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Very interesting article. You can read the original article here: http://www.nature.com/articles/ncomms10676. The heart of the study is differences in gene expression. Gene expression looks at which genes in the DNA are active, that is, these sections of DNA are being copied into RNA, which is then used to make proteins which perform specific functions in the cell.

The authors attribute three possible mechanisms for these changes: "Such rapid adaptation could occur via three complementary mechanisms: (i) selection could result in small allele frequency changes at many loci, as in traditional quantitative genetics models17, (ii) selection could act directly on a few regulatory loci18 or (iii) there could be physical changes to the genome that are functionally relevant but that do not involve a change in the nucleotide sequence (that is, heritable epigenetic modifications)19. These three mechanisms leave different signatures at the genomic level, but all create changes that can be directly detected by measuring the global patterns of gene expression."

I would predict that many of the changes are due to mechanism 3 - epigenetic changes in which additions/substractions to DNA impacts how readily a gene is expressed. One epigenetic process, methylation, decreases the rate that a gene is expressed; a second epigenetic process, acetylation, increase the rate that a gene is expressed. Both processes occur in response to environmental signals. And epigenetic markers are removed in subsequent generations (though not all at once), allowing formerly "hatchery" fish to revert to "wild" patterns of gene expression.

Very very interesting and explains quite a lot.

Steve
 

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Very interesting article. You can read the original article here: http://www.nature.com/articles/ncomms10676. The heart of the study is differences in gene expression. Gene expression looks at which genes in the DNA are active, that is, these sections of DNA are being copied into RNA, which is then used to make proteins which perform specific functions in the cell.

The authors attribute three possible mechanisms for these changes: "Such rapid adaptation could occur via three complementary mechanisms: (i) selection could result in small allele frequency changes at many loci, as in traditional quantitative genetics models17, (ii) selection could act directly on a few regulatory loci18 or (iii) there could be physical changes to the genome that are functionally relevant but that do not involve a change in the nucleotide sequence (that is, heritable epigenetic modifications)19. These three mechanisms leave different signatures at the genomic level, but all create changes that can be directly detected by measuring the global patterns of gene expression."

I would predict that many of the changes are due to mechanism 3 - epigenetic changes in which additions/substractions to DNA impacts how readily a gene is expressed. One epigenetic process, methylation, decreases the rate that a gene is expressed; a second epigenetic process, acetylation, increase the rate that a gene is expressed. Both processes occur in response to environmental signals. And epigenetic markers are removed in subsequent generations (though not all at once), allowing formerly "hatchery" fish to revert to "wild" patterns of gene expression.

Very very interesting and explains quite a lot.

Steve
What is meant by expressed?

So what does this mean impact wise? Does it mean that the impact will be limited? Does it mean that hatcheries always change the way the genes are expressed? Could changes in hatch practices change the way the genes are expressed?

I find this science fascinating. Unfortunately it is generally dumbed down in these articles rendering it almost meaningless. The original paper is often too much to digest.

Go Sox,
cds
 

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I believe expressed means 'shown.' Genes can turn on and off (think cancer) and when "on" a certain trait is 'expressed.' I have taken very minimal genetics classes so I could definitely be wrong.
 

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Sculpin Enterprises
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What is meant by expressed?

So what does this mean impact wise? Does it mean that the impact will be limited? Does it mean that hatcheries always change the way the genes are expressed? Could changes in hatch practices change the way the genes are expressed?

I find this science fascinating. Unfortunately it is generally dumbed down in these articles rendering it almost meaningless. The original paper is often too much to digest.

Go Sox,
cds
Let me try to explain expression by using humans as an example. In every one of our cells, we have approximately 20,000 genes (a region of the DNA double helix). Each gene has the instructions to produce the 100,000 proteins which actually perform tasks in the body (e.g., enzymes for chemical reactions, contractile proteins in muscle, structural molecules likes collagen in tendons and ligaments). Because DNA has to last the life of the cell (which, in some cases, is the life of the organism), it is kept relatively safe in the nucleus. When a cell needs more copies of a specific protein, a copy of the gene is made in the form of RNA (a process called transcription) which travels to the cytoplasm where the nucleotides are used by a structure called the ribosome to indicate the order of the 20 amino acids that make up proteins (a process called translation). All the cells in your body have the same DNA, plus or minus a few copying errors. Any particular cell makes only a subset of those proteins and accesses (expresses) just a subset of those genes. For example, while a muscle cell has the DNA information on making the hormone insulin, it does not "express" that information. A pancreatic cells has the information to synthesize hemoglobin, but it is not expressed in these cells.
When an egg is first fertilized, it appears to be capable of expressing all of the genes in its arsenal. But as the embryo develops, cells begin to specialize into tissue types (endoderm on the inside, mesoderm in the middle, ectoderm on the outside). Specialization occurs within these major tissue types too (e.g., ectoderm into skin and into neurons). During this specialization process (also known as differentiation), chemical markers may be added to some of the genes that prevent them form being copied into RNA, essentially turning them off (a process called methylation). Others become easier to express (copy into RNA) when other chemical markers are added to structural proteins that support these gene regions (a process called acetylation). [There are other mechanisms that have these impacts too.] These kinds of changes fall into the broad category of epigenetics because they occur during the lifetime of the organism. The DNA information is still there, but its access has been changed.
In subsequent generations, these epigenetic markers (acetylation / methylation) are removed and the organism returns to its original state. In some cases, the markers last only a single generation, but in other cases, the markers persist for several generations. For example, extreme starvation in Holland near the end of the Second World War resulted in a series of epigenetic changes in fetuses that developed during that time (see http://www.naturalhistorymag.com/features/142195/beyond-dna-epigenetics). They were born at a smaller size and stayed small throughout their lives (and had a lower risk of diabetes); these epigenetic changes for efficient use of energy were passed onto their children even though they suffered no starvation during their own development.
One way to think of these epigenetic changes in humans (and hatchery fish) is that there are teams of genes that work best under one set of environmental conditions and other teams that work best under other environmental conditions. As the world is a variable place, epigenetics allows an organism to activate the suite that will work best and silence the ones that won't as an organism adapts to its current environment.
Some speculation. From this study of hatchery vs. wild steelhead, it appears that the crowded conditions of the hatchery favor one suite of genes, while the conditions in the wild favor another suite. And it would appear that expressing the wrong suite is very bad for growth and survival. The overall DNA in the two groups (hatchery vs. wild) is probably quite similar, but the expression is different because of their different rearing environments. And these differences in expression may persist for more than one generation. This would explain the very poor survival of the offspring of hatchery fish that spawn in the wild, even when half of the genes come from a wild parent - wrong epigenetic markers for survival in the wild. However, some of these offpring do survive and the more generations they are in the wild the more their epigenetic markers revert to the wild conditions and the hatchery imprints are lost.
Steve
 

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Let me try to explain expression by using humans as an example. In every one of our cells, we have approximately 20,000 genes (a region of the DNA double helix). Each gene has the instructions to produce the 100,000 proteins which actually perform tasks in the body (e.g., enzymes for chemical reactions, contractile proteins in muscle, structural molecules likes collagen in tendons and ligaments). Because DNA has to last the life of the cell (which, in some cases, is the life of the organism), it is kept relatively safe in the nucleus. When a cell needs more copies of a specific protein, a copy of the gene is made in the form of RNA (a process called transcription) which travels to the cytoplasm where the nucleotides are used by a structure called the ribosome to indicate the order of the 20 amino acids that make up proteins (a process called translation). All the cells in your body have the same DNA, plus or minus a few copying errors. Any particular cell makes only a subset of those proteins and accesses (expresses) just a subset of those genes. For example, while a muscle cell has the DNA information on making the hormone insulin, it does not "express" that information. A pancreatic cells has the information to synthesize hemoglobin, but it is not expressed in these cells.
When an egg is first fertilized, it appears to be capable of expressing all of the genes in its arsenal. But as the embryo develops, cells begin to specialize into tissue types (endoderm on the inside, mesoderm in the middle, ectoderm on the outside). Specialization occurs within these major tissue types too (e.g., ectoderm into skin and into neurons). During this specialization process (also known as differentiation), chemical markers may be added to some of the genes that prevent them form being copied into RNA, essentially turning them off (a process called methylation). Others become easier to express (copy into RNA) when other chemical markers are added to structural proteins that support these gene regions (a process called acetylation). [There are other mechanisms that have these impacts too.] These kinds of changes fall into the broad category of epigenetics because they occur during the lifetime of the organism. The DNA information is still there, but its access has been changed.
In subsequent generations, these epigenetic markers (acetylation / methylation) are removed and the organism returns to its original state. In some cases, the markers last only a single generation, but in other cases, the markers persist for several generations. For example, extreme starvation in Holland near the end of the Second World War resulted in a series of epigenetic changes in fetuses that developed during that time (see http://www.naturalhistorymag.com/features/142195/beyond-dna-epigenetics). They were born at a smaller size and stayed small throughout their lives (and had a lower risk of diabetes); these epigenetic changes for efficient use of energy were passed onto their children even though they suffered no starvation during their own development.
One way to think of these epigenetic changes in humans (and hatchery fish) is that there are teams of genes that work best under one set of environmental conditions and other teams that work best under other environmental conditions. As the world is a variable place, epigenetics allows an organism to activate the suite that will work best and silence the ones that won't as an organism adapts to its current environment.
Some speculation. From this study of hatchery vs. wild steelhead, it appears that the crowded conditions of the hatchery favor one suite of genes, while the conditions in the wild favor another suite. And it would appear that expressing the wrong suite is very bad for growth and survival. The overall DNA in the two groups (hatchery vs. wild) is probably quite similar, but the expression is different because of their different rearing environments. And these differences in expression may persist for more than one generation. This would explain the very poor survival of the offspring of hatchery fish that spawn in the wild, even when half of the genes come from a wild parent - wrong epigenetic markers for survival in the wild. However, some of these offpring do survive and the more generations they are in the wild the more their epigenetic markers revert to the wild conditions and the hatchery imprints are lost.
Steve
Thank you Steve. I am smarter right now than I was 10 minutes ago. That's quite a gift.

Go Sox,
cds
 

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Sculpin Enterprises
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Very nice Steve! Would this help to explain in part, the failure of some brood stock programs?
Hi WW,
That would be a potential explanation for the challenges facing brood stock programs. They are using wild fish that have wild-fish epigenetic markers and their offspring have to survive under the crowded, stressful conditions of a hatchery with the wrong suite of expressed genes. Certainly, hatchery managers have had a much easier time transferring their lab rat strains (e.g., Chambers Creek) from hatchery to hatchery on different watersheds, even continents, presumably because the hatchery conditions are reasonably similar even if the water shed is different.
Steve
 

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However, some of these offpring do survive and the more generations they are in the wild the more their epigenetic markers revert to the wild conditions and the hatchery imprints are lost.
The next question would be how long would this take?
 

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ok so again the reports and not the first time that I have read it .Says that hatchery genes can and do breed out but Im still wrong.Guess I just have to drink the kool aid and get a membership to Wfc.Then I can be one of the kool kids.
 

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ok so again the reports and not the first time that I have read it .Says that hatchery genes can and do breed out but Im still wrong.Guess I just have to drink the kool aid and get a membership to Wfc.Then I can be one of the kool kids.
Your most recent assertion is that there are no true wild fish. This would seem to indicate that any short term genetic differences created by hatchery fish spawning in the wild will be mitigated by time. Thus leaving our wild fish as wild as they have ever been.
 

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ok so again the reports and not the first time that I have read it .Says that hatchery genes can and do breed out but Im still wrong.Guess I just have to drink the kool aid and get a membership to Wfc.Then I can be one of the kool kids.
Wolf,

Why do you keep saying the same nonsense over and over? It looks to me like you don't understand what you read and don't even understand what you write. This makes it hard to have even a basic discussion with you.

As mentioned going on a hundred times it seems like, the issue is not black and white, but includes many shades of gray. If you cannot understand and accept that, then any amount of conversation with you is wasted.

Hatchery genetics are not good for survival in the natural environment. Wild genetics are not as good for survival in a hatchery as hatchery fish. But some hatchery steelhead can survive in the wild (summer steelhead more than winter steelhead, and Chambers Creek fish have the least adaptibility to the natural environment.) under certain conditions. If you cannot understand this less than all or nothing black and white answer, you are wasting your time trying to discuss it.

Sg
 

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Salmo funny I have seen on other sites you dont talk so down about the hatchery fish infact you seem to be behind and have said there is other problems facing wild steelhead than hatchery fish.But here al of a sudden its like you did a 180 on it.Show me where I ever said I have all the ansewrs you have several times told me to do the research.ok did Have read in several reports that the hatchery gene can be bread out with in as soon as a couple of generations.I have also never lied and said that I hate hatchery fish and it should be wild fish only.Yes I do enjoy fishing hatchery fish because me and my family enjoy eating fish.I would rather eat a hatchery brat as you all like to call them than eat something from a fish farm.Which from what I have read up on is a whole lot worse for wild fish and our enviroment .Salmo you said do the research which I have and from what I can see we should be fighting a differant fight than the hatchery one.I havnt read anything that says 100% that hatchery fish are the down fall of wild fish.But I have read alot about the down side of over fishing both tribal/no tribal fishiers.About the down side of poor habitat.Im not a bio but have spent enough time in the wilds to know habitat can only handle so many animals/fish=carrying capacity.I know you have said that steelhead dont use the esturies like some of the salmon species do.But on that note could the esturies be more important to steelhead than we think or that belive.The nisqually runs where doing poorly.But know a few years after returning the nisqually delta back to its more natural state .we are now seeing a up turn in steelhead numbers.I have read in a couple reports where the bios working/studing the nisqually runs where seeing a higher number of smolts staying as resident rainbows than out migrateing to become steelhead.So could it be that part of the problem was the outmigrating smolts hit the estury found poor condtions.then instaed of countiuing on the out bound turned around and headed back upstream.Where now they find better conditions and go ahead and head on out into the sound then the oceacen to become our beloved steelhead.I mean it would seem if it was all the hatchery fish fault as some want us to believe.Then we should have seen better returns alot sooner seeing as there has been no hatchery releases of steelhead in that river in over 20 years.But now after repairing the delta we are seeing the numbers starting to increase.yes hatchery fish can poise a problem.Are they the biggest threat no.So if we really care then we need to focus are energy on the real problems/threats not the easy low hanging fruit.Would support the wfc if they put their energy to fighting the real problems not on bogus lawsuits that do nothing but increase their coffers.
 

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Salmo funny I have seen on other sites you dont talk so down about the hatchery fish infact you seem to be behind and have said there is other problems facing wild steelhead than hatchery fish.But here al of a sudden its like you did a 180 on it.Show me where I ever said I have all the ansewrs you have several times told me to do the research.ok did Have read in several reports that the hatchery gene can be bread out with in as soon as a couple of generations.I have also never lied and said that I hate hatchery fish and it should be wild fish only.Yes I do enjoy fishing hatchery fish because me and my family enjoy eating fish.I would rather eat a hatchery brat as you all like to call them than eat something from a fish farm.Which from what I have read up on is a whole lot worse for wild fish and our enviroment .Salmo you said do the research which I have and from what I can see we should be fighting a differant fight than the hatchery one.I havnt read anything that says 100% that hatchery fish are the down fall of wild fish.But I have read alot about the down side of over fishing both tribal/no tribal fishiers.About the down side of poor habitat.Im not a bio but have spent enough time in the wilds to know habitat can only handle so many animals/fish=carrying capacity.I know you have said that steelhead dont use the esturies like some of the salmon species do.But on that note could the esturies be more important to steelhead than we think or that belive.The nisqually runs where doing poorly.But know a few years after returning the nisqually delta back to its more natural state .we are now seeing a up turn in steelhead numbers.I have read in a couple reports where the bios working/studing the nisqually runs where seeing a higher number of smolts staying as resident rainbows than out migrateing to become steelhead.So could it be that part of the problem was the outmigrating smolts hit the estury found poor condtions.then instaed of countiuing on the out bound turned around and headed back upstream.Where now they find better conditions and go ahead and head on out into the sound then the oceacen to become our beloved steelhead.I mean it would seem if it was all the hatchery fish fault as some want us to believe.Then we should have seen better returns alot sooner seeing as there has been no hatchery releases of steelhead in that river in over 20 years.But now after repairing the delta we are seeing the numbers starting to increase.yes hatchery fish can poise a problem.Are they the biggest threat no.So if we really care then we need to focus are energy on the real problems/threats not the easy low hanging fruit.Would support the wfc if they put their energy to fighting the real problems not on bogus lawsuits that do nothing but increase their coffers.
OMG! You don't know Salmo G at all.
 
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