Unnatural selection of salmon life histories in a modified riverscape

Altered river flows and fragmented habitats often simplify riverine communities and favor non‐native fishes, but their influence on life‐history expression and survival is less clear. Here, we quantified the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed two decades of Chinook salmon monitoring data to explore the influence of regulated flows on juvenile emigration phenology, abundance, and recruitment. We then followed seven cohorts into adulthood using otolith (ear stone) chemical archives to identify patterns in time‐ and size‐selective mortality along the migratory corridor. Suppressed winter flow cues were associated with delayed emigration timing, particularly in warm, dry years, which was also when selection against late migrants was the most extreme. Lower, less variable flows were also associated with reduced juvenile and adult production, highlighting the importance of streamflow for cohort success in these southernmost populations. While most juveniles emigrated from the natal stream as fry or smolts, the survivors were dominated by the rare few that left at intermediate sizes and times, coinciding with managed flows released before extreme summer temperatures. The consistent selection against early (small) and late (large) migrants counters prevailing ecological theory that predicts different traits to be favored under varying environmental conditions. Yet, even with this weakened portfolio, maintaining a broad distribution in migration traits still increased adult production and reduced variance. In years exhibiting large fry pulses, even marginal increases in their survival would have significantly boosted recruitment. However, management actions favoring any single phenotype could have negative evolutionary and demographic consequences, potentially reducing adaptability and population stability. To recover fish populations and support viable fisheries in a warming and increasingly unpredictable climate, coordinating flow and habitat management within and among watersheds will be critical to balance trait optimization versus diversification.