Scientific consequences / benefits of hatchery vs native breeding

[DLJeff]

I asked a question on another thread about a steelhead report. Jason rightfully reminded me I had hijacked the thread and I apologize for that. Alosa posted a great summary of some research by fishery biologists that helps explain the potential consequences and benefits of introducing hatchery bred fish into a native population. Thanks for that, I much appreciate it and learned a little. Here's his responses to my query:


I'll chime in on this (if that's ok Loren). First, my background is fisheries conservation genetics, so what I am about to say isn't my opinion, but what has been demonstrated repeatedly by multiple independent studies of various anadromous fish species (primarily salmonids). Just to show that I'm serious about that, I've listed some of those key studies below, but I'll provide the cliff notes here:

1) The negative effects of stocking practices on the genetic integrity and fitness of wild fish populations have been well documented;

2) There are two general categories of stocking:
i) supportive breeding - reproduction of a segment of the wild population is conducted in captivity followed by the release of the captive progeny to supplement that same wild populations. Here, no genes from other populations are introduced into the system (but there are OTHER negative effects);
ii) stock transfers - the relocation of individuals between wild populations that can introduce genes that would otherwise not normally be observed in that population;

3) Supportive breeding favours the reproductive rate of one segment of the wild population. This can lead to an increase in the variance in family size and a corresponding decrease in genetically effective population size (Ne). Maintaining a large Ne is important for long term population persistence, because the rate of inbreeding, and thereby the loss of genetic diversity, is proportional to the inverse of Ne. The effects of supportive breeding on Ne are particularly important in small populations, b/c stocking can reduce Ne below what it could have been had no stocking occurred at all. This is important b/c the loss of genetic diversity can impede the capacity of populations to respond to environmental change and increase extinction risk;

4) Domestication selection in hatcheries are another important consequences of supportive breeding. Traits that are important in a hatchery are not necessarily beneficial in the wild, and selection in hatcheries can shift trait distributions away from their wild optimum. If many hatchery raised individuals (with traits that are optimized for life in captivity) are released into a wild population, this can result in a reduction in the average fitness of the wild population, and may negatively impact population persistence;

5) Stock transfers among genetically different populations can reduce fitness and jeopardize the long term persistence of those populations. Many anadromous fishes home to their natal rivers and this restricts gene flow leading to the establishment of genetically distinguishable populations and local adaptations that optimize population fitness. Stock tranfers remove the reproductive barriers established through homing, and create opportunities for non-native genes to introgress among wild populations, and can eliminate those important local adaptations.

This is an abridged version of some of the details. There is more to the story, but I think I've highlighted the key points without getting too technical (I hope). Those of you interested in specifics can check out the references below (Laikre et al. 2010 provide an EXCELLENT comprehensive review). If anyone wants it and has difficulty finding it, PM me and I'll try to pass it along.


Here are a few key references:

Araki, H., B. Cooper, and M.S. Blouin. 2007. Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318: 100-103.

Hasselman DJ, Limburg KE (2012) Alosine restoration in the 21st century: challenging the status quo. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 4: 174-187.

Hindar, K., N. Ryman, and F. Utter. 1991. Genetic effects of cultured fish on natural fish populations. Canadian Journal of Fisheries and Aquatic Sciences 48: 945-957.

Laikre L, Schwartz MK, Waples RS, Ryman N (2010) Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends in Ecology and Evolution 25: 520-529.

Lynch, M., and M. O’Hely. 2001. Captive breeding and the fitness of natural populations. Conservation Genetics 2: 363-378.

Pearse DE, Martinez E, Garza JC (2011) Disruption of historical patterns of isolation by distance in coastal steelhead. Conservation Genetics 12: 691-700.

So if I can carry this conversation onward for a little bit...

Regarding "supportive breeding": Good point about reducing the gene diversity along with the accumulated hereditary resistance to detrimental environmental factors. The counter effects could also true if properly managed, correct? For instance, could you not introduce beneficial genetic markers that could counter negative environmental factors, such as introducing genes that resist whirling disease? Maybe this is getting too close to playing God and meddling in Mother Natures' garden which usually raises her hackles.

I understand and agree with the point that survival traits learned in hatcheries are rarely beneficial in the wild. Obviously way wild fish are nearly always harder to fool than hatchery fish. Let's ignore the "homing trait" for a minute and allow me to ask, is there any data that indicates how long it takes a fish to "re-learn" the old survival traits? I know several rivers in southern Missouri that were regularly stocked back in the 50's - 70's but hadn't been stocked since. A naturally reproducing population survives. And those fish are as hard to catch as any native fish, at least from my experience.

This is really interesting to me. Being a chemical engineer (retired now) I typically like to remove the emotion from issues like this and rely on the science to formulate my position. You're first reply is very educational. I'm not trying to start some big pissing contest. I am just interested in the science. If this turns into something else I hope the administrater will delete the whole thing.

[Darian]

Happy that you moved this subject to this forum. The info passed on by Alosa is very interesting but the subject is a difficult one to bring up for discussion on this board without it becoming a train wreck.

[Larry S]

Doug,
Nice gesture! Some posters are well meaning, but, a bit too intense to realize that we're all after the same
goal. Nothing stirs the pot like wild vs hatchery! Hope to cross paths with you both some day. Darian does have
that ability to amp up the activity.
Best to all,
Larry S

[DLJeff]

Heh heh, I suppose I should have searched the archives because I'm sure you're right, there is probably plenty of discussion and cussin' on this subject. Ironheaders in particular I think take this issue to heart. I honestly was just intrigued by the position to remove the hatchery fish and recalling some of the beneficial aspects from the streams in Missouri I wondered if there is good science behind that position. That's all there was behind my question. I hope it's taken in that manner.

I'll fish with you Larry. I'm moving to Oregon end of the month and will be sort of busy getting settled for a bit and then I'm headed to south Andros for a week mid-April. But after that if you want to plan a little camp out somewhere that'd be great.

[the_gnarwhale]

Alosa can probably explain this in depth but there have been studies done showing the extremely low survival/return rate of the offspring of a hatchery/wild fish. So if a hatchery fish is allowed to spawn with a wild fish those wild eggs are effectively ruined. Those fish don't get a chance to "re-learn" because they simply don't survive.

[JasonB]

I'm quite interested in this discussion, mostly from a perspective of pondering and (hopefully) learning a bit myself. Thanks for moving it here. I'm afraid I'm not much of an expert at any of the genetics, but I do tend to have a natural hesitancy towards any of our own attempts to improve upon nature. I've said it in another post on this very debate, but I think it's worth restating: I'm not entirely convinced that we really know as much as we would like to about anadromous fish (or the natural world as a whole for that matter). I'm also one of those who's kind of ok with the concept that there is usually more to things than meets our eyes, and that we may well never fully comprehend the future ramifications of certain "small" changes that we make.

Clearly there is no way we can NOT impact the "natural" process here, but I'm always a bit nervous about taking any big steps towards trying to improve things ourselves. Sometimes less is more...

Now, I'm gonna go hide on the corner and watch the fray. Hopefully we can stay mostly civil, and hopefully we might all learn another thing or two :cool:
Cheers,
JB

[DLJeff]

Now, I'm gonna go hide on the corner and watch the fray. Hopefully we can stay mostly civil, and hopefully we might all learn another thing or two

All I ask is that any posts to this thread include the science to support it. Opinions, individual experience, and 'clear generalities' are too easily refuted and we all know what they say about opinions - everybody has one. That's not what this thread is about.

[Darian]

This subject has come up a couple of times a year in the Salmon/Steelhead Forum and in this Forum. Each time it comes up there's been some very good information exchanged including citations. If you can sort the wheat from the chaff, it would be a good idea to look back into those threads to pick up some of that information. The first one you might try is titled Natural vs Hatchery Bred in the Salmon/Steelhead Forum. Work backward from there. You can't really miss the titles.... :cool:

[ycflyfisher]

I was hoping that Alosa would return to this conversation to provide answers to your questions. I think Alosa’s original post was very interesting. I think it's sad that you felt it necessary to state that that the moderators should kill this thread if it gets out of control. IMO what the moderators should do is kill the participation of the individuals who feel compelled to trainwreck every scientific discussion. These discussions should be like any other.

I’ve tried to read a grand total of one paper on the genetics of anadromous fishes (Neilsen’s Sacto Chinook Study) and I didn’t understand a word of it. I think anyone with a slightly above rudimentary understanding of biology can read and understand most of the basic science of steelhead that largely deals with life history and survival strategy. Genetics however are not intuitive and I can't tell you the difference between a ribosome and a chromosome. Consequently what I don't also understand what governs the life histories the progeny of the spawning interaction of a wild 1 salt female with a wild 3 salt male fish will be predisposed to follow. Are they predominantly going to follow a one salt LH, a 3 salt LH? I have no idea, so I can't explain it to you in genetic terms like Alosa.

For each life history expressed by the fish, you’ve got an even larger set of potential survival strategies that correspond to each localized population (deme) of wild steelhead within each watershed. The nuts and bolts of exactly how those successful survival strategies are efficiently passed from one generation to the next via some kind of genetic flow is also something I can’t explain. But I do know that it does happen. I think I can shed some light on your questions, but I can’t explain it as completely as Alosa likely could because I’ve got to attempt to explain it in layman’s terms because that was the only way it was explained to me that I could comprehend.

If you look at the MFE summer steelhead, we know as soon as the fry emerge from the gravel, get zipped up and gulp enough air to fill their swim bladders, they immediately start moving upstream, against the elevated spring run off to push high into the tribs. The MFE is probably the harshest environs in CA where we still have wild summer runs. The MFE dries up in the summer. The pools become isolated ponds where water temps typically approach 80 deg F. The riffles become dried rock gardens and what little streamflow is present is largely subsurface to the riverbed. If those YOY didn’t push hard for the viable upstream riffle habitat and thermal refugia, they would never likely grow and mature enough to hit the smoltification window. In other words there would likely be no MFE summer fish. That would be an example of a successful survival strategy that somehow is passed genetically.

The MFE summer fish from what I’m told, are exclusively 2-2 fish. A grand total of one LH. They however are not the only 2-2 deme of fish in the Eel basin. Those fish have been honed by eons of evolution and have developed an extremely specialized set of survival strategies and specialized adaptations (the adults actually summer over in that 80 deg F pond water in the main stem for severalbmonths) that have allowed them to exploit an ever so slight ecological niche in an extremely unlikely environs and survive in the MFE.

That’s probably the most extreme example of adaptation by a race of wild steelhead that I’m familiar with. I would hope that you don’t need to a professional geneticist or even a biologist to realize that if one were to dump truckloads of any of the existing strains of summer hatchery fish or even 2-2 fish from the same basin into an environment like the MFE, your efforts to give those transplanted fish a foothold, is going to end in futility. Simply put as possible, the MFE would kill any strain of summer fish except the fish that have evolved in basin and found probably the only LH and corresponding strategies that allow them to survive. The MFE is definitely an extreme example, but is nowhere near unique in that all wild steelhead have evolved in the basins where they exist and likewise have been honed by eons of evolution to carve out strategies and adaptations that work in those basins.

You can’t replace those wild fish with fish grown in a bucket, particularly when those bucket grown fish when placed into a unfamiliar wild environment, are going to follow the LH/SS that they’re genetically predisposed to follow. They are not going to have any link to the LH and survival strategies the wild fish are expressing which work for that basin.

When you read in a science paper about steelhead how the introduction and potential spawning interaction between wild and hatchery fish “reduces the fitness” of the population as a whole, it does not mean that the resulting progeny have less stamina or strength than the wild fish. It's referring to the genetic fitness of the population.

[Charlie S]

Interesting thread.....I've enjoyed it and the information provided. Thanks all.

[ycflyfisher]

If you take Alosa’s second point:
supportive breeding - reproduction of a segment of the wild population is conducted in captivity followed by the release of the captive progeny to supplement that same wild populations. Here, no genes from other populations are introduced into the system.

Most that read that statement probably think that’s a good thing and that no damage really could be done if a few bucket grown fish “with the same genetics” spawn with wild fish of the same basin. What they miss is:“reproduction of a SEGMENT of the wild population…”

Using another CA example: KMP fish, or what we collectively refer to as “Klamath River steelhead” is in reality, comprised of numerous dozens if not hundreds of distinct localized demes. All of which are unique, and have differing predominant LH’s and corresponding SS’s that all work for specific basins within the Klamath watershed that they occupy. They also pass those LH’s and SS’s down genetically somehow. Again, I can’t explain the particulars on how they do it.

I have little doubt that IF you took truckloads of presmolting steelhead from either Irongate or the Trinity hatchery (i.e. the same basin) and dumped them into Blue Creek, Dillon Creek, or one of the forks of the Salmon, that it would have a detrimental effect on the population dynamics of the wild fish that have evolved in those tribs. Some of those hatchery fish are going to survive to smoltification, and some of those smolts will survive to return to those tribs as adults. Again, I can’t explain how it happens genetically but I don't think you need to be a professional to see they’re likely going to throw a wrench in the machine that drives the passing down of survival strategies that work for those particular tribs. Same goes it you were to transplant wild fish from Blue to Dillon or vice versa. They might be wild fish but they're not the wild fish that evolved in basin.

The problem is hatchery fish often elect to spawn in basin with wild fish, and unfortunately they do it in droves. I once was told that PIT tagged Coho that had origins from the Rogue River hatchery showed up the carcass surveys on the SF Trinity. We’re not talking dozens, but hundreds of out of basin fish. It only happened in mass once, but eons of evolution was potentially unhinged in one season.

It also doesn’t help that fisheries managers of past generations have already tried to “play god”. If you look at the Skamania/Washougal strain of summer hatchery fish, the fisheries managers who created that batch of frankenfish purposely introduced “selective breeding” into the supportive breeding process. 90+ percent of the fish native to the Washougal were one or two salt fish. The Washougal hatchery fish were selected for size (hit the egg quotas with fish >30 inches, 3 salt fish only) because the thought was bigger had to be better. So you’ve got a hatchery strain that’s a bastardized mish-mash, that at best represents 10 percent of the total, naturally occurring gene pool. Ironically, Washougals are the summer strain that has been transplanted out of basin all over the US. Truth be told, they’re probably ill adapted to survive in what’s left of the Washougal basin let alone anywhere else. McMillan’s Males As Vectors paints a pretty good picture of how the larger hatchery fish on the W have spawned the smaller one salt fish that left the main stem and went up the tribs into extirpation. The W is far from the only hatchery where this type of “selective” supportive breeding has occurred. Hatchery fish have been selected for numerous criteria from size (larger fish only), to early run timing and late run timing so the "season" would last longer. When you purposely select for a specific criteria,genetic variation which drives adaptation gets tossed to the wayside. It’s happened everywhere and isn't always intentional.

Even when you take a river like the Feather, where out of basin transfers were kept to a comparative minimum, and they were not “selectively” bred for size or run timing, what you’ve still got is a bastardized, genetic mess of the fish from all the dozens to hundreds of localized demes that were once native to the three forks of the Feather. A mess that isn’t really fit for anything but a hatchery environment that are piss poor, nonadaptable copies of the wild fish they replaced.

Hopefully all that explaining establishes a basis to work with to get to the point of attempting to answer your questions.


From a legal/ESA standpoint, a population of streamborn steelhead can never be considered wild IF they’re the progeny of hatchery fish transferred from out of basin. We actually have a population of those fish that are recognized as such here in CA. Ironically, they’re Washougals. They have temporal and spatial separation from the other fish in the basins where they exist. Where they are acknowledged in the ESU for that basin they were transplanted to, there’s a very specific disclaimer that they are not to be considered part of the ESU (Evolutionary Significant Unit). So no, they’re never going to be considered “wild fish”.

Do they act like wild fish? I would have to again say no. Not IMO. Planting of Washougals in that particular basin was discontinued in the mid 1970’s. They’ve been a self sustaining population since then. Meaning they have had close to 40 years to evolve in that basin and show by my account, no LH variation. I’ve never caught one in the one or two salt size range, and back when I was a fish whore, I never stopped fishing for steelhead regardless of season and have caught a pretty large sample of those fish. So I’d have to say it’s something of a fluke that there’s some niche in that basin that the most bastardized race of summer fish in existence somehow gained a foothold. All Wild fish show variation in a percentage of the population. The MFE is an exception because the fish have limited SS's that would be sucessful.

Could a potentially less genetically screwed up strain of hatchery steelhead be introduced to some watershed and begin to show LH variation and adaptation that actually allows them to not only survive but adapt fast enough to drive an increase in abundance? I think the answer to that question is yes with some caveats. The first being yes, in the same fashion that bigfoot and the Loch Mess Monster could be real. Possible yes. Likely no. The second caveat is how many watersheds are you willing to seed with hatchery fish then discontinue stocking, and how long of a timeline are you willing to give them to adapt and increase abundance? Seed hundreds of rivers and give them several hundred generations and some will probably be successful at increasing abundance.

I think your Missouri example of a self sustaining fishery being established from stocking is an apples to orange type comparision to PNW steelhead. The fact is most of the hatcheries here on the west coast are mitigation facilities. They can’t by law discontinue stocking. The streamborn fish are constantly being diluted by spawning interaction with hatchery fish.
The fish you cited are not. They’ve actually had a chance to evolve and adapt. Most “wild” fish caught on hatchery rivers in CA like the American, Feather,Russian, Mad, etc are simply the progeny of hatchery fish. The chance of any “wild” fish on said rivers being the progeny of 2 actual streamborn fish is very slim. the chances of said fish on those watersheds being a 2nd generation “wild” fish is even smaller. 3rd generation and you’re going back to LochNess/bigfoot odds IMO. Steelhead are the fastest adapting of the anadromous salmonids. But there's simply not enough adaptation happening and occuring for enough generations to lead to variance on CA hatchery rivers. And that variance IS necessary to drive not only the extreme specialization the MFE fish possess, but the specialization that all native populations of steelhead possess.

Without the variation a population can’t change and evolve to find those specialized SS’s that are tailored to the specific habitat they depend on.


Hope that sheds some light. Just my opinions.

[Walter]

Excellent discussion. Thank you.

[JasonB]

Indeed this has been quite interesting, and informative.

Cheers, JB