Endangered Cultus Lake sockeye salmon exhibit genomic evidence of hypoxic and thermal stresses while rearing in degrading freshwater lacustrine critical habitat.

Water quality degradation due to lake eutrophication and climate change contributes to the risk of extirpation for the endangered Cultus Lake sockeye salmon. Sockeye salmon juveniles experience both low-oxygen water in profundal lake habitats and elevated temperatures above the thermocline during diel vertical migrations in summer and fall when the lake is thermally stratified. We used a transcriptomic tool (Salmon Fit-Chip) to determine whether salmon were experiencing thermal and/or hypoxic stress during this period. The results showed that over one-third of the fish were responding to either hypoxic (35.5%) or thermal stress (40.9%) during periods when these environmental stressors were pronounced within the lake, but not during periods when profundal dissolved oxygen was elevated and the water column was isothermal and cool. The most consistent signs of hypoxic stress occurred during July (52.2%) and September (44.4%). A total of 25.7% of individual fish sampled during months when both stressors were occurring (July, September, October) showed signatures of both stressors. When a combination of hypoxic and thermal stress biomarkers was applied, 92% of fish showed evidence of one or both stressors; hence, for at least several months of the year, most sockeye salmon juveniles in Cultus Lake are experiencing anthropogenically environmentally induced stress. We also detected the presence of pathogenic ciliate