Survival of a threatened salmon is linked to spatial variability in river conditions

Extirpation of the Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha) evolutionary significant unit (ESU) from the San Joaquin River is emblematic of salmonid declines across the western seaboard of the United States. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. Two regional mortality sinks were evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll a, fluorescent dissolved organic matter (fDOM), turbidity, and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Key words: juvenile salmon, migration, habitat, survival, FLAMe La disparition locale de l'unite evolutionnaire significative (UES) du saumon chinook (Oncorhynchus tshawytscha) a migration printaniere de la vallee centrale dans la riviere San Joaquin est representative des declins de salmonides a la grandeur de la cote ouest des Etats-Unis. Si des efforts de restauration d'habitats et de reintroduction de poissons sont en cours, des etudes telemetriques recentes revelent une faible survie des juveniles lors de la devalaison vers l'ocean. Les etudes anterieures se sont axees sur la modelisation de la survie en fonction du debit et de la region geographique, mais n'ont generalement pas considere les effets de la variabilite des habitats. Afin d'evaluer le lien entre les conditions environnementales et la survie des saumons chinooks a migration printaniere juveniles, nous avons jumele des approches de cartographie d'habitats a haute resolution spatiale a la telemetrie acoustique le long d'un troncon de 150 km de la riviere San Joaquin durant le printemps 2019. Si la survie globale durant la devalaison etait faible (5 %), notre schema de classification base sur l'habitat decrit mieux les variations de la survie de saumoneaux dotes d'etiquettes acoustiques que d'autres modeles possibles bases sur la geographie ou la distance. Deux puits de mortalite regionaux sont ressortis le long du profil longitudinal de la riviere, revelant une faible survie dans des secteurs ayant en commun des temperatures elevees, mais dont les valeurs de chlorophylle a, matiere organique dissoute fluorescente (MODf), turbidite et oxygene dissous different. Ces constatations demontrent la pertinence d'integrer des cadres de classification des habitats fluviaux pour ameliorer la comprehension de la dynamique de la survie de populations de poissons menacees. [Traduit par la Redaction] Mots-cles : saumon juvenile, migration, habitat, survie, FLAMe
Introduction Pacific salmon populations native to California, USA have declined throughout the last century, shifting once economically viable runs to critically low numbers (Yoshiyama et al. 1998; Katz et al. [...]