Life History and Smoltification Shape Genomic Signatures of Thermal Tolerance in Chinook Salmon

Temperature is a key determinant of survival and distribution in ectothermic species, but how variation in thermal resilience is influenced by developmental transitions, life-history strategies, and their interaction with population-specific genomic variation is poorly understood. Using Chinook salmon (Oncorhynchus tshawytscha), an ecologically and culturally important species of conservation concern, we investigated how population-specific life histories influence thermal tolerance and its underlying genomic architecture. We assessed thermal tolerance using critical thermal maximum (CT_max), a nonlethal measure of acute thermal tolerance that determines the temperature at which fish can no longer maintain equilibrium during a thermal ramp. CT_max was measured in four populations representing two life-history types, stream-type and ocean-type, that differ in freshwater residency and age at smoltification. Stream-type populations exhibited lower CT_max than ocean-type populations in both freshwater and saltwater, revealing consistent life-history differences in thermal tolerance. Smoltification significantly reduced CT_max across all populations, indicating that physiological transformation for seawater readiness comes at a cost to thermal performance. Thermal tolerance was more variable in saltwater, highlighting the influence of environmental context on phenotypic expression. Although populations exhibited distinct genetic variants and expression profiles, all populations showed enrichment of common functional pathways, including the unfolded protein response and ion transport. These findings suggest that similar physiological outcomes are achieved through distinct regulatory architectures across life-history types and developmental stages. Together, our results provide insight into the polygenic nature of thermal tolerance in Chinook salmon, emphasising how life history, environment and genetic background interact to shape resilience to thermal stress.