Broodstock hatcheries/ epigenetics

[charles sullivan]

In speaking with some fellow hamsters/ Whatcomites recently, a few questions came up. If possible, I think that @Cabezon @Smalma and @Salmo_g all may be able to provide some insight if you all choose. I am willing to pick up a check or two in appreciation of any thoughts. Like I always say, "She'll make more."
I am mixing a couple convo's here. I was only drinking during one of them so hopefully I can do this justice.

We were speaking of the failed Nooksack hatchery and how the genetics portion seems to be almost designed to fail given how they must operate. The thought being that keeping the requirement from the state hatchery management plan to only use hatchery broodstock from Nooksack hatchery fish creates an inevitable reduction in fitness. The reduction compounds itself with each successive generation. It seems to me that it's likely that the reduction in genetic diversity is caused by agressively selecting for early spawning fish. Diversity seems to increase population resilience. Nooksack hatch fish have become homogenous. Nooksack hatchery broodstock are as fragile as management egos.
No one in the group has a real strong grasp on epigenetics and its effect on fitness. My punnett square exercises from long ago did not speak to it, that for sure. Can anyone here speak to this? Can anyone explain what epigenetics are and their effect? I know only enough to be wrong.

Our discussion moved to a bit of a comparison between the current failed hatchery and the broodstock hatchery that had been run by the local steelhead club. I have only heard good things about that hatchery, at least anecdotally. I suspect @Smalma has a bit of knowledge on how that was run. I am curious as to what the basic differences are in how it was run compared to the current Kendall debacle. I suspect that a similar type hatchery would run afoul of the hatchery managment plan. Someone showed a WDFW post on the twitters teasing us with the idea via their own social media. They were also speaking about cooperating with the Nooksack tribe. If they partnered with a tribal entity, would that be a way to have a native broodstock hatchery? The tribes can't be held to the same standard as WDFW when designing and operating a hatchery right? They would not be required to follow WDFW's guidelines outlined in the hatchery management plan.

After working through our thoughts @Pink Nighty had the idea to try and reduce the fitness issues by transforming hatcheries and hatchery practices to reduce the epigenetic issues by more closely mimicking natural conditions. Seems logical. I can't think of any hatchery that has really tried to do this. My assumption is that this would be space and water intensive. I then I thought of the pinnacle of fisheries management called the Fulton spawning channel. It seems to be a great beginning to such a facility. With any luck we could avoid the resultant harvest impacts on wild fish, or we'll all be defending some steelhead crazed, chlorine dumping lunatic. Anyone have any idea if this would be feasible in any way? Has anyone else tried this sort of thing?
Does anyone know anything about WDFW's plans for a change in Nooksack hatchery practices?

I know.....that's a lot of questions. Time for a beer.

Thanks to anyone who answers any of my rambling questions. I know that there are a few more bio's that frequent here than the 3 that I tagged. We'd love to hear from you all too.

 

[Cabezon]

Hi Charles,
[Sorry, long, but this is a complex topic. But I will pat myself on the back as I had predicted some of the impacts of hatchery rearing on epigenetics in salmonids in a old post in WFF...] I can't speak specifically about the Nooksack situation, but I'm happy to provide some background on epigenetics. In brief, epigenetics studies the impact of environment and individual history on the activity of genes and therefore on the presence and quantity of specific proteins that drive cellular physiology. Yes, this likely wasn't taught when you were in school as the insights into epigenetics have only become clear in the last 30ish years (and there is still so much to discover). Proteins do a majority of the heavy-lifting in a cell; they act as enzymes, receptors, transport molecules, structural molecules, etc. Humans, for example, make about 100,000 different proteins - the human parts list.

In traditional genetics, you would have learned about protein synthesis. This is part of the central dogma of biology: DNA -> RNA -> proteins. DNA, the master recipe book for proteins, is found primarily in the nucleus of an animal cell; there are also some genes found in mitochondria, the energy powerhouse. A gene, a section of DNA, is copied ("transcribed") into messenger RNA (mRNA), a working text of an individual recipe. At the protein factory, the ribosome, the order of nucleotides on the mRNA is used to direct the order that the 20 different amino acids are bonded together to form a polypeptide ("transcription"), the actual meal. The ribosome uses the genetic code to convert ("read") the genetic instruction, called a codon (blocks of three RNA nucleotides) into which specific amino acids that will be added next to a growing polypeptide. A single polypeptide (or several that link together, such as the protein hemoglobin composed of 4 polypeptides) will then fold to form its functional shape ("conformation") due to interactions among the amino acids in the polypeptide chain. For example, the difference between sickle cell hemoglobin and non-sickle-cell hemoglobin is the genetic substitution of one amino acid for another that changes the structure on the beta polypeptides in hemoglobin. This cascades up to impact the final shape of hemoglobin, the shape the red blood cells, and a slew of physiological impacts. Some proteins can fold themselves but others require the assistance of other proteins (chaperonins). Protein shape can be modified by the environment or actively by the cell to turn a protein "on" or "off".

[When I first stared teaching intro biology in 1993, I would tell my students that there was a single gene for each polypeptide. But as a result of the human genome project and other research, we now know that one gene can produce several different polypeptides. Individual cells can modify the original mRNA molecule ("post-transcriptional modification") by removing some sections of the original mRNA and leaving others ("alternative splicing"), all under the control of other genetically-coded enzymes. This is kind off like a menu where for your meal you can choose have soup or salad, rice or potatoes, but the meat is fried chicken and the desert is apple pie. Some elements of the mRNA (and therefore the final protein) are modifiable and others are not. Thus, a single gene may result in the synthesis of different polypeptides (isoforms), that are typically subtle modifications of an overall structure that is fine-tuned for the needs of a specific cell type. For example, mammals have seven different isoforms of myosin, the protein that powers muscle contraction; these different isoforms differ in their speed of contraction and power generation. Because of alternative splicing, the 100,000 proteins in humans are produced by just 20,000 genes (salmonids appear to have about 31,000 genes).]

But how does epigenetics fit into this? First, all cells in the body contain the same DNA (plus or minus a few copying errors and some other factors such as transposon) and this is the same DNA present in the very first cell, the zygote. But all cells do not produce all the same proteins. All cells make certain "house-keeping" proteins (such as enzymes for glycolysis), but during development, cells begin to specialize to perform specific tasks and this is done by regulating access to the genes in their DNA. For example, pancreatic cells makes digestive enzymes but not neurotransmitters, and neurons produce neurotransmitters but not digestive enzymes, even though both cells have the genes for both types of proteins. That is because some genes are turned off (and others on) in the pancreatic cells and different genes are turned on (and off) in neurons. The basic DNA is not modified but the ability of a cell to access specific genes is changed (a change in "gene expression"), typically for a long time (even multi-generational). Enzymes are activated by the environment / individual history / development that direct when enzymes will add or remove factors, such as methyl groups ("methylation") to individual genes, These factor impact whether a cell can access ("read" = transcribe) a specific gene or not into mRNA (and then translate the mRNA into a polypeptide). These epigenetic changes can be reversed during a cell's life, but they can also be inherited (passed on to offspring via the egg or sperm).

Why epigenetics? Epigenetic changes may allow organisms to fine-tune their physiology, by modifying gene expression, to better fit where they are in their development, to respond to specific challenges during their life, or to better fit specific environmental conditions. Epigenetic regulation of DNA provides phenotypic plasticity (the ability to modify the physical/physiological traits of an organism) from the same pool of genes. Some groups of genes may be a better fit to one set of environmental conditions (for example, high food vs. low food, crowded vs. dispersed social conditions). For example, two groups of trout eggs raised at different temperatures demonstrated different methylation patterns (and this pattern was also influenced by the genetic background of the trout).

Yes, there is evidence that epigenetics (aka, environmental) impacts the biology of trout and that these changes are inheritable. For example, hatchery trout fed different diets (high protein vs. high carbohydrates) produced offspring that differed in energy metabolism and mitochondrial dynamics. More generally, there is evidence that hatchery rearing leads to different epigenetic patterns in hatchery trout versus their wild counterparts. In particular, this study by Michael Skinner at WSU on Methow River steelhead is particularly compelling in demonstrating that hatchery rearing conditions result in a wide range of epigenetic changes that impact growth and maturation rate among other factors versus wild trout. Further, these epigenetic changes persist in sperm ("epigenetic transgenerational inheritance").

Here is the conclusion of that study:
"Clearly, the current study supports a critical role for epigenetics when considering the molecular source for hatchery impacts, however, it will be an integration of epigenetics and genetics that will influence the molecular control of phenotypic variation. Since the sperm were found to have epigenetic alterations, the generational impacts through epigenetic inheritance also need to be considered. The potential that these epigenetic germline effects can be transmitted in the absence of direct exposure through epigenetic transgenerational inheritance now needs to be assessed. In hatchery operations involving food production, such as aquaculture, or when the hatchery fish are not allowed to breed with the wild fish population, impacts on the wild population will be reduced. However, in the event a hatchery population can breed with a wild fish population, the long-term impacts on the wild population and the environment could be dramatic and alter the future trajectory of the wild population. Further research into environmental epigenetic impacts on hatchery and wild fish populations is now needed. Interestingly, the epigenetic alterations observed could be used as biomarkers to further identify hatchery impacts on the fish, as well as correlate with phenotypic alterations observed in the future."

Hopefully, others who know more about the specifics of the Nooksack system and its hatchery history can build on this.

Steve

 

[Matt B]

I would like a cup of the same coffee Steve is having, please.
Great info!

 

[Rob Allen]

I'll keep my mostly ignorant comments short. In terms of restoration , mitigation and enhansment efforts all methods will fail until we have consistently good ocean survival. We have sparks of success for a few years, Snake river sockeye for example, but ultimately the projects fail or have extremely inconsistent results because of ocean survival. So inconsistent that we have very little ability to know what works or doesn't or why.

 

[Salmo_g]

Cabezon posted the best summary of epigenetics I have ever seen! Genetics isn't my background, and I only took one course in it in college that I remember. I hadn't even heard of epigenetics until maybe 8 years ago. Steve's description illustrates how epigenetics provide that heritable archetypal knowledge that tells a juvenile wild trout or steelhead that critical survival information about how and when to forage and when to shelter from predation, a distinction that hatchery fish don't have to know.

As the Nooksack hatchery steelhead program struggles to meet minimum broodstock requirements, the genetic diversity within that small population becomes ever smaller and less fit to survive until it is "circling the drain" so to speak. I think this is also what happened to steelhead at the Puyallup hatchery on the Carbon River.

This might also explain the demise of the Chambers Creek hatchery steelhead program at Chambers Creek. Before US v. WA, Chambers Creek and South Tacoma Hatchery served as the origin and ongoing support system for the hatchery winter steelhead program in western WA. The program began and succeeded there because of the presence of warm spring water that accelerated maturation of adult brood stock, egg incubation, and early juvenile rearing. At that time (late 1940s and early 1950s) a fish was a fish, and there was no particular intent to make the hatchery stock different in any way from the innumerable wild stocks where Chambers fish were eventually planted. But the continuing selection for early timed spawning and the warm water developed a steelhead stock that was and is significantly different from all wild steelhead stocks. The purpose of the early timing selection was to add more months on the front end to raise steelhead smolts to the necessary release size in one year instead of the typical two years for wild smolts.

The program was very successful with large numbers of returning adults. So it was only natural that the former Dept. of Game expanded the program and provided fingerling juvenile Chambers hatchery steelhead to rearing ponds located on most major river systems throughout western WA. The key element here is that Chambers was the donor stock, providing those warm water fast growing juveniles to the satellite locations every year, with no need or desire to collect returning broodstock at those remote satellite locations. Even with the deliberate unnatural selection for early run timing and spawn timing, there were a large number of returning adults to Chambers Creek, thereby maintaining that important remnant of genetic diversity.

Then a couple of things happened. The Puyallup Tribe took note that Chambers Creek was within the Tribal Usual & Accustomed fishing area and decided to fish the creek for steelhead. So the number of returning adults dropped significantly. And fisheries science was evolving so that managers believed that hatcheries could produce better results using broodstock from the watershed where the hatchery was located. The intuitive interpretation of that would be to use broodstock of the endemic population of fish native to that watershed. But gov't agencies being about doing what they think they've always done, it translated into using the broodstock returning to those respective hatcheries. This is why Green River hatchery fall Chinook are the stock of fish raised in every hatchery fall Chinook program in Puget Sound (PS). And Chambers Creek steelhead are the stock raised in the remaining 6 hatchery winter programs in PS. There is another factor playing a role in the hatchery steelhead issue. By the time this hatchery decision was being made, WDG, WDW, and now WDFW understood that wild stocks are different from hatchery stocks. So it was (is) better to maintain those differences through timing separation than to use watershed native broodstocks in the hatchery program, thereby massively increasing the genetic introgression between hatchery and wild fish. It's worth noting that not all fisheries folks agree about this. There is a lot of support for so called "broodstock" hatchery programs whereby wild native fish in the watershed are used as donor broodstock to a hatchery program effort. This is certainly how every single hatchery program anywhere begins, with locally adapted and sourced broodstock.

The moment that "broodstock" hatchery program begins, genetics and epigenetics begin exerting both their intended beneficial and unintended deliterious effects. The traditional programs then use subsequent returns to the hatchery as future broodstock, which serves to intensify effects, both positive and negative. To minimize the negative effects, some of these programs use only wild broodstock to minimize the negative impacts that inbreeding and epigentics would cause. This is how wild populations are "mined" to provide brood for a hatchery program. This can be a sustainable practice if, and only if, the wild population is in good enough health to consistently produce returning adult numbers "surplus" to the needs of natural spawning escapement to fully, or nearly fully, seed the natural habitat. Short of that, the practice "mines" a wild population of adult fish to nearly the point of extirpation.

Back to the Nooksack hatchery steelhead program of Chambers origin fish. Unless I'm missing something, Kendall Creek hatchery does not have a water supply that allows replicating what was done at Chambers Creek and South Tacoma. That works against the program's success. And everyone knows that brothers and sisters and cousins are not supposed to mate, or adverse genetic effects will occur and amplify. That is likely happening in hatchery programs that are small in scale and becoming even smaller. Add to this the severely decreased ocean smolt to adult survival rates, and hatchery programs struggle to maintain themselves. It's almost as if someone were to write a script that would cause a successful fish hatchery program to fail, they would have written just about exactly what has happened in the PS region over the past 40 years.

 

[tomb]

Cabezon posted the best summary of epigenetics I have ever seen! Genetics isn't my background, and I only took one course in it in college that I remember. I hadn't even heard of epigenetics until maybe 8 years ago. Steve's description illustrates how epigenetics provide that heritable archetypal knowledge that tells a juvenile wild trout or steelhead that critical survival information about how and when to forage and when to shelter from predation, a distinction that hatchery fish don't have to know.

As the Nooksack hatchery steelhead program struggles to meet minimum broodstock requirements, the genetic diversity within that small population becomes ever smaller and less fit to survive until it is "circling the drain" so to speak. I think this is also what happened to steelhead at the Puyallup hatchery on the Carbon River.

This might also explain the demise of the Chambers Creek hatchery steelhead program at Chambers Creek. Before US v. WA, Chambers Creek and South Tacoma Hatchery served as the origin and ongoing support system for the hatchery winter steelhead program in western WA. The program began and succeeded there because of the presence of warm spring water that accelerated maturation of adult brood stock, egg incubation, and early juvenile rearing. At that time (late 1940s and early 1950s) a fish was a fish, and there was no particular intent to make the hatchery stock different in any way from the innumerable wild stocks where Chambers fish were eventually planted. But the continuing selection for early timed spawning and the warm water developed a steelhead stock that was and is significantly different from all wild steelhead stocks. The purpose of the early timing selection was to add more months on the front end to raise steelhead smolts to the necessary release size in one year instead of the typical two years for wild smolts.

The program was very successful with large numbers of returning adults. So it was only natural that the former Dept. of Game expanded the program and provided fingerling juvenile Chambers hatchery steelhead to rearing ponds located on most major river systems throughout western WA. The key element here is that Chambers was the donor stock, providing those warm water fast growing juveniles to the satellite locations every year, with no need or desire to collect returning broodstock at those remote satellite locations. Even with the deliberate unnatural selection for early run timing and spawn timing, there were a large number of returning adults to Chambers Creek, thereby maintaining that important remnant of genetic diversity.

Then a couple of things happened. The Puyallup Tribe took note that Chambers Creek was within the Tribal Usual & Accustomed fishing area and decided to fish the creek for steelhead. So the number of returning adults dropped significantly. And fisheries science was evolving so that managers believed that hatcheries could produce better results using broodstock from the watershed where the hatchery was located. The intuitive interpretation of that would be to use broodstock of the endemic population of fish native to that watershed. But gov't agencies being about doing what they think they've always done, it translated into using the broodstock returning to those respective hatcheries. This is why Green River hatchery fall Chinook are the stock of fish raised in every hatchery fall Chinook program in Puget Sound (PS). And Chambers Creek steelhead are the stock raised in the remaining 6 hatchery winter programs in PS. There is another factor playing a role in the hatchery steelhead issue. By the time this hatchery decision was being made, WDG, WDW, and now WDFW understood that wild stocks are different from hatchery stocks. So it was (is) better to maintain those differences through timing separation than to use watershed native broodstocks in the hatchery program, thereby massively increasing the genetic introgression between hatchery and wild fish. It's worth noting that not all fisheries folks agree about this. There is a lot of support for so called "broodstock" hatchery programs whereby wild native fish in the watershed are used as donor broodstock to a hatchery program effort. This is certainly how every single hatchery program anywhere begins, with locally adapted and sourced broodstock.

The moment that "broodstock" hatchery program begins, genetics and epigenetics begin exerting both their intended beneficial and unintended deliterious effects. The traditional programs then use subsequent returns to the hatchery as future broodstock, which serves to intensify effects, both positive and negative. To minimize the negative effects, some of these programs use only wild broodstock to minimize the negative impacts that inbreeding and epigentics would cause. This is how wild populations are "mined" to provide brood for a hatchery program. This can be a sustainable practice if, and only if, the wild population is in good enough health to consistently produce returning adult numbers "surplus" to the needs of natural spawning escapement to fully, or nearly fully, seed the natural habitat. Short of that, the practice "mines" a wild population of adult fish to nearly the point of extirpation.

Back to the Nooksack hatchery steelhead program of Chambers origin fish. Unless I'm missing something, Kendall Creek hatchery does not have a water supply that allows replicating what was done at Chambers Creek and South Tacoma. That works against the program's success. And everyone knows that brothers and sisters and cousins are not supposed to mate, or adverse genetic effects will occur and amplify. That is likely happening in hatchery programs that are small in scale and becoming even smaller. Add to this the severely decreased ocean smolt to adult survival rates, and hatchery programs struggle to maintain themselves. It's almost as if someone were to write a script that would cause a successful fish hatchery program to fail, they would have written just about exactly what has happened in the PS region over the past 40 years.

Nice summary SalmoG…one addition: I’d note that a wild population being mined to support a broodstock hatchery need not have a surplus to completely replace all wild fish taken for brood because some of the hatchery fish produced that return and spawn jn the wild will produce wild fish and partially offset the mining. However those hatchery fish likely won’t produce as many wild offspring per capita as the wild fish being mined, and careful attention must occur to make sure the over mining scenario you allude to doesn’t occur.

 

[BriGuy]

Hi Charles,
[Sorry, long, but this is a complex topic. But I will pat myself on the back as I had predicted some of the impacts of hatchery rearing on epigenetics in salmonids in a old post in WFF...] I can't speak specifically about the Nooksack situation, but I'm happy to provide some background on epigenetics. In brief, epigenetics studies the impact of environment and individual history on the activity of genes and therefore on the presence and quantity of specific proteins that drive cellular physiology. Yes, this likely wasn't taught when you were in school as the insights into epigenetics have only become clear in the last 30ish years (and there is still so much to discover). Proteins do a majority of the heavy-lifting in a cell; they act as enzymes, receptors, transport molecules, structural molecules, etc. Humans, for example, make about 100,000 different proteins - the human parts list.

In traditional genetics, you would have learned about protein synthesis. This is part of the central dogma of biology: DNA -> RNA -> proteins. DNA, the master recipe book for proteins, is found primarily in the nucleus of an animal cell; there are also some genes found in mitochondria, the energy powerhouse. A gene, a section of DNA, is copied ("transcribed") into messenger RNA (mRNA), a working text of an individual recipe. At the protein factory, the ribosome, the order of nucleotides on the mRNA is used to direct the order that the 20 different amino acids are bonded together to form a polypeptide ("transcription"), the actual meal. The ribosome uses the genetic code to convert ("read") the genetic instruction, called a codon (blocks of three RNA nucleotides) into which specific amino acids that will be added next to a growing polypeptide. A single polypeptide (or several that link together, such as the protein hemoglobin composed of 4 polypeptides) will then fold to form its functional shape ("conformation") due to interactions among the amino acids in the polypeptide chain. For example, the difference between sickle cell hemoglobin and non-sickle-cell hemoglobin is the genetic substitution of one amino acid for another that changes the structure on the beta polypeptides in hemoglobin. This cascades up to impact the final shape of hemoglobin, the shape the red blood cells, and a slew of physiological impacts. Some proteins can fold themselves but others require the assistance of other proteins (chaperonins). Protein shape can be modified by the environment or actively by the cell to turn a protein "on" or "off".

[When I first stared teaching intro biology in 1993, I would tell my students that there was a single gene for each polypeptide. But as a result of the human genome project and other research, we now know that one gene can produce several different polypeptides. Individual cells can modify the original mRNA molecule ("post-transcriptional modification") by removing some sections of the original mRNA and leaving others ("alternative splicing"), all under the control of other genetically-coded enzymes. This is kind off like a menu where for your meal you can choose have soup or salad, rice or potatoes, but the meat is fried chicken and the desert is apple pie. Some elements of the mRNA (and therefore the final protein) are modifiable and others are not. Thus, a single gene may result in the synthesis of different polypeptides (isoforms), that are typically subtle modifications of an overall structure that is fine-tuned for the needs of a specific cell type. For example, mammals have seven different isoforms of myosin, the protein that powers muscle contraction; these different isoforms differ in their speed of contraction and power generation. Because of alternative splicing, the 100,000 proteins in humans are produced by just 20,000 genes (salmonids appear to have about 31,000 genes).]

But how does epigenetics fit into this? First, all cells in the body contain the same DNA (plus or minus a few copying errors and some other factors such as transposon) and this is the same DNA present in the very first cell, the zygote. But all cells do not produce all the same proteins. All cells make certain "house-keeping" proteins (such as enzymes for glycolysis), but during development, cells begin to specialize to perform specific tasks and this is done by regulating access to the genes in their DNA. For example, pancreatic cells makes digestive enzymes but not neurotransmitters, and neurons produce neurotransmitters but not digestive enzymes, even though both cells have the genes for both types of proteins. That is because some genes are turned off (and others on) in the pancreatic cells and different genes are turned on (and off) in neurons. The basic DNA is not modified but the ability of a cell to access specific genes is changed (a change in "gene expression"), typically for a long time (even multi-generational). Enzymes are activated by the environment / individual history / development that direct when enzymes will add or remove factors, such as methyl groups ("methylation") to individual genes, These factor impact whether a cell can access ("read" = transcribe) a specific gene or not into mRNA (and then translate the mRNA into a polypeptide). These epigenetic changes can be reversed during a cell's life, but they can also be inherited (passed on to offspring via the egg or sperm).

Why epigenetics? Epigenetic changes may allow organisms to fine-tune their physiology, by modifying gene expression, to better fit where they are in their development, to respond to specific challenges during their life, or to better fit specific environmental conditions. Epigenetic regulation of DNA provides phenotypic plasticity (the ability to modify the physical/physiological traits of an organism) from the same pool of genes. Some groups of genes may be a better fit to one set of environmental conditions (for example, high food vs. low food, crowded vs. dispersed social conditions). For example, two groups of trout eggs raised at different temperatures demonstrated different methylation patterns (and this pattern was also influenced by the genetic background of the trout).

Yes, there is evidence that epigenetics (aka, environmental) impacts the biology of trout and that these changes are inheritable. For example, hatchery trout fed different diets (high protein vs. high carbohydrates) produced offspring that differed in energy metabolism and mitochondrial dynamics. More generally, there is evidence that hatchery rearing leads to different epigenetic patterns in hatchery trout versus their wild counterparts. In particular, this study by Michael Skinner at WSU on Methow River steelhead is particularly compelling in demonstrating that hatchery rearing conditions result in a wide range of epigenetic changes that impact growth and maturation rate among other factors versus wild trout. Further, these epigenetic changes persist in sperm ("epigenetic transgenerational inheritance").

Here is the conclusion of that study:
"Clearly, the current study supports a critical role for epigenetics when considering the molecular source for hatchery impacts, however, it will be an integration of epigenetics and genetics that will influence the molecular control of phenotypic variation. Since the sperm were found to have epigenetic alterations, the generational impacts through epigenetic inheritance also need to be considered. The potential that these epigenetic germline effects can be transmitted in the absence of direct exposure through epigenetic transgenerational inheritance now needs to be assessed. In hatchery operations involving food production, such as aquaculture, or when the hatchery fish are not allowed to breed with the wild fish population, impacts on the wild population will be reduced. However, in the event a hatchery population can breed with a wild fish population, the long-term impacts on the wild population and the environment could be dramatic and alter the future trajectory of the wild population. Further research into environmental epigenetic impacts on hatchery and wild fish populations is now needed. Interestingly, the epigenetic alterations observed could be used as biomarkers to further identify hatchery impacts on the fish, as well as correlate with phenotypic alterations observed in the future."

Hopefully, others who know more about the specifics of the Nooksack system and its hatchery history can build on this.

Steve

Wow! That's about the best synopsis on the topic I have read.

On a NFR note, my mom was recently diagnosed with cardiac amyloidosis, which is a fairly rare disease that involves abnormal proteins that did not "fold" properly. Also, the condition can be genetic and passed down to children.

So, we're learning quite a bit about this process. Your explanation about epigenetics is the best I've seen. It's fascinating to me that our scientists and doctors know so much about this. I'm amazed they were able to make the diagnosis, develop a medication, and determine that her "flavor" of the disease is not hereditary -- all through the examination of these proteins and DNA. This would not have been possible a few short years ago.

Back on topic, hopefully science continues to find novel ways to apply epigenetics to fisheries biology to the benefit of our fishy friends.

Science is cool.

 

[speedbird]

Really good write up. Regarding hatcheries that integrate wild stock and simulate natural conditions. Is that not what is currently happening to outstanding success at the Baker Lake Sockeye hatchery?

 

[charles sullivan]

Hi Charles,
[Sorry, long, but this is a complex topic. But I will pat myself on the back as I had predicted some of the impacts of hatchery rearing on epigenetics in salmonids in a old post in WFF...] I can't speak specifically about the Nooksack situation, but I'm happy to provide some background on epigenetics. In brief, epigenetics studies the impact of environment and individual history on the activity of genes and therefore on the presence and quantity of specific proteins that drive cellular physiology. Yes, this likely wasn't taught when you were in school as the insights into epigenetics have only become clear in the last 30ish years (and there is still so much to discover). Proteins do a majority of the heavy-lifting in a cell; they act as enzymes, receptors, transport molecules, structural molecules, etc. Humans, for example, make about 100,000 different proteins - the human parts list.

In traditional genetics, you would have learned about protein synthesis. This is part of the central dogma of biology: DNA -> RNA -> proteins. DNA, the master recipe book for proteins, is found primarily in the nucleus of an animal cell; there are also some genes found in mitochondria, the energy powerhouse. A gene, a section of DNA, is copied ("transcribed") into messenger RNA (mRNA), a working text of an individual recipe. At the protein factory, the ribosome, the order of nucleotides on the mRNA is used to direct the order that the 20 different amino acids are bonded together to form a polypeptide ("transcription"), the actual meal. The ribosome uses the genetic code to convert ("read") the genetic instruction, called a codon (blocks of three RNA nucleotides) into which specific amino acids that will be added next to a growing polypeptide. A single polypeptide (or several that link together, such as the protein hemoglobin composed of 4 polypeptides) will then fold to form its functional shape ("conformation") due to interactions among the amino acids in the polypeptide chain. For example, the difference between sickle cell hemoglobin and non-sickle-cell hemoglobin is the genetic substitution of one amino acid for another that changes the structure on the beta polypeptides in hemoglobin. This cascades up to impact the final shape of hemoglobin, the shape the red blood cells, and a slew of physiological impacts. Some proteins can fold themselves but others require the assistance of other proteins (chaperonins). Protein shape can be modified by the environment or actively by the cell to turn a protein "on" or "off".

[When I first stared teaching intro biology in 1993, I would tell my students that there was a single gene for each polypeptide. But as a result of the human genome project and other research, we now know that one gene can produce several different polypeptides. Individual cells can modify the original mRNA molecule ("post-transcriptional modification") by removing some sections of the original mRNA and leaving others ("alternative splicing"), all under the control of other genetically-coded enzymes. This is kind off like a menu where for your meal you can choose have soup or salad, rice or potatoes, but the meat is fried chicken and the desert is apple pie. Some elements of the mRNA (and therefore the final protein) are modifiable and others are not. Thus, a single gene may result in the synthesis of different polypeptides (isoforms), that are typically subtle modifications of an overall structure that is fine-tuned for the needs of a specific cell type. For example, mammals have seven different isoforms of myosin, the protein that powers muscle contraction; these different isoforms differ in their speed of contraction and power generation. Because of alternative splicing, the 100,000 proteins in humans are produced by just 20,000 genes (salmonids appear to have about 31,000 genes).]

But how does epigenetics fit into this? First, all cells in the body contain the same DNA (plus or minus a few copying errors and some other factors such as transposon) and this is the same DNA present in the very first cell, the zygote. But all cells do not produce all the same proteins. All cells make certain "house-keeping" proteins (such as enzymes for glycolysis), but during development, cells begin to specialize to perform specific tasks and this is done by regulating access to the genes in their DNA. For example, pancreatic cells makes digestive enzymes but not neurotransmitters, and neurons produce neurotransmitters but not digestive enzymes, even though both cells have the genes for both types of proteins. That is because some genes are turned off (and others on) in the pancreatic cells and different genes are turned on (and off) in neurons. The basic DNA is not modified but the ability of a cell to access specific genes is changed (a change in "gene expression"), typically for a long time (even multi-generational). Enzymes are activated by the environment / individual history / development that direct when enzymes will add or remove factors, such as methyl groups ("methylation") to individual genes, These factor impact whether a cell can access ("read" = transcribe) a specific gene or not into mRNA (and then translate the mRNA into a polypeptide). These epigenetic changes can be reversed during a cell's life, but they can also be inherited (passed on to offspring via the egg or sperm).

Why epigenetics? Epigenetic changes may allow organisms to fine-tune their physiology, by modifying gene expression, to better fit where they are in their development, to respond to specific challenges during their life, or to better fit specific environmental conditions. Epigenetic regulation of DNA provides phenotypic plasticity (the ability to modify the physical/physiological traits of an organism) from the same pool of genes. Some groups of genes may be a better fit to one set of environmental conditions (for example, high food vs. low food, crowded vs. dispersed social conditions). For example, two groups of trout eggs raised at different temperatures demonstrated different methylation patterns (and this pattern was also influenced by the genetic background of the trout).

Yes, there is evidence that epigenetics (aka, environmental) impacts the biology of trout and that these changes are inheritable. For example, hatchery trout fed different diets (high protein vs. high carbohydrates) produced offspring that differed in energy metabolism and mitochondrial dynamics. More generally, there is evidence that hatchery rearing leads to different epigenetic patterns in hatchery trout versus their wild counterparts. In particular, this study by Michael Skinner at WSU on Methow River steelhead is particularly compelling in demonstrating that hatchery rearing conditions result in a wide range of epigenetic changes that impact growth and maturation rate among other factors versus wild trout. Further, these epigenetic changes persist in sperm ("epigenetic transgenerational inheritance").

Here is the conclusion of that study:
"Clearly, the current study supports a critical role for epigenetics when considering the molecular source for hatchery impacts, however, it will be an integration of epigenetics and genetics that will influence the molecular control of phenotypic variation. Since the sperm were found to have epigenetic alterations, the generational impacts through epigenetic inheritance also need to be considered. The potential that these epigenetic germline effects can be transmitted in the absence of direct exposure through epigenetic transgenerational inheritance now needs to be assessed. In hatchery operations involving food production, such as aquaculture, or when the hatchery fish are not allowed to breed with the wild fish population, impacts on the wild population will be reduced. However, in the event a hatchery population can breed with a wild fish population, the long-term impacts on the wild population and the environment could be dramatic and alter the future trajectory of the wild population. Further research into environmental epigenetic impacts on hatchery and wild fish populations is now needed. Interestingly, the epigenetic alterations observed could be used as biomarkers to further identify hatchery impacts on the fish, as well as correlate with phenotypic alterations observed in the future."

Hopefully, others who know more about the specifics of the Nooksack system and its hatchery history can build on this.

Steve

This should be nominated for scientific post of the year. Thank you for the homework.

 

[HauntedByWaters]

I think the simplistic issue with broodstock is that it is expensive and only works with a lot of volunteer support. Hatcheries have high densities and other less natural conditions to get more fish per dollar.

 

[charles sullivan]

Continued thoughts and questions from a steelheader without an open river:

@Salmo_g
The creek that goes Kendall hatchery (Kendal creek?) very much appears to be spring influenced. I do not know for sure if it is or if the state has any water rights to use it even. At this point, it may not matter anyhow given the dismal performance of the hatchery and the constraints that are placed on it.

Also, I am quite disappointed that I was unable to bait you into publicly endorsing/ planning some form of environmental terrorism to solve that Fulton Spawning Channell up north. There must have been too much drag in my presentation to get such an educated fish to rise. I guess that is why I prefer steelhead over trout.

@tomb
These convo's are always improved when you come out to play.

@Cabezon is it correct to say that we do not know what environmental factors are turning on or off the different expressions of DNA? Is it correct to say we do not know the extent that epigenic factors influence survival of hatchery fish from egg to adult or at what point in the fish's life span the epigenetic changes caused by the hatchery environment are likely to be causing increased mortality?

I am also curious about the Hamma Hamma rescue hatchery effort. If I recall correctly (and I very well may not), adult steelhead were captured (possibly post-spawn) and held in captivity to use as brood stock the following year. In this way, you are using fish that have already had the opportunity to spawn in the wild. The captured broodstock are unlikely to spawn again given the low percentage of fish that live to spawn a second time. Would this be a way have an integrated hatchery and dramatically reducing the impact of "mining" wild origin fish? So, taking a post spawn fish would be equivalent of mining 0.1 wild fish. I understand that this is something of a mathematical analysis rather than the simplified 1+1=2 sort of math the average human understands.

Does anyone know much about the Hamma Hamma project or using post spawn fish as broodstock the following year? Is that crazy for any reason? My wife has already told me that one idea that I had was crazy this morning. She told me again using only non-verbals. I am prepared to be told in written form.

Adding to the intrigue, apparently this happened:



Aside from the somewhat asinine river mouth netting comment, this is a fascinating twit from WDFW. My thought is that any integrated hatchery would almost have to be operated by a tribe to be permitted. My thought is that WDFW would have too many challenges such as the requirements of ESA and the hatchery management plan that they are beholden to. It seems to me that the Wild Fish Conservancy, The Conservation Angler or any number of other anti-hatchery three letter acronym groups (TLA) are out there waiting to sue if there is anything out of line. WFC did leave the door open for a wild broodstock hatchery on the Skagit in their settlement with the state. Maybe I will call in to The Conservation Angler. Their executive director has been willing to have a dialogue in the past. He seemed to be a guy who could disagree without being disagreeable.

Do any of the bio's or TLA representatives' members here have any thoughts on how in the world an integrated hatchery could be permitted? Would tribal cooperation help? Would tribal ownership or operation be required to get it permitted since they are not restricted by state level policy and the more litigious TLA's have been unwilling to sue them or the Fed's?

 

[Emily27]

is it correct to say that we do not know what environmental factors are turning on or off the different expressions of DNA? Is it correct to say we do not know the extent that epigenic factors influence survival of hatchery fish from egg to adult or at what point in the fish's life span the epigenetic changes caused by the hatchery environment are likely to be causing increased mortality?

This probably wont give you the fullest answer you could be looking for but this study https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0257407#ack by Mike Blouin at OSU talks about genetic changes accrued in hatchery fish.

Also I haven't looked into it much but over in Europe there are at least a couple programs/studies looking at reconditioning of Atlantic salmon kelts with at least some success in getting viable eggs, and I found this link from CRITFC talking about steelhead reconditioning

 

[Smalma]

See I'm late to the party but the "Steves" have done a good job addressing part of the issues.

It should be understood that the hatchery steelhead smolts will always survive at lower rates than wild produced fish. In the wild it would be pretty typical to have only a fish or two per 1,000 eggs to survive to become a smolt. That heavy selection culls the potential to the to the point only the best adapted (to avoid predators, find food, etc.) survive. With hatchery fish one might see as much as 800 smolts per 1,000 eggs. During their fresh rearing to the smolt stage they receive significant less selective pressure and many of the surviving fish will not be as "fit" as the wild. However, at even significantly lower smolt survivals hatchery can produce more adults/female thus their ability to support higher fishing rates.

With the collecting of improved information during the late 1970s and 1980s it was noted that the PS hatchery steelhead smolt was variable with the highest survivals seen in the Snohomish and as one move either north or south those survivals averaged less. Staring in the late 1980s it was noted that marine survival rates for south sound fish declined significantly. That decline mirrored what was seen with the coho. For example, coho smolt survival in the Deschutes was typically 20 to 25% in the 1970s but the late 1980s was down in the 5%. Those declining survivals over time up up sound until by 1990s returns were down everywhere. That poor survivals were seen through the Salish sea for both the wild and hatchery smolts.

Some of radio tagging has shown that much of the increased mortality is occurring in Puget Sound itself. With the smolts experiencing some pretty mortalities. For example, wild smolts leaving the Skagit and traveling through Deception pass typically reach the Port Angeles area in 6 days or so while losing up to half of their numbers. In short at least part of the poor performance is happening after they leave the hatchery.

That does not mean that problems with the brood stock and/or rearing practices are not also playing key roles. On the surface I would think that relying on brood stock that had successfully migrated to the salt and returned to spawn would be a strong survival selection to produce the next generation. I would be curious to know whether there has been changes in fecundity, age at maturing, etc. Does it take more adults to meet a constant goal? As I recall the water supply situation at Kendall relies on both the Creek water which has some spring influence and well water. Wonder if which is used to release the steelhead and whether source would make a difference. Noticed in the future brood document the program goal for the steelhead was for a target release in April and May with a target size of 5/#. During the 1980s on the Snohomish it was noted that the returns (adults/smolts released) on the Skykomish high than that on the Snoqualmie. Looking more closely at those returns and potential diffences between the two releases it was noted that the Snoqualmie (Tokul) were being released at a larger size and earlier than the Skykomish (Reiter ) fish. AT the time it seemed that the best release strategy was a early May release of fish 6/#. Noticed that many of the State's hatcheries similar release targets as Kendal. Wonder if the State has new studies to update their release targets? It might be interesting to look at the details of the Kendal releases. This successfully rearing fish can be tricky business at times.

Curt

 

[Pink Nighty]

Continued thoughts and questions from a steelheader without an open river:

@Salmo_g
The creek that goes Kendall hatchery (Kendal creek?) very much appears to be spring influenced. I do not know for sure if it is or if the state has any water rights to use it even. At this point, it may not matter anyhow given the dismal performance of the hatchery and the constraints that are placed on it.

Also, I am quite disappointed that I was unable to bait you into publicly endorsing/ planning some form of environmental terrorism to solve that Fulton Spawning Channell up north. There must have been too much drag in my presentation to get such an educated fish to rise. I guess that is why I prefer steelhead over trout.

@tomb
These convo's are always improved when you come out to play.

@Cabezon is it correct to say that we do not know what environmental factors are turning on or off the different expressions of DNA? Is it correct to say we do not know the extent that epigenic factors influence survival of hatchery fish from egg to adult or at what point in the fish's life span the epigenetic changes caused by the hatchery environment are likely to be causing increased mortality?

I am also curious about the Hamma Hamma rescue hatchery effort. If I recall correctly (and I very well may not), adult steelhead were captured (possibly post-spawn) and held in captivity to use as brood stock the following year. In this way, you are using fish that have already had the opportunity to spawn in the wild. The captured broodstock are unlikely to spawn again given the low percentage of fish that live to spawn a second time. Would this be a way have an integrated hatchery and dramatically reducing the impact of "mining" wild origin fish? So, taking a post spawn fish would be equivalent of mining 0.1 wild fish. I understand that this is something of a mathematical analysis rather than the simplified 1+1=2 sort of math the average human understands.

Does anyone know much about the Hamma Hamma project or using post spawn fish as broodstock the following year? Is that crazy for any reason? My wife has already told me that one idea that I had was crazy this morning. She told me again using only non-verbals. I am prepared to be told in written form.

Adding to the intrigue, apparently this happened:

View attachment 50857

Aside from the somewhat asinine river mouth netting comment, this is a fascinating twit from WDFW. My thought is that any integrated hatchery would almost have to be operated by a tribe to be permitted. My thought is that WDFW would have too many challenges such as the requirements of ESA and the hatchery management plan that they are beholden to. It seems to me that the Wild Fish Conservancy, The Conservation Angler or any number of other anti-hatchery three letter acronym groups (TLA) are out there waiting to sue if there is anything out of line. WFC did leave the door open for a wild broodstock hatchery on the Skagit in their settlement with the state. Maybe I will call in to The Conservation Angler. Their executive director has been willing to have a dialogue in the past. He seemed to be a guy who could disagree without being disagreeable.

Do any of the bio's or TLA representatives' members here have any thoughts on how in the world an integrated hatchery could be permitted? Would tribal cooperation help? Would tribal ownership or operation be required to get it permitted since they are not restricted by state level policy and the more litigious TLA's have been unwilling to sue them or the Fed's?

Charles that idea of using post spawn kelts is intriguing. It stands to reason that fish would have lived it's full life with all the epigenetic influences resulting in a fish that successfully spawned in that watershed. This is the heart of the thought I posed in our group message.

What are the epigenetic influencing factors that cause issue with hatchery steelhead? The big ones are obviously mate finding and redd digging/spawning success as adult fish, and then hatching, feeding, predation evasion and flood/drought management as juveniles.

To the bios out there, do you believe it is possible to have a hatchery with traditional goals (increase of harvestable fish) operate in a manner that appreciably reduces the negative impacts of hatchery genetics?

My simple thoughts are along the lines of a natural spawning channel (with controllable flows) and a series of natural holding ponds ala a beaver complex to rear fish in. The game would be creating the conditions to maximize bug growth to rear the fry naturally, and having a flow regime that both flooded and dried areas periodically. Allow the fish to naturally escape the ponds as their instinct tells them to.

Is something like this even possible or is trying to play God a fools errand?

 

[Smalma]

In 2020 WDFW's ad hoc Puget Sound Steelhead Advisory Group (PSSAG) published their "Quicksilver Porfilio" with a number of recommendations to address improve PS steelhead recreational opportunities. Include where to two recommendations to consider on the Nooksack. One was wild steelhead brood stock potentially considering using early timed wild steelhead (mid-river spawners?) and evaluate the effectiveness of using sonar to estimate wild steelhead run sizes.

Anecdotal reports were that the creeks like Bertrand, Fish Trap, Double Ditch, Anderson and Smith were populated by early time (early spawning) winter steelhead, and they might provide a better option for an integrated steelhead brood stock. While such a effort would have its own set of logistic problems those would not be as difficult to overcome than a more traditional program using the later timed steelhead. Potential might be a tool to assist with recovery of those earlier timed populations.

PSSAG had some in-depth discussion about an Intergrated wild winter steelhead brood stock program on the Skagit. Such a program on the Nooksack would have many of the same issues to resolve. The idea of any such program would to have a brood stock as similar as possible as the wild fish., same genetics and rearing selective pressures. The requirement to rear steelhead fry for 1 to 2 years before releases assures that the hacthery environment will be exerting selective pressures that the wild fish would not cause a divergence from the parent stock. The late and extended spawning time (mid-March into July) present a fish culture problem. An integrated brood would require a representative cross section collection of eggs across that whole time period. To produce true smolts from the eggs from the later portion would difficult to produce with just one year of rearing. If a portion of the fish would require two years of rearing one would one to rear the whole group for two years. To assure that at the time of release that all the smolts be similar size (less selection) they problem would have to be reared in 3 different rearing containers to allow for different feeding regimes. If the program is to an annual those 3 containers become six. Few hatcheries are set up to provide that flexibility.

While solving the above fish culture programs could potentially be solved with dollars the fisheries management would be more difficult and would likely result in a program much smaller than most would hope for.

Curt

 

[Salmo_g]

Really good write up. Regarding hatcheries that integrate wild stock and simulate natural conditions. Is that not what is currently happening to outstanding success at the Baker Lake Sockeye hatchery?

I can't really say. When someone petitioned to list Baker sockeye under the ESA, NMFS concluded that they didn't qualify for ESA consideration because they didn't consider the fish to be a "wild" population, given that their life history consisted of spawning natural in artificial spawning channels, or beaches. Under the Baker project FERC license, the adult fish are put in three "baskets", if you will. Some adults are held and artificially spawned with the eggs incubated in a fairly traditional hatchery, some adults are placed in artificial spawning beaches to spawn naturally, and some adults are placed in Baker Lake to seek out natural spawning areas on their own. The main reason for all this separation effort is because sockeye are extremely susceptible to IHN virus. By spreading out the adults, and therefore the risks, the probability of a major loss of fish due to disease outbreak is significantly reduced. It would be difficult to take the same approach with other species of fish because sockeye life history is so different from the others.

 

[Salmo_g]

Also, I am quite disappointed that I was unable to bait you into publicly endorsing/ planning some form of environmental terrorism to solve that Fulton Spawning Channell up north. There must have been too much drag in my presentation to get such an educated fish to rise. I guess that is why I prefer steelhead over trout.

First off, we adherents of environmental monkey-wrenching reject the term environmental terrorism. It reeks of negativity and distorts the definition of terrorism since environmental monkey-wrenching has no intention of terrifying anyone. Secondly, the main reason I haven't and won't monkey-wrench the Fulton River spawning channel is because I'm not a Canadian, and it is therefore not my place to do it. Thirdly, and quite important, security and surveillance measures are vastly improved and more sophisticated these days, making it extremely difficult for a traditional monkey-wrencher to go about his business.

 

[Salmo_g]

Does anyone know much about the Hamma Hamma project or using post spawn fish as broodstock the following year?

The measures being employed on the Hamma Hamma and other Hood Canal (HC) streams for steelhead recovery do not use post-spawn fish unless something has changed. The measures employed have included mining natural steelhead redds for eyed eggs that are then transported to the Long Live the Kings (LLTK) hatchery. Juveniles from those eggs are reared to smolt stage, with some of them released to the river of origin to replace the otherwise lost production and the remainder raised at one of the sites to become captive broodstock.

A prospective integrated wild steelhead broodstock hatchery program is likely more possible than feasible. It is possible if the affected treaty tribes approve of it (they most likely would because it would serve their interests) and if NMFS approves it. NMFS would approve it if the biological analysis concludes that it wouldn't jeopardize the survival and recovery of the PS ESA-listed steelhead Distinct Population Segment (DPS). I think the conclusion depends upon who does the analysis and of course the details of how the program would be operated. I'm not sure how the alphabet NGOs would react; some of them seem to like integrated wild broodstock, i.e., the transitioning Skykomish summer steelhead program.

 

[charles sullivan]

The measures being employed on the Hamma Hamma and other Hood Canal (HC) streams for steelhead recovery do not use post-spawn fish unless something has changed. The measures employed have included mining natural steelhead redds for eyed eggs that are then transported to the Long Live the Kings (LLTK) hatchery. Juveniles from those eggs are reared to smolt stage, with some of them released to the river of origin to replace the otherwise lost production and the remainder raised at one of the sites to become captive broodstock.

A prospective integrated wild steelhead broodstock hatchery program is likely more possible than feasible. It is possible if the affected treaty tribes approve of it (they most likely would because it would serve their interests) and if NMFS approves it. NMFS would approve it if the biological analysis concludes that it wouldn't jeopardize the survival and recovery of the PS ESA-listed steelhead Distinct Population Segment (DPS). I think the conclusion depends upon who does the analysis and of course the details of how the program would be operated. I'm not sure how the alphabet NGOs would react; some of them seem to like integrated wild broodstock, i.e., the transitioning Skykomish summer steelhead program.

Nothing changed. I just got shit wrong. It does seem like a potentially good idea to investigate using post spawn fish as broodstock. The first issue is finding a way to capture the fish post spawn and nurse them back to health to spawn in the following year. I am not sure how difficult the process of getting them back and fit would be. Would you need to store them in saltwater for a year? Would they figure out what hatchery food was?

 

[charles sullivan]

Charles that idea of using post spawn kelts is intriguing. It stands to reason that fish would have lived it's full life with all the epigenetic influences resulting in a fish that successfully spawned in that watershed. This is the heart of the thought I posed in our group message.

What are the epigenetic influencing factors that cause issue with hatchery steelhead? The big ones are obviously mate finding and redd digging/spawning success as adult fish, and then hatching, feeding, predation evasion and flood/drought management as juveniles.

To the bios out there, do you believe it is possible to have a hatchery with traditional goals (increase of harvestable fish) operate in a manner that appreciably reduces the negative impacts of hatchery genetics?

My simple thoughts are along the lines of a natural spawning channel (with controllable flows) and a series of natural holding ponds ala a beaver complex to rear fish in. The game would be creating the conditions to maximize bug growth to rear the fry naturally, and having a flow regime that both flooded and dried areas periodically. Allow the fish to naturally escape the ponds as their instinct tells them to.

Is something like this even possible or is trying to play God a fools errand?

Aside from cost, I can see some challenges:

I think the portion where the fish leave when they are ready would be tough. I am not sure how you clip them. If they were unclipped would make the harvestable fish part difficult.

Then there is the water right part. Either you are using an existing stream and modifying it or you would have to use diverted river water or groundwater. Groundwater rights are hard to come by in Whatcom County. I do know that there has been one large farm corp. who added groundwater water to a stream in the Nooksack basin. In that way, they were able to use their water and did not lose the water right by abandoning it. Since the fish/river are senior water right holders and the issues with water rights are generally due to the connectivity of ground water to the stream, maybe you could make a case to the state that the fish and the river were the water right users actually using the water?

Flooding could also be a huge problem.

I think that the idea is excellent. It seems uber expensive.