gardening, fishing and thoughts about genetics

[rolmops]

Ok, this may sound crazy,but I have been called that all my life so that does not bother me.

Anybody who gardens or farms knows that when the rains do not come, the plants get pressured and will start setting flowers in order to produce their seeds and make sure that there will be a next generation.

In times of plenty, water fleas are exclusively female and reproduce by cloning, but when their ponds dry up there will be male fleas and on top of cloning there is also sexual reproduction which causes more genetic variety which in turn increases survival chances for the species.

Now for the last few years fish were smaller and  there has been a lot of two year old salmon coming up the streams in order to reproduce. And as we all know, the three year olds and, very rarely , some 4 year olds are supposed to do that, not two year olds.

We also know that a few years ago we had harsh winters and not so much bait, relative to the amount of fish that came out of the hatcheries and natural reproduction. The fish we caught was smaller. We started thinking that there was  genetic change happening, favoring smaller fish. 

Now this year there were die offs of bait fish and the salmon was gorging on this plentiful source of food specially in June when many of us got skunked while the salmon lay on the bottom with their bellies full of easy pickings. It seems that the fish is plentiful and larger compared to the last few years. 

My theory is that there was no genetic change, but a survival mechanism that caused reproduction urge to start at an earlier age, much like happens with plants and water fleas when there is environmental pressure. Of course the process in fish would be slower due to their longer life cycle compared to water fleas.

If what I think is correct, then this fall run should have fewer 2 year olds running relative to the overall amount and the size of fish will be larger, although the overall amount of running fish will be smaller because we lost a lot fish due to two year olds running last year instead of now.

Unless there is an awful winter which would throw everything in disarray , next year should show larger fish continuing the trend we see this year.

These are just my not completely uneducated thoughts.

Please  tune in and give me your opinion on these thoughts. 

Edited September 11, 2025 by rolmops

[Gill-T]

Theory says more bait, less predators = bigger predators 

Edited September 11, 2025 by Gill-T

[LongLine]

Which is bigger?  A basketball center that is 6'10" tall and 240 Lbs or a football lineman that is 6"0" and 300 Lbs?  

 

The weight of each was determined by their diet but their height was a matter of genetics. The basketball center could go well over 300 Lbs with a different diet but the football player will not grow 10" taller.

 

Back in the 60's when the beer company gave fish awards, one had to give a length and a girth as well as weight in order to win an award.  Today we only go by weight to win a tournament.

 

 

The DEC data for 2022 said the average length of a 3 Yr old female was 36.9" and in the 2023 report they said the average length of the same 3 yr old female was 33.8".  Quite a difference!  However, the 3 yr old males were the same for both years at 35.8". 

 

They however do a lot of fancy logarithmic regression analysis to calculate the wet weight of 36" fish and report that as a 3 yr old fish.  The 2024 summary says the 3 yr old Chinook was 19 Lbs.  The full 2024 report still hasn't been published so the jury is still out on that one.  For years there was opposition to adding random sampling to the preyfish assessment but when they finally did and added some whole lake trawls the results were different than anticipated.  

 

I'd be all in favor of the tournaments recording not only weights of fish but length and girth also.  That lineman obviously has a greater girth than the basketball player. 

[GAMBLER]

10 hours ago, LongLine said:

Which is bigger?  A basketball center that is 6'10" tall and 240 Lbs or a football lineman that is 6"0" and 300 Lbs?  

 

The weight of each was determined by their diet but their height was a matter of genetics. The basketball center could go well over 300 Lbs with a different diet but the football player will not grow 10" taller.

 

Back in the 60's when the beer company gave fish awards, one had to give a length and a girth as well as weight in order to win an award.  Today we only go by weight to win a tournament.

 

 

The DEC data for 2022 said the average length of a 3 Yr old female was 36.9" and in the 2023 report they said the average length of the same 3 yr old female was 33.8".  Quite a difference!  However, the 3 yr old males were the same for both years at 35.8". 

 

They however do a lot of fancy logarithmic regression analysis to calculate the wet weight of 36" fish and report that as a 3 yr old fish.  The 2024 summary says the 3 yr old Chinook was 19 Lbs.  The full 2024 report still hasn't been published so the jury is still out on that one.  For years there was opposition to adding random sampling to the preyfish assessment but when they finally did and added some whole lake trawls the results were different than anticipated.  

 

I'd be all in favor of the tournaments recording not only weights of fish but length and girth also.  That lineman obviously has a greater girth than the basketball player. 

You don't pick a 5'6" 140 lb kid as a lineman or basketball player.  You pick the 240 6'10" 240lb guy for your basketball team or the 6' 0" 300lb guy for your line.  If you pick the 5'6" 140lb kid, you will not be successful. 

[rolmops]

I don’t play basketball or football. 
My meanderings centered around genetics and the influence of genetic potential which may be mistaken for mutations.

Edited September 12, 2025 by rolmops

[ifishy]

rolmops what i think your hinting at is called epigenetics. 

essentially the DNA has the blue prints for multiple combinations of length and girth as well as a number of other factors.  However a fish cant be all of those at the same time. What happens is environmental factors and conditions which include but are not limited to prey abundance.  temperature. photo period. water clarity. pollutants. and others will trigger the genes to be "turned on or turned off" in turn so in one set of circumstances you can have a king get to 30lbs and a genetically identical fish in a different set up may only end up at 19lbs.   the mechanisms that this works through are the focus of a lot of todays genetic research as ways to potentially treat various human disease and conditions. there are may other potential applications both good and bad. 

 

fish in lake O running at 2 years is likely influenced by multiple factors and has been going on for many years.  it is reasonably possible that the  increase in natural reproduction these days vs 20 years ago is in part because of the increase of 2 year olds running.  this means that even with better predator/prey ratio we may still see a significant portion of 2 year olds run.  

Edited September 12, 2025 by ifishy

[Gator]

Okay, since we're playing in my wheelhouse, let's make this even more complicated.

 

Epigenetic changes can persist over not just one or two but multiple generations, like a molecular memory that projects far into the future. For example, children of obese parents have a tough time losing weight. Emerging evidence suggests that their grandchildren may as well. In model organisms, stress responses to adverse environmental conditions can strengthen those responses generations down the line. In my lab, we've just shown (unpublished data under review) that animals expressing toxic Alzheimer's Disease related Tau protein in their neurons have less progeny, and this effect persists for four generations after the toxic Tau is removed completely. Unfortunately, I don't think that this has anything to do with human disease but instead represents a transgenerational response to intrinsic stress, but hey, it's cool.

 

So all of these factors that weigh on reproductive success and vitality of the progeny need to be considered - as IFishy suggests above - as part of a continuum rather than as a single generation effector. This hasn't happened yet, but it needs to in order to provide a better understanding of the relevant impacts and consequences.

Edited September 12, 2025 by Gator

[salmoseine]

Epigenetics... fascinating entry into this discussion by ifishy. Thankyou!  Pulled the following from Prof Google (edited) attempting to gather the "basics":  

 

Epigenetic changes, particularly DNA methylation, significantly affect salmon size and reproduction by influencing gene expression in response to environmental factors. Research on both wild and farmed salmon shows that factors like temperature, stress, and nutrition can alter an individual's growth and timing of maturation. These changes can sometimes be passed to offspring, impacting future generations. 

Factors causing epigenetic changes:

 

Captive vs. wild rearing

A central area of study compares the epigenetics of hatchery-raised salmon with their wild counterparts.

• Reprogramming fitness: Captive rearing induces distinct DNA methylation patterns in salmon, including regions associated with stress response, immune function, and neuro-muscular regulation.
• Reduced fitness: These epigenetic changes likely contribute to the reduced survival and reproductive success observed in hatchery-reared fish when released into the wild, even in the absence of significant genetic differences.
• Transgenerational inheritance: Research has shown that these environmentally-induced epigenetic marks can persist into adulthood and be transmitted to offspring through the sperm, potentially affecting the fitness of future generations. 

Competition and nutrition

Environmental conditions at sea, such as competition for food, are a major driver of changes in salmon size and age at maturation. 

• Food availability: Increased competition from other salmon populations in the ocean can limit food resources. This affects overall growth rates, causing fish to be smaller at a given age.
• Age structure: A more significant factor in overall size decline, however, is a shift toward younger maturation. Under stressful oceanic conditions, salmon are returning to spawn at younger ages, and therefore at smaller sizes.
• Feed composition: In aquaculture, manipulating micronutrients in feed can induce changes in gene expression and DNA methylation related to growth and metabolism. These changes can also be inherited by offspring. 

Impact on reproduction and size

The epigenetic changes driven by these environmental and rearing factors directly impact salmon fitness and survival.

• Reproductive cycles: Manipulating environmental factors like light and water temperature can artificially alter the spawning seasons of Atlantic salmon broodstock for aquaculture, showing how sensitive their reproductive cycles are to environmental cues.
• Egg production: The widespread declines in salmon body size due to younger maturation can lead to a significant reduction in per-capita egg production, threatening the sustainability of salmon populations.
• Intergenerational effects: Epigenetic modifications in the sperm and eggs due to stress can affect metabolic rates and physiology in the offspring, influencing their growth, development, and overall fitness. 

Edited September 12, 2025 by salmoseine
formatting

[Gator]

I won't attempt to professionally evaluate Prof. Google, but remember that he told everybody Hochul had signed the crossbow bill back in June.

 

And if we ask for a reference on a particular topic, I've found him capable of making up publications..."how did I miss that?!?"...because it doesn't exist lol. But a casual glance at the intel above looks generally accurate.

[LongLine]

Brian - Depends on what the definition of a "kid" is.  I agree that a 5'6" "kid" on a pro team is not a good choice but that same "kid" for pop-warner would probably be a great choice. 

 

Previous annual reports seem to indicate that King salmon grow more (%) between 1 & 2 yrs old than they do between 2 & 3 yrs old.  There is a lot of literature out there that indicates Nat Repro fish are smaller than stocked fish and that they run sooner. It's logical that many generations of inter-breeding have lead to smaller length fish which has reduced the weight potential and differences which the tournaments are seeing.  Going strictly by tournament weight could be misleading as that data doesn't give a complete picture

 

Based on west coast literature, the larger the eggs, the bigger the kings will be as the fry is large and hence, they would have a head start on growth.  The stockers record the quantity of fish along with the weight per pound of those put into pens. The number per pound is an indication of their size. A year with lower No./Lb (bigger fish) should have a head start on growth over those with a higher No./Lb.  

The numbers look like this:

 

The 2023 pen fish were much larger than other years. Initial size doesn't appear to be a factor. Although  Preyfish abundance is up over last couple years however numbers for years before random sampling & all lake sampling could be suspect.  Also, there's variation in last few years. 
  
Genetics is interesting.  If you look at Yank's data in other thread, there's a big difference between 2005 and 2025 BUT look at it in 4-year groupings.  Look at group 2025, 2024, 2023 and 2022...They're practically the same.  Look at group 2021, 2020, 2019 and 2018...they're practically the same but the 2nd group is different than the 1st grouping.  And so on down the list.

 

Genetics doesn't explain why all the fish seem affected. (Does it run in 4 year cycles?)  If genes can turn on/off why aren't there big fish as well as small fish?  Conditions change every year. Mild winter, cold winter, wet year/dry year. Early spring/late spring. High water/low water. Different times in pens. Nat Repo seems different each year. Fish on CN side bigger. etc.  

 

I'd like to see more about Chinooks. Literature from west coast generally shows big differences between the different species of salmon. 

 

(Yeah, I know...too many questions)
 

[ifishy]

Gator I'm a ways removed from my lab days (went cooperate to pay the bills) but am known to pursue the occasional research article if you ever end up publishing id love to take a read. I started my research life in developmental genetics but took a detour through the medical field (not a doctor) before going where I am now

[Gill-T]

I am pretty sure I have been epigenetically altered to preferably fish for salmon. 

[Gator]

13 hours ago, ifishy said:

Gator I'm a ways removed from my lab days (went cooperate to pay the bills) but am known to pursue the occasional research article if you ever end up publishing id love to take a read. I started my research life in developmental genetics but took a detour through the medical field (not a doctor) before going where I am now

Awesome! We have a couple papers nearly accepted now that are on BioRxiv (search "Nehrke"), including one on the AD model where we can selectively induce Tau depletion, but the epigenetic stuff will be in the Supplement of the next paper. We should be posting it later this year - I will shoot you a pm.

 

Sorry for the digression, guys. Science turns my crank.

 

We are currently on an epic tear in terms of our ability to manipulate genes. Unfortunately, this doesn't necessarily equate to understanding what we've done...lol not lol. Kind of scary, even for an "expert".

 

And when it comes to salmon epigenetics, I know enough to appreciate that I know crap. I like Longline's questions though. Simple answers don't suffice. If they did, I'd be out of a job.

[GAMBLER]

On 9/12/2025 at 5:02 PM, LongLine said:

Brian - Depends on what the definition of a "kid" is.  I agree that a 5'6" "kid" on a pro team is not a good choice but that same "kid" for pop-warner would probably be a great choice. 

 

Previous annual reports seem to indicate that King salmon grow more (%) between 1 & 2 yrs old than they do between 2 & 3 yrs old.  There is a lot of literature out there that indicates Nat Repro fish are smaller than stocked fish and that they run sooner. It's logical that many generations of inter-breeding have lead to smaller length fish which has reduced the weight potential and differences which the tournaments are seeing.  Going strictly by tournament weight could be misleading as that data doesn't give a complete picture

 

Based on west coast literature, the larger the eggs, the bigger the kings will be as the fry is large and hence, they would have a head start on growth.  The stockers record the quantity of fish along with the weight per pound of those put into pens. The number per pound is an indication of their size. A year with lower No./Lb (bigger fish) should have a head start on growth over those with a higher No./Lb.  

The numbers look like this:

 

The 2023 pen fish were much larger than other years. Initial size doesn't appear to be a factor. Although  Preyfish abundance is up over last couple years however numbers for years before random sampling & all lake sampling could be suspect.  Also, there's variation in last few years. 
  
Genetics is interesting.  If you look at Yank's data in other thread, there's a big difference between 2005 and 2025 BUT look at it in 4-year groupings.  Look at group 2025, 2024, 2023 and 2022...They're practically the same.  Look at group 2021, 2020, 2019 and 2018...they're practically the same but the 2nd group is different than the 1st grouping.  And so on down the list.

 

Genetics doesn't explain why all the fish seem affected. (Does it run in 4 year cycles?)  If genes can turn on/off why aren't there big fish as well as small fish?  Conditions change every year. Mild winter, cold winter, wet year/dry year. Early spring/late spring. High water/low water. Different times in pens. Nat Repo seems different each year. Fish on CN side bigger. etc.  

 

I'd like to see more about Chinooks. Literature from west coast generally shows big differences between the different species of salmon. 

 

(Yeah, I know...too many questions)
 

Funny you bring up pen rearing.  The Pen project with the best growth rate year in and year out got pulled a bunch of years ago......

[GAMBLER]

If we want some big kings in the mix, why not throw some Triploid kings in the mix.  Big sterile kings that do not spawn and will get BIG.  They can continue their methods and appease the guys that want some giant kings every once and a while.  What would it hurt?  It wouldn't screw with the Lake O genetics they already have.  IN the past, they didn't want to add fresh genetics to disrupt the kings that have adapted to Lake O.  Sounds like a win win to me!  

[Gill-T]

Can of worms potentially if someone catches a record. You would need an asterisk next to name like the home run record during steroid era. 

[GAMBLER]

1 hour ago, Gill-T said:

Can of worms potentially if someone catches a record. You would need an asterisk next to name like the home run record during steroid era. 

Records?  Without it, we will never see a record king out of Lake Ontario again.  Bring on the steroid Era!

[Gill-T]

I would like to know which stream some of those recent Michigan giants came from. 

[ut_falcon]

There's your  40+ pound Chinook making it way up the Ganaraska yesterday, just gotta try harder to catch it guys!  I think the 122cm (48") length is a bit exaggerated but even still based on the thickness of this monster it's well over 40.

 

 

 

I posted this last fall but the Lake Superior salmon have been massive the last two years. The derby in Wawa Canada had a winning salmon of 39.7 pound in 2024 and 35.7 this year.  Crazy thing is this derby only runs for a weekend on lake superior and they had fish of that class weighted in. I heard there was a record cisco hatch a few years ago that's driving the large weights.  Considering the biggest chinook previously caught in Superior was low 30's in the 1980's it really shows you the genetics are there if the predator/prey ratio supports it.

 

I bet we'll be seeing some bigger fish next year in Lake Ontario with the huge 1 year old class of alewife in the lake this year if they have a good survival rate this winter.

 

 

 

 

 

 

 

 

Edited September 16, 2025 by ut_falcon

[LongLine]

Ocean run Kings get much bigger than fresh water bred.  Lake Ontario Kings came from the Green River near Seattle Washington I.E. Puget Sound. Literature indicates that all west coast salmon are now smaller and less abundant than they were 50 years ago.

 

Ocean run large Kings (80-90 Lbs) have been caught recently (2019) in Chile, South America.  Looking up the history of Kings in Chile (where they lack other salmon) revealed that they unsuccessfully river stocked a couple rivers with Kings in the 70's.  In the early 80's entrepreneurs successfully "ocean ranched" brood stock Kings from Washington State.  They turned to ocean net pens and the 90"s had many pen failures with major King escape.  They were considered a harmful invasive as they took over rivers to the demise of natural inhabitants. The Kings spawned in hundreds of Chilean rivers and their range is expanding. 

 

Ocean run Kings predominantly feed on Herring. Ours prefer Alewife. They are basically the same. Difference being the Alewife can live in freshwater.  

 

West coast states have enacted strict regulations on salmon fishing with some closing fishing seasons. So have the west coast Canadiens. But the CNs have also detected a decline in Herring populations and have enacted higher restrictions on commercial fishing for them.  (Harvested for feed and oil)  Chile has proposed regulations on Herring harvest but has not enacted them yet.

 

All five groups have the same genetic background.  IMO, food seems the driving force.  Larger schools of alewife on North shore.  Superior fish eating Cisco. West coast fish struggling and Chilean fish gorging themselves. Food abundance appears a stressor that triggers "survival mode" which in turn triggers growth, gut function and reproduction size and age.  

 

Questions for all the genetics guys:  Can the genetics "thing" as described in Yank's video be reversed?  If the 2yr old mixed with 3 yr olds results in more 2 yr old spawners, why doesn't it also result in more 2 yr olds becoming 3 yr olds spawners? Additionally, what would happen genetically if some larger Garnaraska fish contributed to the egg collection effort on the SR?

[Gill-T]

When I was in Chile, I saw atlantics in the fish markets also. Very fertile ocean and unbelievable tribs. 

[LongLine]

From what I've found is that ocean farming of Atlantics is really big business in Chile. They export them all over the world. (Chances are good that salmon in our grocery stores came from Chile.) They enacted strict regulations on farming after the King "fiascos." They do not have natural runs of Atlantics, and they have no Pinks, Chum or Sockeye.