Does this published results constitute the negatives of broodstock programs? I my book it does:
Hood River Native Broodstock Program:

In 1994 the Oregon Department of Fish and Wildlife and tribes began to evaluate the reproductive success of native broodstock and compared them to the wild fish they were derived from. Kathryn Kostow evaluated the data collected on wild, native broodstock, and old hatchery stock to determine whether there is a life history and behavior difference between them. The following is taken from the abstract in a paper published by Kostow in 2004.

Juvenile phenotypes and fitness as indicated by survival were compared for naturally produced steelhead (Oncorhynchus mykiss), a new local hatchery stock, and an old nonlocal hatchery stock on the Hood River, Oregon, U.S.A. Although the new hatchery stock and the naturally produced fish came from the same parent gene pool, they differed significantly at every phenotype measured except saltwater age. The characteristics of the new hatchery stock were similar to those of the old hatchery stock. Most of the phenotypic differences were probably environmentally caused. Although such character changes would not be inherited, they may influence the relative fitness of the hatchery and natural fish when they are in the same environment, as selection responds to phenotypic distributions. A difference in fitness between the new hatchery stock and naturally produced fish was indicated by significant survival differences. Acclimation of the new hatchery stock in a “seminatural” pond before release was associated with a further decrease in relative smolt-to-adult survival with little increase in phenotypic similarity between the natural and hatchery fish. These results suggest that modified selection begins immediately in the first generation of a new hatchery stock and may provide a mechanism for genetic change.

Kostow notes in her study that ‘new hatchery fish’ derived from the wild population and called ‘native brood stock’ had poor survival.” She said, “Average smolt to adult survival for the naturally produced winter and summer steelhead were five to six times higher than for the new hatchery stock. “

“…large phenotypic responses by fish from the same parent gene pool to the differences between the captive and natural environments are consistent with the process of domestication.”

“This study demonstrates large average phenotype and survival differences between hatchery-produced and naturally produced fish from the same parent gene pool. These results indicate that a different selection regime was affecting each of the groups. The processes indicated by these results can be expected to lead to eventual genetic divergence between the new hatchery stock and its wild source population, thus limiting the usefulness of the stock for conservation purposes to only the first few generations.”

Source: Can. J. Fish. Aquat. Sci. 61: 577-589, 2004