Evaluating the Effectiveness of Managed Gene Flow to Reduce Adaptation to Captivity in Supportive Breeding Programs

Conservation and management programs are increasingly reliant on captive rearing in aquaculture to support declining wild populations. However, adaptation to captivity can decrease the fitness of captive individuals when released in the wild and may reduce the fitness and genetic diversity of wild populations.  Managed gene flow, or incorporating wild individuals as broodstock in breeding programs, can theoretically reduce genetic differentiation caused by adaptation to captivity, but the effectiveness of this strategy is uncertain. We examined the potential of this practice to reduce genetic differentiation using two hatchery lines of Chinook salmon, Oncorhynchus tshawytscha. The “integrated” line uses natural origin individuals as broodstock, while the “segregated” line has no gene flow from the wild. The founding wild population and three generations (sampled in 2002, 2006, 2010) of both hatchery lines were compared at thousands of molecular markers identified through restriction site associated (RAD) sequencing. Measures of population differentiation (F_ST) compared to the wild founders were small for all populations. However, F_ST for the 2010 segregated population (F_ST=0.0085±0.030, p<0.001) was more than an order of magnitude higher than the 2010 integrated population (F_ST=0.00016±0.019, p>0.05). A Chinook salmon linkage map developed in our lab was used to conduct genome scans of divergence from the founder population across the chromosomes. We detected a number of “outlier” regions in the segregated line that are consistent with directional selection. These results suggest that managed gene flow has reduced genetic differentiation in captivity and can be used to maximize the success of conservation-focused aquaculture programs.