RT Journal Article SR Electronic T1 What can genomics tell us about the success of enhancement programs in anadromous Chinook salmon? A comparative analysis across four generations JF bioRxiv FD Cold Spring Harbor Laboratory SP 087973 DO 10.1101/087973 A1 Charles D. Waters A1 Jeffrey J. Hard A1 Marine S.O. Brieuc A1 David E. Fast A1 Kenneth I. Warheit A1 Robin S. Waples A1 Curtis M. Knudsen A1 William J. Bosch A1 Kerry A. Naish YR 2016 UL http://biorxiv.org/content/early/2016/11/17/087973.abstract AB Population enhancement through the release of cultured organisms can be an important tool for marine restoration. However, there has been considerable debate about whether releases effectively contribute to conservation and harvest objectives, and whether cultured organisms impact the fitness of wild populations. Pacific salmonid hatcheries on the West Coast of North America represent one of the largest enhancement programs in the world. Molecular-based pedigree studies on one or two generations have contributed to our understanding of the fitness of hatchery-reared individuals relative to wild individuals, and tend to show that hatchery fish have lower reproductive success. However, interpreting the significance of these results can be challenging because the long-term genetic and ecological effects of releases on supplemented populations are unknown. Further, pedigree studies have been opportunistic, rather than hypothesis driven, and have not provided information on “best case” management scenarios. Here, we present a comparative, experimental approach based on genome-wide surveys of changes in diversity in two hatchery lines founded from the same population. We demonstrate that gene flow with wild individuals can reduce divergence from the wild source population over four generations. We also report evidence for consistent genetic changes in a closed hatchery population that can be explained by both genetic drift and domestication selection. The results of this study suggest that genetic risks can be minimized over at least four generations with appropriate actions, and provide empirical support for a decision-making framework that is relevant to the management of hatchery populations.