Data from: Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program

While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho USA. We expanded upon previous estimates of relative reproductive success (RRS) to include two full generations and used generalized linear models to determine if origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the 1st generation and mean of 2.52 times in the 2nd generation). Overall when spawning in nature, hatchery-origin fish demonstrated a trend towards lower RS compared to natural-origin fish (p0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.Master_Genotype_DataThis is the raw genetic data for all samples used in the analyses of this manuscript.Gt-Seq_Primers_ProbesThis is the list of the primers and probes used for GT-seq SNP genotyping.Koch_et_al_2018_Rscripts_DataAnalysesThis is the R script used for all analyses associated with this manuscript.final_genetics_dataThis is the R object to load into the Rscript for easy start-up of script