The Native Fish Society under attack


Active Member
Hookedonthefly -
Thanks for the link; some may find it interesting reading.

I was all ready familiar with that study having read both early and final drafts. I have discussed it with several of those involved in the work. Lots of interesting nuggets of information in the study and certainly lots of stuff to get those creaky wheels in my brain turning again. However it remains unclear how much "introgression" is occurring between hatchery and wild Skagit steelhead. It is clear that there is shared genetics between the hatchery and wild Skagit stocks. The mechanism for that share genetics remains unclear. Suggest that reading section 10 might be of interest of interest to some though it can be heavy going.

From that study in 10.4.1 in discussing the conclusions of the genetic studies -

"The SPAN microsatellite loci lack sufficient power to reliably quantify Marblemount
Hatchery (Chambers Creekorigin) introgression into the wild Skagit River winter steelhead
populations, or reliably identify pure unmarked hatchery or hatcheryancestry fish using the
program STRUCTURE."

Same study in 10.4 the author states -

"Part of the reason for the inability to clearly distinguish hybrid from pure fish lies in the fact that the wild Skagit River steelhead and Chambers Creek origin... share a recent common ancestor and are currently weakly (though significantly) differentiated..."

I also from the same report I found the following of interest; it is from section 8.4.3 Genetic Profile of Natural-Origin Sauk Adult Steelhead -

"These tests provide data to show that the genetic profile of steelhead within the Sauk River has not changed over the 30 year time period."

This constant profile remains in spite of significant changes in the temporal and spatial overlap between the hatchery and wild Sauk steelhead.

I'm sure that studies such as this one will allow future researchers to ask more refined questions to tease out some more detailed answers but in the meantime I kind of like it that there remains much that we do not know about one of my favorite fish and rivers. The mystery is part of the attraction.

Okay guys....continue to cut each other to pieces and let the status quo continue. The bottom line is why continue a program that has gotten less and less productive. If you are going to kill most of the fish before they return to the river, why keep stocking them? Why make habitat improvements if you are going to kill the fish before they return to the river. All the anglers are fighting over the tail and ignoring the whole cow. Some day you are going to realize you are all on the same side!

Your right Jim, we are on the same side, we just have some different ideas about how to continue the struggle. I sure hope that Curt doesn't take my responses personally, I like Curt, his input on this site is invaluable, he and the other bios who post on this site are a wealth of knowledge that is hard to find anywhere else.
If my responses seem a bit curt( pun intended), please forgive me, it is not meant to be presonal.

Thanks, Chris


I don't think those anglers who prefer the hatchery programs above wild steelhead are on the same side as those who would like to see less hatchery steelhead and more wild steelhead.

As far as I can tell, some salmon/steelhead anglers would gladly wipe out every single wild fish as long as hatcheries keep dumping in fish for them to catch and kill.

I don't feel that I have much in common with those folks.


Active Member
Chris -
I agree with current low returns it makes little economic sense to continue many of the Puget Sound steelhead hatchery programs. In another world the logical thing to do would be to suspend all but the best (highest return rates) of the PS program during periods of low marine survival until such time as the smolt to adult survivals improve to the point that it makes sense. The problem with that approach is that I'm not sure whether current state steelhead polices would allow for the start of those programs (would have to import brood stock from outside of each basin). Further same policies with the ESA listings dictate that the rivers would have to close. Where would the displaced effort land? The coast?

That does rise a related issue. Where in the heck are all the hatchery fish coming from that are hybridizing with the wild fish. The mean of the values provide by hookedonthefly from table 27 is an introgression rate of 19%. On an average year where the wild steelhead escapement is at the 6,500 goal more than 1200 wild fish would have to spawned with a hatchery fish to result in a 19% introgression rate. It is generally thought that with the temporal separation in the spawning of the hatchery and wild Skagit steelhead that the interbreeding has to be mostly hatchery males spawning with wild females. That would imply that there are at least 2,400 uncaught hatchery fish swimming around the Skagit River. Actually it would have to be significantly more than 3,000 hatchery fish since the hatchery females have completed their spawning by the end of January or early February. For the hatchery males to spawn with that many wild females that interbreeding would have to continue well into May some 3 months after hatchery females have finished one would expect a considerable loss of vigor in those hatchery males; especially considering that to successfully spawn they would have to out compete the larger more vigor wild males; this implies that there may be several times more than 2,400 uncaught hatchery fish in the Skagit potentially spawning with the wild fish.

Some questions quickly come to mind when thinking about the above.

Are the hatchery smolts really surviving that well?

How come we can not catch more of those hatchery fish?

Why don't/didn't we see more hatchery kelts from those HXW crossing in the spring CnR fishery?

If those big numbers of hatchery fish don't exist does that mean that those juveniles from hatchery/wild crosses have a huge survival advantage over those from wild parents?

Are those hatchery males able to significantly out competing those wild males for spawning rights?

Or what was thought to be juveniles produced by hatchery/wild crosses the result of some other factor?

Just some of the things that cause me to scratch my head when I look beneath the surface on some of these issues.


Chris Bellows

Your Preferred WFF Poster
...That does rise a related issue. Where in the heck are all the hatchery fish coming from that are hybridizing with the wild fish...
are there any studies on the % of hatchery fish that residualize in the skagit? are the numbers as high as on the coast?

smaller resident hatchery fish might explain some gene flow that wouldn't result from the few returning adults. we know the importance of resident rainbows to steelhead genetics.


Active Member
KJ -
Hope I answered most of your questions in my follow-up posts to Chris and hookedonthefly.

As always is the case the ideas, observations, etc that I express in these discussions unless attributed directly to some one are my own. My goal in nearly all these discussions is present information so that the readers can be in a position to make informed decisions. Typically the information and observations that I try to pass along are a combination of from my reading, professional experience and an avid angler that considers the Skagit/Sauk my home water. As an angler with biologically training, a natural curiosity about all things fishy, a decent ability to observe and 50 years of experience on the river I think I provide a perspective that might be of interest to at least some of the readers here. As an angler I spend dozens of days a year chasing and enjoying the wonderful and diverse fish resource found in the basin. I have casted a fly over (and caught an anadromous fish) on very mile of the Skagit from the power house at Newhalem to the salt at La Conner and nearly every mile of the Sauk and its forks and have left boot tracks on significant portions of the rest of the anadromous portion of the Skagit basin.

I rarely express an opinion in these discussion and when I do so I try to make sure that it is labeled as my opinion.

Since you asked I'm not a particularly big fan of steelhead hatcheries and at this point in my angling career could easily live without them. That said I do recognize the value and opportunities they provide for many anglers. In regard to the issue of genetic introgression between hatchery and wild steelhead to day in 2013 on the Skagit basin it is my OPINION that it is a minor issue that represents little threat to the wild steelhead of the Skagit. That is not to say that the Skagit steelhead would not be better off without hatchery steelhead; they would. It is my OPINION that the threat of hatchery/wild introgression to the wild Skagit steelhead is similar to the threat to that resource we might see from a steelhead spring CnR season.

I'm often wrong and certainly don't expect everyone to agree with what I have to say (what a boring place it would be if we all thought the same!) but I do hope that many find my ramblings of some interest that at least occasionally cause them to pause and think a minute.



Active Member
Chris -
I don't know of any studies on what the number of residual hatchery steelhead might be on the Skagit. Generally speaking have some residuals is the "norm" for a hatchery program though the hatchery folks can reduce the numbers of those residuals by careful attention to the size and condition of the smolts that are produced and released. Those fish most likely become residuals are those potential smolts that do not reach sufficient size to be true smolts or have grown so large that they seem to lose the urge to migrate.

For those residuals to interact with the wild population (either the adult steelhead or resident rainbows) they would have to rear to the adult stage (which for most would be an additional two years of year in the river). Remembering that those "smolts" are essentially catchable size rainbows. There are lots of studies showing that the survival of catchable rainbows is quite low with many disappearing within weeks or a month or two. That said clearly some do survive and one can find fin clipped adult "rainbows" most of our rivers if you look hard enough. Such fish (especially the males) would have the potential to spawn with either other resident rainbows or adult female steelhead as "sneak spawners".

While one would expect to see similar initial rates of residuals between the Skagit hatcheries and say the ones on the Quillayute river on the coast the fate of those fish would be very different. Like almost everything in the steelhead world answers can be shaped by the particulars of a given system. In this case the flow regimes between the Skagit and the Quillayute are very different. The Quillayute is basically has a rainfall driven hydrograph while the Skagit hydrograph is dominated by the snow melt pattern; especially this time of the year. The average daily flows on the Quillayute has been falling since March and at the time of smolt release (early May) and the period after release the flows on the various Quillayute tributaries are pretty benign. The situation on the Skagit is very different. With the snow melt (typically starting in May) the Skagit goes through a significant period of very high flows (lasting through July) with the highest daily average flows of the year. The highest daily flows on most western Washington rivers happen in the late fall/early winter during the flood season while on the Skagit it is in the spring/early summer. It is this difference that shapes so many life history patterns (run timing, spawn timing, etc) that makes the Skagit such a different situation than many other rivers.

On the Skagit in addition to the impacts of the flow condition on the longer survival of those hatchery residuals there is also a habitat issue. The main stem Skagit has a surprising lack of suitable juvenile steelhead/trout over winter habitats. It is this fact that accounts for how unproductive the main stem Skagit is in raising juvenile steelhead and why its steelhead escapement goal is so low given the size of the river. As a result between the combination of the natural poor survivability of those hatchery fish, the high flows, and lack of juvenile over-winter (high flow refuges) in the Skagit the fate of the vast majority of those fish is death by the early summer. Though clearly some do survive and eventually reach adulthood (at about 14 inches and two years in the river).

The number of the residuals that do reach adulthood has be quite low. In the nearly 30 years since all the steelhead hatchery production has been fin clipped (with adipose fin removal) I would guess between 1 and 2% of the adult sized resident rainbows that I have encountered in the basin were adipose clipped. In fact it would be fair to say I have encounter more wild resident rainbows over 24 inches in length than the total number of adults that were adipose clipped.

The short answer rather than the lengthy on above is that because of the uniqueness of the Skagit basin in my opinion the potential interaction between hatchery residuals and the wild steelhead population on the Skagit is much lower than on most coastal rivers.


Jim Wallace

Smells like low tide.
In the new fishing regs, I noticed that for most coastal rivers, any adipose fin-clipped trout can be retained, regardless of size. Perhaps we should bonk any fin-clipped "resident" rainbows or hatchery steelhead smolts that we catch in these rivers. We are allowed to retain 2 trout per day, but since we are releasing the wild ones, that leaves room to remove two fin-clipped hatchery dinkers from the river.
In the new fishing regs, I noticed that for most coastal rivers, any adipose fin-clipped trout can be retained, regardless of size. Perhaps we should bonk any fin-clipped "resident" rainbows or hatchery steelhead smolts that we catch in these rivers. We are allowed to retain 2 trout per day, but since we are releasing the wild ones, that leaves room to remove two fin-clipped hatchery dinkers from the river.
But then you would have to stop fishing after keeping the second one, right, since you can't keep fishing, even C&R, if you have caught your limit.

I know you are probably being a bit tongue in cheek in suggesting we keep smolts as a means of reducing hatchery impact, but since mortality at sea is a huge factor in steelhead returns, bonking a few smolt is likely to have a small impact.