Epigenetics and hatcheries

jwg

Active Member
#3
Can anyone explain how this differs from what we already know?
I think there are members of this forum that did already know this, from reading primary research papers and from science news articles that came out about those research papers.

The topic of epigenetics is not as well understood here, as indicated by past threads and current discussion in another thread. I thought this article provide a nice explanatory analogy about epigenetics.

that is, the genetic code for a species is like each member having the same audiotape, but over the course of playing their tapes, i.e. individuals living their lives, the expression of whats on the tape changes. Those changes in how the tape is expressed, i.e. sounds when played, are like the epigenetic changes on an individuals DNA, that changes how the DNA is expressed, i.e. which proteins are made and not made and then the metabolic changes that follow.

hatchery environments and wild environments lead to different epigenetic changes and gene expression.



j
 

cabezon

Sculpin Enterprises
#4
Hi jwg,
Cool new article on coho. I agree that the scientific understanding of epigenetics is still incomplete. An embryonic cell has access to the complete repertoire of genes in its DNA. As the embryo develops, cells specialize for specific functions and as part of that differentiation process, some genes are turned off and others are turned on. The source of the signals for turning genes on or off may be intrinsic (within) to the cell or extrinsic (produced by other cells or the environment). A pancreatic cell has the genes (DNA sequences) for making neurotransmitters, but those genes are turned off in that cell, often by adding methyl groups to that DNA sequence. [These methyl groups are added by specific enzymes and can be removed by other enzymes.]

A key aspect of epigenetics is that the actual sequence of DNA is not changed, but which DNA sequences (which genes) are available for producing a protein (gene expressions) changes. If epigenetic changes occur to regulatory genes (think of these as middle or upper management that control a large number of structural or worker genes), a large cluster of genes can be silenced (or activated). While the analogy in the Hakai magazine article has some merit, I like to think of the epigenetic differences between hatchery and wild salmonids are equivalent to alternate developmental programs (alternate suites of genes that work cooperatively). This provides individuals with the flexibility to acclimate in a variable world by activating the appropriate suite that would be favorable to the current environmental conditions.

[What follows is highly speculative..] A developing salmonid has both a high nutrient program and a low nutrient program (could be high social stress / low social stress) [in fact, there could be several alternate programs for a range of conditions]. When developing in a hatchery environment, the high nutrient developmental program (a suite of genes) is activated and the low nutrient program (another suite of genes) is turned off. When developing in a stream, the low nutrient program is activated and the high nutrient program is turned off. Whichever program is selected at this early stage continues throughout the life of the individual fish.

Some epigenetic controls are removed during the formation of gametes for the next generation, wiping the slate clean for the next generation. But we do know that some epigenetic controls persist across generations and can control the development of the subsequent generations, albeit in weaker form. When a pair of hatchery steelhead (using the high nutrient program) reproduce in a river, most of their offspring are still using the high nutrient program, which is not the best strategy for life in a river. Therefore, most in this second generation do poorly. By the third generation developing in a river, the high nutrient program has been turned off in a greater percentage of the offspring and more of these offspring develop via the more appropriate low nutrient program; survival, growth, and reproduction improves. The genes have not changed but which genes are accessed has changed.

If I were entering gradual school (and interested in fish molecular genetics), this would be an area that I would choose for my Ph.D. It has tremendous potential.

Steve
 

jwg

Active Member
#5
Hi jwg,
Cool new article on coho. I agree that the scientific understanding of epigenetics is still incomplete. An embryonic cell has access to the complete repertoire of genes in its DNA. As the embryo develops, cells specialize for specific functions and as part of that differentiation process, some genes are turned off and others are turned on. The source of the signals for turning genes on or off may be intrinsic (within) to the cell or extrinsic (produced by other cells or the environment). A pancreatic cell has the genes (DNA sequences) for making neurotransmitters, but those genes are turned off in that cell, often by adding methyl groups to that DNA sequence. [These methyl groups are added by specific enzymes and can be removed by other enzymes.]

A key aspect of epigenetics is that the actual sequence of DNA is not changed, but which DNA sequences (which genes) are available for producing a protein (gene expressions) changes. If epigenetic changes occur to regulatory genes (think of these as middle or upper management that control a large number of structural or worker genes), a large cluster of genes can be silenced (or activated). While the analogy in the Hakai magazine article has some merit, I like to think of the epigenetic differences between hatchery and wild salmonids are equivalent to alternate developmental programs (alternate suites of genes that work cooperatively). This provides individuals with the flexibility to acclimate in a variable world by activating the appropriate suite that would be favorable to the current environmental conditions.

[What follows is highly speculative..] A developing salmonid has both a high nutrient program and a low nutrient program (could be high social stress / low social stress) [in fact, there could be several alternate programs for a range of conditions]. When developing in a hatchery environment, the high nutrient developmental program (a suite of genes) is activated and the low nutrient program (another suite of genes) is turned off. When developing in a stream, the low nutrient program is activated and the high nutrient program is turned off. Whichever program is selected at this early stage continues throughout the life of the individual fish.

Some epigenetic controls are removed during the formation of gametes for the next generation, wiping the slate clean for the next generation. But we do know that some epigenetic controls persist across generations and can control the development of the subsequent generations, albeit in weaker form. When a pair of hatchery steelhead (using the high nutrient program) reproduce in a river, most of their offspring are still using the high nutrient program, which is not the best strategy for life in a river. Therefore, most in this second generation do poorly. By the third generation developing in a river, the high nutrient program has been turned off in a greater percentage of the offspring and more of these offspring develop via the more appropriate low nutrient program; survival, growth, and reproduction improves. The genes have not changed but which genes are accessed has changed.

If I were entering gradual school (and interested in fish molecular genetics), this would be an area that I would choose for my Ph.D. It has tremendous potential.

Steve
Steve:

I like very much your more informative explanation here, touching on several key aspects of epigenetics.

I also like very much your thought on low nutrient and high nutrient programs.

I also think of the hatchery as a nutrient rich environment. Then, the fish to most efficiently acquire the food outcompete the others, while in a river environment (low nutrient), the fish to most efficiently transform limited food into biomass outcompete the others.

To put it crudely, the hatchery winners may acquire the food but shit a lot of it out or otherwise metabolize it wastefully, whereas the wild fish make sure to efficiently process their limited food into body mass and ultimately reproduction.

to me, this thinking came from microbial community ecology (not my field but I collaborate with microbiologists--I'm a chemist). The ecological question is which microbes in a community outcompete the others in abundant resources--without limitations in flux of those resources to their location-- vs which microbes compete in limited resource fluxes.

So, for example, consider a microbial community in liquid media culture on a shaker table in the lab (the microbial hatchery): the nutrient resources in the culture are abundant and accessible until they are exhausted. The microbes that use them the fastest, before they are exhausted, win. They don't have to be efficient in what they do with the nutrients. As long as they convert some of the nutrients into progeny, and prevent other microbes from getting the nutrients by consuming nutrients faster, they win.

Now consider a microbial community in subsurface environments like soil, a porous medium which allows water and nutrient transport to the site of a microbial community, but limits the rate of transport (the wild native environment). Limited amounts of nutrients are available, at a limited rate. In this community, those microbes that most efficiently pr0cess those nutrients into biomass, i.e. progeny, win. They still need to capture the nutrients in competition with the other microbes, but there is no advantage in wastefully processing those nutrients, since there is not an unlimited supply. And they will succeed in getting more resources by increasing their numbers, not by processing the nutrients faster. They cannot get nutrients faster by processing them faster, because they have to wait for additional nutrients to arrive.

j
 

cabezon

Sculpin Enterprises
#6
Steve:

I like very much your more informative explanation here, touching on several key aspects of epigenetics.

I also like very much your thought on low nutrient and high nutrient programs.

I also think of the hatchery as a nutrient rich environment. Then, the fish to most efficiently acquire the food outcompete the others, while in a river environment (low nutrient), the fish to most efficiently transform limited food into biomass outcompete the others.

To put it crudely, the hatchery winners may acquire the food but shit a lot of it out or otherwise metabolize it wastefully, whereas the wild fish make sure to efficiently process their limited food into body mass and ultimately reproduction.

to me, this thinking came from microbial community ecology (not my field but I collaborate with microbiologists--I'm a chemist). The ecological question is which microbes in a community outcompete the others in abundant resources--without limitations in flux of those resources to their location-- vs which microbes compete in limited resource fluxes.

So, for example, consider a microbial community in liquid media culture on a shaker table in the lab (the microbial hatchery): the nutrient resources in the culture are abundant and accessible until they are exhausted. The microbes that use them the fastest, before they are exhausted, win. They don't have to be efficient in what they do with the nutrients. As long as they convert some of the nutrients into progeny, and prevent other microbes from getting the nutrients by consuming nutrients faster, they win.

Now consider a microbial community in subsurface environments like soil, a porous medium which allows water and nutrient transport to the site of a microbial community, but limits the rate of transport (the wild native environment). Limited amounts of nutrients are available, at a limited rate. In this community, those microbes that most efficiently pr0cess those nutrients into biomass, i.e. progeny, win. They still need to capture the nutrients in competition with the other microbes, but there is no advantage in wastefully processing those nutrients, since there is not an unlimited supply. And they will succeed in getting more resources by increasing their numbers, not by processing the nutrients faster. They cannot get nutrients faster by processing them faster, because they have to wait for additional nutrients to arrive.

j
Hi J,
The situation may be somewhat similar, except that in the case of eukaryotes, the same individual could follow the spend-thrift or the miserly strategy depending on early factors that influenced its development, rather than competition among strains or species. And while my fleshed out scenario focused on nutrients, it could easily be social stress as a trigger.

I remember back to a seminar that I heard while in gradual school from a fish biologist from Montana that highlights the importance of stress and rearing environment. This study occurred when some sections of the Madison were still stocked with hatchery trout. In areas where hatchery trout were released the number of wild trout crashed. One explanation was food depletion by the hatchery fish but the wild trout were feeding just fine. The problem was social as much as energetic. The hatchery trout had no boundaries / no recognition of social signals and would swim into the feeding territories of the wild trout. The wild trout would rush to drive them off and the hatchery trout would skedaddle off only to blunder into the territory of the next trout. This induced added energetic costs to the wild trout and added stress, both of which impacted their survival.

One wonders if the choice of a young Oncorhynchus mykiss to stay in its home river (resident rainbow) versus head out to sea (a steelhead) might be the result of an epigenetic switch triggered early on during its development that has dramatic repercussions on the whole life history of that individual.
Steve
 

FinLuver

Active Member
#7
that is, the genetic code for a species is like each member having the same audiotape, but over the course of playing their tapes, i.e. individuals living their lives, the expression of whats on the tape changes. Those changes in how the tape is expressed, i.e. sounds when played, are like the epigenetic changes on an individuals DNA, that changes how the DNA is expressed, i.e. which proteins are made and not made and then the metabolic changes that follow.
Explains a LOT about the human species and its current behavior and thinking...;)
 

FinLuver

Active Member
#8
Some epigenetic controls are removed during the formation of gametes for the next generation, wiping the slate clean for the next generation. But we do know that some epigenetic controls persist across generations and can control the development of the subsequent generations, albeit in weaker form. When a pair of hatchery steelhead (using the high nutrient program) reproduce in a river, most of their offspring are still using the high nutrient program, which is not the best strategy for life in a river. Therefore, most in this second generation do poorly. By the third generation developing in a river, the high nutrient program has been turned off in a greater percentage of the offspring and more of these offspring develop via the more appropriate low nutrient program; survival, growth, and reproduction improves. The genes have not changed but which genes are accessed has changed.
Again...
Explains a LOT about the human species and its current behavior and thinking...;)
 

chromie

Active Member
#9
Hi J,
The situation may be somewhat similar, except that in the case of eukaryotes, the same individual could follow the spend-thrift or the miserly strategy depending on early factors that influenced its development, rather than competition among strains or species. And while my fleshed out scenario focused on nutrients, it could easily be social stress as a trigger.

I remember back to a seminar that I heard while in gradual school from a fish biologist from Montana that highlights the importance of stress and rearing environment. This study occurred when some sections of the Madison were still stocked with hatchery trout. In areas where hatchery trout were released the number of wild trout crashed. One explanation was food depletion by the hatchery fish but the wild trout were feeding just fine. The problem was social as much as energetic. The hatchery trout had no boundaries / no recognition of social signals and would swim into the feeding territories of the wild trout. The wild trout would rush to drive them off and the hatchery trout would skedaddle off only to blunder into the territory of the next trout. This induced added energetic costs to the wild trout and added stress, both of which impacted their survival.

One wonders if the choice of a young Oncorhynchus mykiss to stay in its home river (resident rainbow) versus head out to sea (a steelhead) might be the result of an epigenetic switch triggered early on during its development that has dramatic repercussions on the whole life history of that individual.
Steve
Engineering is my background so pardon the lack of proper biological terminology.

Could this scenario play out on wild vs wild interactions? I’m curious about the trigger for population crashes being limited by how much boundary space vs nutrient density. Certainly both matter. What was interesting in the Madison example was not a lack of nutrients but a lack of boundary space.

For example estuarine rearing habitat. Let’s use the Skagit as an example. The Skagit delta has a fair amount of dikes for farmland which limit channel migration and open natural estuarine development processes. With this limited variability in habitat space, does that cause stress factors on smolts in general as they compete not only for nutrients but safe harbor? Do some wild fish show that same of clueless hatchery fish behavior of boundary awareness and move into other territories as a means of survival? I see a lot of salmon nutrient enrichment dumps (tails cut off) on upper Skagit tributaries. I now wonder what kind of impact it has if habitat/boundary space is limited down stream.

It would seem to me, the more it could create a severe negative feedback loop for all species that develop in limited rearing habitat, let alone nutrient density.

I wonder too about about the weighted impact of shoreline development with bulkheads in the Puget Sound and the impact of sediment transport in regards to eelgrass development would create this same problem.

Interesting to me in regards to what types of habitat preserved give the most bang for the buck. I recognize that’s a heavy generalization and it depends on species in where they rear.....

I remember back when engineered log jams were becoming a topic of conversation (Tetra engineers?) on the NF Stilliguamish and chuckling at the concept. As time went on and they were implemented above C Post, I snorkeled it and could see first hand the positive impact it was having with the creation of new formed holding pools. I’m thinking they were even more impactful now as you talk about available boundary space.

PS: thanks Cabezon and JWG for a fantastic read. With all the doom and gloom of fish populations in the PNW, realizing the amount we can still learn is exciting.
 
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jwg

Active Member
#10
Engineering is my background so pardon the lack of proper biological terminology.

Could this scenario play out on wild vs wild interactions? I’m curious about the trigger for population crashes being limited by how much boundary space vs nutrient density. Certainly both matter. What was interesting in the Madison example was not a lack of nutrients but a lack of boundary space.

For example estuarine rearing habitat. Let’s use the Skagit as an example. The Skagit delta has a fair amount of dikes for farmland which limit channel migration and open natural estuarine development processes. With this limited variability in habitat space, does that cause stress factors on smolts in general as they compete not only for nutrients but safe harbor? Do some wild fish show that same of clueless hatchery fish behavior of boundary awareness and move into other territories as a means of survival? I see a lot of salmon nutrient enrichment dumps (tails cut off) on upper Skagit tributaries. I now wonder what kind of impact it has if habitat/boundary space is limited down stream.

It would seem to me, the more it could create a severe negative feedback loop for all species that develop in limited rearing habitat, let alone nutrient density.

I wonder too about about the weighted impact of shoreline development with bulkheads in the Puget Sound and the impact of sediment transport in regards to eelgrass development would create this same problem.

Interesting to me in regards to what types of habitat preserved give the most bang for the buck. I recognize that’s a heavy generalization and it depends on species in where they rear.....

I remember back when engineered log jams were becoming a topic of conversation (Tetra engineers?) on the NF Stilliguamish and chuckling at the concept. As time went on and they were implemented above C Post, I snorkeled it and could see first hand the positive impact it was having with the creation of new formed holding pools. I’m thinking they were even more impactful now as you talk about available boundary space.

PS: thanks Cabezon and JWG for a fantastic read. With all the doom and gloom of fish populations in the PNW, realizing the amount we can still learn is exciting.
I can't answer your questions myself.
But they extend the conversation

We talked about high and low nutrient programs
We talked about population density stress.

The transition from fresh to salt has certainly changed, both with regard to habitat and then the fish opportunity to respond, and it's a major affect, and so maybe this is a stressor that affects subsequent survivability and reproductive success
 

Shad

Active Member
#11
I tried, but I can't hang. Some serious science being bantered here. Over my head serious.

I understood that Darwin's principles played out pretty well with regard to hatchery fish survival... Is that the gist of this discussion?
 

Rob Allen

Active Member
#12
I tried, but I can't hang. Some serious science being bantered here. Over my head serious.

I understood that Darwin's principles played out pretty well with regard to hatchery fish survival... Is that the gist of this discussion?
Yup simple natural or in this case unnatural selection. Information we have known for a couple decades no more hatchery research us needed ever. We know they don't work knowing every detail about why is not helpful.
 

Salmo_g

Well-Known Member
#13
Yup simple natural or in this case unnatural selection. Information we have known for a couple decades no more hatchery research us needed ever. We know they don't work knowing every detail about why is not helpful.
What a classic example of a closed mind Rob. "We know all we need to know about topic X, so we don't need to know anything more about it ever again." Some real stupid shits have said that or similar many times over the ages, and were dead wrong every single time. Knowledge is the enemy only to the closed mind. I wish you the best Rob, but you're your own worst enemy.
 

Rob Allen

Active Member
#14
What a classic example of a closed mind Rob. "We know all we need to know about topic X, so we don't need to know anything more about it ever again." Some real stupid shits have said that or similar many times over the ages, and were dead wrong every single time. Knowledge is the enemy only to the closed mind. I wish you the best Rob, but you're your own worst enemy.
Sorry Salmo not agreeing with you is not the definition of closed mindedness.
Hatcheries are never going to be operated in such a way as to increase survival while reducing impacts on wild stocks.
It's time to stop pretending that there is a magic bullet to fix hatcheries. Especially when we don't have the money to act on what we already know.
Knowledge for it's own sake is pointless.
You have to be able to demonstrate how that knowledge is useful before it's of any value.
We spend way too much money in science that adds no value to society.
Fortunatly this study is Canadian so they didn't spend my money to do it.

As for here in WA. We need to be spending our money monitoring what we have already done to determine if it's been of any value.
 

Salmo_g

Well-Known Member
#15
Knowledge for it's own sake is pointless.
You have to be able to demonstrate how that knowledge is useful before it's of any value.
Rob, please don't act stupid. I didn't say that not agreeing with me is the definition of closed minded. It's about what I just quoted from your post up above.

I wasn't referring just to hatcheries BTW. Often you can't know if knowledge is useful until after you have it, sometimes long after. With your attitude of saying that knowledge for its own sake is pointless, damn near everything we know would never have been discovered, because its use or many, many uses were not known and could not be known for years and years to come. For instance, take something simple, like Leonardo Da Vinci inventing the bicycle long before anyone knew how to build one or what practical value it might someday have. Are you going to tell me that was pointless? Hell, there must be a million such examples.

Studying hatcheries and hatchery fish could lead to currently unknown useful things that are unknowable today. Fishery genetic information is exploding at an exponential pace. There's a ton of good that can come from that, all without trying to replace wild salmon and steelhead. There are other species of fish too, ya' know.
 

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