For Duroboat15, et al:

Whenever hatchery practices utilize steelhead that are not native to the planted river system (ie. non-Broodstock systems, as are most common), they are introducing fish that are genetically different from the natives of that river system. This has been shown by protein electrophoretic and more modern nucleic acid-based data comparing native fish populations with hatchery stocks obtained elsewhere. Gots nothing to do with the fins man. It's in the double helix.

In fact, there are demonstrable genetic differences between, say, native steelhead in the Sky system vs. native steelhead in the Stilly system (much less a Chambers Cr clone vs. a Hoh native). This is so beautifully put together from an evolutionary standpoint, that an upper Sky native fish will have, on average, a different genetic makeup than a lower Snohomish spawner. There are genetically distinct subpopulations even within the same river system. These are preserved when lower system fish reproducibly spawn down there, and the upper river smolts return back up there to spawn with some fidelity. If you look at certain proteins the cells produce, there are reproducible allelic differences in how they are expressed, reflecting differences in gene expression and thereby indicating they are genetically different. These are interpreted in the context of a population of fish, and broad patterns of gene expression (tough to tell much about a population from just one fish). We see the difference phenotypically in how the fish are put together from different systems.

Please tell me how a Cowlitz steelhead has much in common with a good ol down home OP native. Seriously.

Much has been discussed aptly on this site about the problems with introducing fish populations with different genomes into native populations. In my opinion, one of the worst effects is crossbreeding of hatchery fish with native fish, resulting in the introduction of hatchery clone (non Broodstock, mind you) genetic material into the native gene pools. This is called introgression, and results in dilution of native genetic makeup. One could view this as another mechanism of genetic drift (which is good from a natural selective standpoint), but I'd disagree in that it is completely artificial and accelerated, and results in loss of native genomes and hence everything that makes the nates special. The concept of introgression was a theoretic one, and if I remember correctly, has been shown to have occured in certain salmonid populations in low gradient river systems like the lower Snohomish, with statistical significance. Once those unique populations are lost, they can never be recovered (it is an extinction). I reviewed the literature on this about 7 years ago for a talk, but I don't have the references handy. I might be able to find them with a lot of work somehow.

I don't want to repeat much of what Smalma and others have explained here. A lot of people are more qualified to explain these things than I am. I just think it's really important to understand that native fish runs are really special, and fragile, and worth fighting for. To say that non-Broodstock hatchery fish are the same as individuals in a native population is way off base.