 7:983–989.