| Abstract | Salmon hatcheries are widely used across the Pacific, yet hatchery fish generally have reduced fitness compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if introgression between hatchery and wild fish occurs. In this study, we examined three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, and their corresponding wild progenitor populations using whole genome sequencing. Each hatchery population was compared to its wild progenitor population using multiple metrics of genomic divergence. While evaluating population-level genomic differentiation (FST), we discovered outlier peaks in each hatchery-wild pair, although no outliers were shared across the comparisons. Further analyses indicated that these relatively small peaks are likely due to genetic hitchhiking on hatchery-selected alleles. Overall, our genome-wide analyses provide fine-scale genetic evidence for domestication and highlight the need to assess if certain management practices can mitigate genetic risks despite multiple pathways of domestication. |
