Using Genetic Data to Determine Origin for Out‐Migrating Smolt and Returning Adult Steelhead Trout (Oncorhynchus mykiss) in a Southeast Alaska Drainage

ABSTRACT Oncorhynchus mykiss is a partially migratory salmonid species, and many migratory populations (known as steelhead) have declined in recent decades in the western United States and Canada. Closely related resident populations (known as rainbow trout) may be an effective resource in the recovery of these declining migratory populations. However, the extent to which different populations of resident rainbow trout produce migratory individuals and how likely these individuals are to return as adults to spawn remains unknown. One limitation to answering these questions is the identification of loci that accurately segregate between migratory and resident populations. To address this limitation, we used existing genomic data from a well‐studied population of O. mykiss from Southeastern Alaska (Sashin Creek) to identify loci that segregate between phenotypes. We then utilized Double Mismatch Allele‐Specific qPCR (DMAS‐qPCR) to genotype 233 smolts out‐migrating from Sashin Creek and 99 returning adult steelhead trout across a five‐year period to determine (a) the origin of out‐migrating smolts and returning adults and (b) to quantify the extent to which the resident population contributes to the migratory population. Our results show that 37.3% of out‐migrating smolts were produced from resident parents, whereas 19.3% of returning adults had resident parents. Ultimately, these results demonstrate that resident populations of rainbow trout produce migrant offspring that successfully complete their migration and return to spawn, increasing population sizes and likely improving genetic diversity. Therefore, conservation efforts should consider landlocked resident populations for producing smolts when developing recovery plans for migratory steelhead populations. We find evidence that resident populations of rainbow trout can and do produce migratory smolts that can successfully return to spawn. There are statistically significant differences in return timing between migrants with migratory parents and migrants with resident parents suggesting there may be selection operating on return timing.