Comprehensive genomic assessments of oolichan population health and range in Haisla territory
Date
2025
Authors
Allison, Michael J.
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Abstract
Protection of aquatic species relies on timely, reliable, and detailed monitoring data, which can be challenging to obtain from species whose life histories and distributions are not well described. The anadromous smelt, oolichan (Thaleichthys pacificus), despite playing vitally important cultural and ecological roles in their ecosystems, have been given relatively little attention from the scientific community due to their lack of value as a commercial fishery. Since the 1990s their populations have experienced steep declines throughout their range, from California to the Alaskan panhandle. The Haisla Nation in Northern BC are one of many Indigenous groups whose traditional relationship with oolichan, also known as “saviour fish” for their importance as a food source after winters, is in peril. Supporting their recovery relies on accurate knowledge of spawning locations, yearly abundance, and organismal health. Herein, I present research examining facets of oolichan spawning distribution, behaviour, and organism-level stress response using the molecular approaches environmental DNA (eDNA) and transcriptomics. This work was conducted as part of the Conservation and Recovery Research on Oolichan in Haisla Territory (CAROOHT) program – a multi-year collaborative initiative between the Haisla Nation, Ecofish Research Ltd., Stantec, the University of Victoria (UVic), the University of Northern British Columbia (UNBC), and Simon Fraser University (SFU). First, I demonstrate the use of unikseq, a tool for the creation of novel eDNA assays from large sequence datasets. Building on top of this and other bodies of work, I present the extensive analysis of hundreds of eDNA samples taken each year from 2019-2024 to elucidate broad- and fine-scale trends in oolichan spawning distribution, timing, and abundance in Haisla Territory. Finally, to assess oolichan organismal health, I have assembled the first de novo transcriptome and developed bioindicator assays targeting gene transcripts that are differentially expressed in oolichan tissue in the presence of oil contaminants. Developing and using these molecular tools in conjunction with conventional monitoring techniques in Haisla Territory, I demonstrate the capacity of harmonized approaches to provide an enriched view of population health, while advancing the capabilities of each individual method.
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Keywords
Environmental DNA, Transcriptomics, Molecular biology, Fisheries, Eulachon, Oolichan, Haisla Nation, Indigenous fisheries, Fish health