Data from: Kokanee-sockeye salmon hybridization predominantly leads to a resident life history with outcomes for a long-term reintroduction program

Stocking programs have been widely implemented to restore extirpated fish species to their historical ranges, and must include careful consideration of potential hybridization dynamics. The sockeye salmon (Oncorhynchus nerka) reintroduction project in Skaha Lake (British Columbia, Canada) provides an excellent opportunity to investigate the outcomes of hybridization between anadromous (migratory) sockeye and resident kokanee over a two-decade long program. Prior research established the presence of hybrids, with the vast majority of F1 spawners exhibiting a resident life history. Yet, it remains unknown whether anadromous hybrid smolts exhibit fitness effects in the form of reduced survival during migration, or whether they predominantly remain resident. Here, we paired cohort-based sampling (age-0 fry, age-1 smolts, adult spawners) in Skaha Lake with SNP genotyping, otolith microchemistry, and morphometrics to: 1) reconstruct trends in stock proportions of sockeye, kokanee and hybrids (F1, B1-sockeye, B1-kokanee) over a 15-year time series; and 2) investigate the morphological, behavioral and fitness outcomes of sockeye-kokanee hybridization. Genetic assignments revealed stock proportions varied widely over time and across cohorts, with hybrids making up a substantial proportion of the population despite earlier suggestions that hybrids may exhibit reduced fitness. Approximately 94% of F1 and 100% of B1-kokanee spawners exhibited microchemical evidence of a resident life history. Conversely, B1-sockeye spawners were evenly split between resident and anadromous, displaying a significant difference in fork length associated with life history and providing further evidence for a genetic basis to migratory behaviour. More broadly, our findings have important management implications for habitat restoration and underscore the need for continued monitoring with consistent sampling among partner organizations.