Broodstock hatcheries/ epigenetics

[Cabezon]

Hi Charles,
1. Is it correct to say that we do not know what environmental factors are turning on or off the different expressions of DNA?
We know some factors (e.g., food availability, thermal shocks) that impact epigenetics in trout/salmonids. But it would be presumptuous to assume that we know all the factors that make hatchery fish different from wild fish. And we don't know how various stimuli interact; those experiments that are being done work on one factor at a time. Because of the density at which fish are raised, the social environment in a hatchery is VERY different (higher densities = more stressful?) than the lower density in the wild (see here for effects but not directly link to epigenetic changes). I suspect that disease exposure is likely VERY different in a hatchery vs. the wild. You would need to find a Ph.D. student working on trout epigenetics; that person would have a much better handle of the current literature (vs. my Google searches).

2. Is it correct to say we do not know the extent that epigenic factors influence survival of hatchery fish from egg to adult or
I doubt that there has been much research on what part of a trout's life history specific epigenetic factors come into play. But to give you some idea of the phenotypic plasticity possible, one of the studies on human epigenetics that I scanned indicated that smokers have different epigenetic markers in their lung tissues than do non-smokers but that these differences are reduced when a person ceases to smoke. Hatchery fish go great in a hatchery: lots of food and few natural predators (but disease outbreaks are possible, but treatment is possible). Unless the hatchery fish is to harvested commercially for food, that hatchery fish will eventually be released into the wild. Not only will the hatchery fish's epigenetics likely be inappropriate for the natural environment but the fish's foraging behavior, anti-predator responses, disease resistance, etc. is likely to be very different from wild fish. Thus any decline in survival by hatchery fish could be do to a slew of factors.

3. Is it correct to say we do not know at what point in the fish's life span the epigenetic changes caused by the hatchery environment are likely to be causing increased mortality?
If you are talking about the life of a single hatchery fish, see #2 above. But where epigenetic changes impact fisheries / survival of wild fish populations is when epigenetic changes that are appropriate to the hatchery environment are carried to the offspring ("epigenetic transgenerational inheritance"). If two hatchery fish spawn in the wild and there are these transgenerational effects, their "wild-spawned" offspring are likely to be less fit (less well adapted) than an offspring whose two parents are wild fish. And there is evidence that the offspring of wild x hatchery matings are less fit than the offspring of wild x wild matings. So, a problem with hatchery fish that "escape" is that they dilute / reduce the fitness of wild fish when they mate with the wild fish. One explanation for this loss of fitness of fish that are totally raised in the wild (but who are the product of hatchery x wild matings) is that these offspring carry some "hatchery" epigenetic markers that are inappropriate to the wild environment. Eventually (? on how many generations this takes), the "hatchery" epigenetic markers will disappear and be replaced by "wild" epigenetic markers. But until this happens, there is a loss of fitness and fewer fish produced.

Steve (close to his intellectual limit on this topic. Can we talk about sculpins next?)

 

[Smalma]

Speaking of using kelts.

One option to assure more consistently meeting brood stock needs at the hatchery (fewer in season closers) would be to live spawn the early tine hatchery brood stock rather than kill spawn them. Would require a change in the spawning protocol; hatchery works find it easier to kill spawn. Fish easier to handle, have more complete spawning (get all the eggs) and often better-quality eggs. If the fish were live spawned the hatchery would have the alternative to retain the kelts as a captive brood stock (hold on site until the next year). It would require a dedicated secure holding area (such fish would be a target for vandals). It might be tricky to get those kelts to start feeding but I think adding a few hatchery conditioned trout to the pond would help to stimulate feeding by the steelhead - the frenzy of the feeding trout seems to excite the steelhead.

The idea would be to have enough brood stock held over to supplement the next year's return thus assuring a higher probability of achieving brood stock needs and lower the likelihood of in-season fishery closures. One benefit of such an approach is the female kelts held over would likely have more eggs than the first time they spawn thus help to more achieve that next year's egg take. I have no idea what other obstacles would be, whether would be additional genetic concerns or even if the hatchery would have the capability, space or wiliness to attempt try such change. Regardless, it might be a fun idea to discuss with the hatchery manager and the State's geneticist and steelhead folks. Also been a fan of out of the box think to stimulate discussions towards a solution.

Curt

 

[charles sullivan]

Hi Charles,
1. Is it correct to say that we do not know what environmental factors are turning on or off the different expressions of DNA?
We know some factors (e.g., food availability, thermal shocks) that impact epigenetics in trout/salmonids. But it would be presumptuous to assume that we know all the factors that make hatchery fish different from wild fish. And we don't know how various stimuli interact; those experiments that are being done work on one factor at a time. Because of the density at which fish are raised, the social environment in a hatchery is VERY different (higher densities = more stressful?) than the lower density in the wild (see here for effects but not directly link to epigenetic changes). I suspect that disease exposure is likely VERY different in a hatchery vs. the wild. You would need to find a Ph.D. student working on trout epigenetics; that person would have a much better handle of the current literature (vs. my Google searches).

2. Is it correct to say we do not know the extent that epigenic factors influence survival of hatchery fish from egg to adult or
I doubt that there has been much research on what part of a trout's life history specific epigenetic factors come into play. But to give you some idea of the phenotypic plasticity possible, one of the studies on human epigenetics that I scanned indicated that smokers have different epigenetic markers in their lung tissues than do non-smokers but that these differences are reduced when a person ceases to smoke. Hatchery fish go great in a hatchery: lots of food and few natural predators (but disease outbreaks are possible, but treatment is possible). Unless the hatchery fish is to harvested commercially for food, that hatchery fish will eventually be released into the wild. Not only will the hatchery fish's epigenetics likely be inappropriate for the natural environment but the fish's foraging behavior, anti-predator responses, disease resistance, etc. is likely to be very different from wild fish. Thus any decline in survival by hatchery fish could be do to a slew of factors.

3. Is it correct to say we do not know at what point in the fish's life span the epigenetic changes caused by the hatchery environment are likely to be causing increased mortality?
If you are talking about the life of a single hatchery fish, see #2 above. But where epigenetic changes impact fisheries / survival of wild fish populations is when epigenetic changes that are appropriate to the hatchery environment are carried to the offspring ("epigenetic transgenerational inheritance"). If two hatchery fish spawn in the wild and there are these transgenerational effects, their "wild-spawned" offspring are likely to be less fit (less well adapted) than an offspring whose two parents are wild fish. And there is evidence that the offspring of wild x hatchery matings are less fit than the offspring of wild x wild matings. So, a problem with hatchery fish that "escape" is that they dilute / reduce the fitness of wild fish when they mate with the wild fish. One explanation for this loss of fitness of fish that are totally raised in the wild (but who are the product of hatchery x wild matings) is that these offspring carry some "hatchery" epigenetic markers that are inappropriate to the wild environment. Eventually (? on how many generations this takes), the "hatchery" epigenetic markers will disappear and be replaced by "wild" epigenetic markers. But until this happens, there is a loss of fitness and fewer fish produced.

Steve (close to his intellectual limit on this topic. Can we talk about sculpins next?)

Thank you for your effort. We are all a bit smaryer for it.

 

[charles sullivan]

Thank you for your effort. We are all a bit smaryer for it.

The fact that I legitimately misspelled smarter is pretty good.

 

[charles sullivan]

Speaking of using kelts.

One option to assure more consistently meeting brood stock needs at the hatchery (fewer in season closers) would be to live spawn the early tine hatchery brood stock rather than kill spawn them. Would require a change in the spawning protocol; hatchery works find it easier to kill spawn. Fish easier to handle, have more complete spawning (get all the eggs) and often better-quality eggs. If the fish were live spawned the hatchery would have the alternative to retain the kelts as a captive brood stock (hold on site until the next year). It would require a dedicated secure holding area (such fish would be a target for vandals). It might be tricky to get those kelts to start feeding but I think adding a few hatchery conditioned trout to the pond would help to stimulate feeding by the steelhead - the frenzy of the feeding trout seems to excite the steelhead.

The idea would be to have enough brood stock held over to supplement the next year's return thus assuring a higher probability of achieving brood stock needs and lower the likelihood of in-season fishery closures. One benefit of such an approach is the female kelts held over would likely have more eggs than the first time they spawn thus help to more achieve that next year's egg take. I have no idea what other obstacles would be, whether would be additional genetic concerns or even if the hatchery would have the capability, space or wiliness to attempt try such change. Regardless, it might be a fun idea to discuss with the hatchery manager and the State's geneticist and steelhead folks. Also been a fan of out of the box think to stimulate discussions towards a solution.

Curt

I agree with regards to outside the box thinking. When it comes to hatcheries it seems like you are either for them or against them. It's all become so dogmatic.

I am hopeful that whatever it is that WDFW is going to propose that it is not rooted in dogma.

 

[Wanative]

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?

The Quinalt tribe biologists and hatchery program managers might know something about this topic.

 

[Chucker]

Speaking of using kelts.

Wasn’t the Warm Springs hatchery looking into using chinook kelts? Or am I remembering things wrong.

Rehabbing kelts would probably be a lot easier with Atlantic salmon than with steelhead. Atlantic salmon kelts recover quite fast and start to feed aggressively on their way downriver. They used to be considered a bit of a pest during early season fishing. A lot of the prized “spring salmon” that you can see pictures of people posing with in the UK are actually kelts that have gone downriver and spent a few weeks - months in the estuary. The term that used to be used is “well mended”.

 

[Salmo_g]

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?

I was talking with a couple biologists from the Yakima Tribe a while back. They live spawned steelheads and kept the kelts and reconditioned them (all freshwater) to have on hand for the following year's spawning needs. The kelts were OK with a freshwater holding pond and readily resumed feeding on some kind of hatchery fish ration. Unfortunately I have no follow up information regarding the outcome as far as fecundity and subsequent egg to fry survival. I think they wanted to learn whether it could be done successfully and may not have continued doing it if it wasn't necessary.

 

[charles sullivan]

The Quinalt tribe biologists and hatchery program managers might know something about this topic.

Which portion? I wrote a hell a lot of thoughts there.

 

[Stonedfish]

I was talking with a couple biologists from the Yakima Tribe a while back. They live spawned steelheads and kept the kelts and reconditioned them (all freshwater) to have on hand for the following year's spawning needs. The kelts were OK with a freshwater holding pond and readily resumed feeding on some kind of hatchery fish ration. Unfortunately I have no follow up information regarding the outcome as far as fecundity and subsequent egg to fry survival. I think they wanted to learn whether it could be done successfully and may not have continued doing it if it wasn't necessary.

I wonder if the tribe is still doing that that program?
The latest report on this page is from 2013.
You’d think if it was super successful they have more updated info about it.

Yakima Basin Steelhead Kelt Reconditioning | Yakama Nation Fisheries

yakamafish-nsn.gov

 

[Wanative]

Which portion? I wrote a hell a lot of thoughts there.

Getting through the permitting legal hoops and working in partnership with the tribes if possible.

 

[Capt Insano Emeritis]

Okay i am a humanities guy not a science guy. So this place right now feels like a patty cake cage battle of fish scientists. I will need to read it all several more times to realize how stupid this post i am making actually is. Impressive nerding out.

 

[JACKspASS]

Okay i am a humanities guy not a science guy. So this place right now feels like a patty cake cage battle of fish scientists. I will need to read it all several more times to realize how stupid this post i am making actually is. Impressive nerding out.

I stopped reading at "humanities"

 

[Gary Knowels]

I'm not a fish bio, just a biochemist teaching HS bio, but I have a few thoughts/questions

1. This science discussion is phenomenal, thank you.

2. Holding kelts for a year would probably also lead to unwanted epigenetic changes, the question would be to compare the specific changes and resulting fitness characteristics to that of the traditional hatchery broodstock.

3. The epigenetic changes that occur during hatchery raising may not make the fish better suited for the hatchery, they may be just be consequences that don't drastically reduce fitness in the hatchery. (anyone have data on this?)

4. Most epigenetic changes happen through some sort of signalling cascade with a single protein or suite of proteins responding to environmental conditions (heat shock, NOS, ROS, energy stress, etc) as the trigger that results in many instances of methylation, acetylation, phosphorylation, and/or ubiquitination (among others). It would be really interesting to see if we have identified specific epigenetic changes that reduce fitness and their upstream triggers. That might lead to understanding that allows us to design better hatchery operations. Epigenetics are endlessly complex webs of biochemical reactions, this type of work is labor, time, and resource intensive.

 

[Capt Insano Emeritis]

I stopped reading at "humanities"

And your moniker does the same for me…

 

[SSPey]

If the question is practical aspects of running hatcheries in a wild broodstock steelhead hatchery program, there are a lot of examples in Oregon to draw upon.

If the question is how these programs (vs traditional hatcheries) affect wild fish, good luck. ODFW was hard pushed by consumption-oriented fishing guides to drink gallons of broodstock kool-aid, with multiple programs on different rivers, but ODFW hasn’t done much to examine impacts on wild fish.

These programs most definitely increase guide pressure, social media hype, overall angling pressure, and total encounters with wild fish through a longer hatchery season

 

[charles sullivan]

If the question is practical aspects of running hatcheries in a wild broodstock steelhead hatchery program, there are a lot of examples in Oregon to draw upon.

If the question is how these programs (vs traditional hatcheries) affect wild fish, good luck. ODFW was hard pushed by consumption-oriented fishing guides to drink gallons of broodstock kool-aid, with multiple programs on different rivers, but ODFW hasn’t done much to examine impacts on wild fish.

These programs most definitely increase guide pressure, social media hype, overall angling pressure, and total encounters with wild fish through a longer hatchery season

Yah, I am sure those are all true.

From a selfish perspective, a longer season on the mighty Nooksack would be welcome. I do not worry about that or encounters much. I think that it is a hugely overstated impact. That is my 2 cents.

There is a very broodstock hatchery to the North that has been running for a long time. That river has habitat that appears even more jacked up than the nookie. I do wonder if the Fraser provides juvenile rearing that the Nooksack can not.

 

[ThatGuyRyRy]

evaluate the effectiveness of using sonar to estimate wild steelhead run sizes.

A position was just posted at WDFW for Coast Ecology Sonar Biologist. So I think they are starting this research.

 

[Canuck from Kansas]

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").
...

Steve

Just came across this. Absolutely great primer on epigenetics @Cabezon, many thanks

Interesting side note, I knew Mike Skinner many years ago. First met him when I was a grad student and he was at Vanderbilt. Our paths crossed many times over the next 15 years at various conferences. Haven't seen him in years (since I left academia). Very nice fellow and a very productive scientist.

Cheers

 

[Old Man]

I tried to read thus, but all them 50 and 75 cents words told me that I should keep ,my fingers still. I will have to look up the 75 cent words to see what they mean. Epigenetics is a 75 cent word if there ever was one.. But the results of me trying to read all of this I became dumber.