Fish in the wild, through natural selection, are adapted to their environment. Fish raised in hatcheries are raised in conditions where natural selection may run a different course. Stocked fish maybe adapted to a relatively stress free environment, and genes that normally would die off in the natural environment care allowed to make their way back into the native population. This can compromise the native populations gene pool making them less capable of survival.
Stocked fish come from a brood stock. Brood stocks are the reproducing fish that produce the progeny which are then stocked into the waters. The brood stock is often of the same species as the wild fish and often from a different population that has adapted to it original environment. For example, salmon were introduced into the Great Lakes and naturally reproduce there. Stocked salmon in the Great Lakes may come from a Pacific coast brood stock where they are adapted to the environment and diseases of the west coast. When the native and stocked fish interbreed it compromises the gene pool of the native fish.
Also, in this article, stocking fish can often hide the state of the native fish population. Artificially high populations because of stocked fish can hide a fishery that is imperiled due to overfishing, habitat loss, and a number of other threats.
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