Primary Contacts: Maddie Betts ([email protected]), Krista Nichols ([email protected]), Mia Nahom ([email protected])
Eulachon (Thaleichthys pacificus, Osmeridae) are anadromous smelts that are endemic to the North Pacific Ocean, with a range that stretches from northern California to the southeastern Bering Sea along the coast of Alaska. Eulachon are an important prey species for birds, marine mammals, and fishes, and culturally important for First Nation and American Indigenous peoples. Recent studies of the population structure of eulachon have identified a number of distinct populations. The southern population of eulachon (ranging from the Nass River in BC, Canada, to the Mad River in CA, USA) has faced sharp population declines in recent decades and was listed as threatened under the Endangered Species Act in 2010.
In collaboration with Fisheries and Oceans Canada (DFO), the primary objective of this project was to identify what genetic stock eulachon bycatch samples caught by the West Coast Ocean Shrimp Fishery belong to, and to what extent the fishery is impacting the threatened Southern population. To do this, we utilized high-throughput sequencing technologies and the genetic baseline designed by Sutherland et al. (2012), which included 521 variant single nucleotide polymorphisms (SNPs), to assign each of ~1600 eulachon bycatch samples to a specific genetic stock.
We selected 1,632 eulachon bycatch fin clip samples from a total of several thousand samples collected between 2013 and 2025. Samples were preserved in 95% ethanol. Samples were extracted using the DNeasy Blood and Tissue kit on a QIAcube high-throughput automated extraction machine. DNA was eluted in 200 uL EB and stored at -20 degrees C.
Samples were sequenced on an Illumina MiSeq using the Genotyping-by-Thousands (GTseq) method developed by Nate Campbell. We utilized and optimized a panel of loci originally developed by DFO for sequencing - the final panel used contained 475 loci.
.fastq files from completed runs were demultiplexed and then analyzed using the GTscore pipeline originally developed by Garrett McKinney (see his github here).
Samples were identified with a genetic stock ID using additional bioinformatics pipelines.
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