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Biology’s new frontier could have big implications for Great Lakes fish

New research shows that epigenetics play a major role in the domestication of hatchery trout.

Posted on December 5, 2016 by Dan O'Keefe, Michigan State University Extension, Michigan Sea Grant

Although steelhead are not native to Michigan, they have been spawning naturally in streams including the Little Manistee River since the late 1800s.
Although steelhead are not native to Michigan, they have been spawning naturally in streams including the Little Manistee River since the late 1800s.

Sometimes two fish that look alike can be very different indeed. Take rainbow trout for example. Some live the majority of their lives in freshwater lakes; others are born in rivers but move to the Pacific Ocean to feed on fish and squid. Some reside in desert streams eating tiny invertebrates; others are reared on pelleted diets in aquaculture facilities.

All of these fish are rainbow trout. They can breed with one another and share the same basic physical characteristics – the position of fins, pattern of spotting on the tail, etc. Even so, we recognize the difference and even call them by different names.

The Kamaloops trout is a lake-strain rainbow trout from interior British Columbia. The steelhead grows fast feeding in ocean currents. The redband trout can tolerate warm daytime temperatures in desert streams, and domesticated rainbow trout tolerate crowded conditions much better than wild fish.

None of this will come as a surprise to anglers and fisheries biologists who are familiar with a long list of “strains” of rainbow trout and other fish that have been stocked for their unique characteristics. Hatcheries have even been involved in selective breeding of rainbow trout to create new strains with desirable characteristics. The long-lived summer run Skamania is one example of this.

What is the difference?

In the past, we generally assumed that differences between strains could be understood by looking at genes. For example, it makes sense that the desert-dwelling redband trout would have genes that allow it to survive in warmer water than, say, a steelhead that spawns in Alaskan rivers.

At the molecular level, a gene is a sequence of DNA. The DNA molecule contains a genetic code that essentially provides a blueprint for an entire organism – in this case a rainbow trout. When comparing wild rainbow trout strains, looking at DNA makes sense. Natural selection allows some trout to survive and breed while others die and fail to pass on their genes.

Over the course of many generations, different strains of rainbow trout develop in ways that reflect differences in their environments. We expect to see this reflected in the DNA of wild redband trout and the Alaskan steelhead, but what about fish reared in hatcheries?

Too fast for natural selection

Domestic fish, like domestic cattle and other livestock, are raised in conditions that are more crowded than natural environments. Previous research has shown that even a single generation of captive breeding and rearing can reduce fitness of rainbow trout (steelhead) by up to 40%. In this context, fitness is not a measure of how healthy an individual fish is. Instead, Darwinian fitness relates to the number of successful offspring produced by an individual fish.

For rainbow trout, this means that first-generation hatchery trout are not as good at producing offspring in natural environments as wild-spawned trout are. For example, first-generation hatchery steelhead in the Hood River, Oregon, produced 15% fewer successful offspring than wild steelhead when spawning in the wild but when spawned in captivity, the first-generation hatchery fish produced twice as many successful offspring. In a single generation, the hatchery fish had adapted in ways that made them more successful in artificial environments but less successful in the wild.

Changes in domesticated fish, and other animals, occur so quickly that changes in gene frequencies (DNA) cannot be the only cause. Several generations of very strong selective breeding are needed to create even minor changes in gene frequencies. Researchers working on Hood River steelhead hypothesized that changes were caused, at least in part, by the way that some genes are expressed (as opposed to changes to the genes themselves).

What they found was astounding (see study). After a single generation of captive breeding and hatchery rearing, the expression of 723 different genes was altered in comparison to wild fish. Many of these genes were related to wound healing, immunity, and metabolism. This makes a lot of sense, seeing that crowded hatchery conditions lead to more wounds and exposure to disease.

The new frontier of epigenetics

These changes in gene expression are not limited to first-generation hatchery fish, either. Molecular tags that control the expression of genes can be inherited by the next generation. The Hood River hatchery steelhead experienced “heritable epigenetic modifications” that were passed on to their offspring.

All this may sound rather esoteric, but this is one of the first studies to demonstrate the importance of epigenetics in fisheries management. Put simply, “epi-” means “above” and “epigenetics” refers to all of the factors that control expression of genes. Think of DNA as the computer hardware of your cells and epigenetics as the software or computer programs that control the use of DNA (see Duke University video).

The emerging field of epigenetic research has made a splash in the news over the past few years, but most studies have dealt with human health. It turns out that diet and stress influence human epigenetics, too. Researchers have investigated epigenetic effects on aging, Alzheimer’s disease, obesity, cancer, and a host of other health issues.

Fisheries scientists have only begun to investigate the role of epigenetics. If the Hood River study is any indication, this new frontier could have big implications for how we understand and manage wild and stocked fish populations in the Great Lakes.

Michigan Sea Grant helps to foster economic growth and protect Michigan’s coastal, Great Lakes resources through education, research and outreach. A collaborative effort of the University of Michigan and Michigan State University and its MSU Extension, Michigan Sea Grant is part of the NOAA-National Sea Grant network of 33 university-based programs.

This article was published by Michigan State University Extension. For more information, visit www.msue.msu.edu. To have a digest of information delivered straight to your email inbox, visit www.msue.msu.edu/newsletters. To contact an expert in your area, visit expert.msue.msu.edu, or call 888-MSUE4MI (888-678-3464).

I'm glad you only posted the "layman'" version. I got an epiheadache trying to understand what O'Keefe was trying to explain!

As far as wildlife is concerned I still think "It's not nice to fool with Mother Nature" when you start playing God with genetics. Natural selection occurs in the wild and makes a species able to cope and survive. Forcing changes to a species to become a series of subspecies over a short period of time could cause other environmental issues. It could cause problems with the food chain in an ecosystem and cause the disappearance of more native forms of a desirable species. I would hate to see some super alewife eating form of steelhead show up even though I love to catch steelhead.

You kill me Mike!!!

Hey Don. What about the genetically altered food we eat and not even aware of it? Scary

I'm happy agri-science has come up with Genetically Modified Organism (GMO) foods. For one, the amount of nasty-azz pesticides that were once required to control weeds and insects has been slashed dramatically. A lot of that stuff used to get into our waters. Anyone remember DDT, chlordane, furidan and other chemicals that used to bio-accumulate in Great Lakes fish? Now the enviro-worry-worts are down to worrying about plastic "fibers" that wash off our laundry getting into the lakes. Don't get me wrong, I'm not in favor of anything other more unnatural than earthworms and fish hooks in the waters I fish, but I'll take fleece fibers over PCBs anytime.

When I was a youth, a book called the Population Bomb was as front and center in environmental news as climate change is now. It claimed the world was heading for a population of four billion and was very near carrying capacity. Even if everyone switched to eating rice and beans, mankind was heading for mass starvation. (This was major - minor was running out of oil, nuclear meltdowns at electrical generating stations, acid rain from coal plants, increasing reliance on organo-phosphates used in crop production, global cooling, overcrowding, mass pandemics from yet-to-be mutated viruses and bacterias and on and on. Humanity was doomed...and soon. That was written in 1968 and the author used the best science (and the worst case scenarios) to make his predictions.

Thanks to GMOs the world population has doubled, humanity in general is better fed now than 50 years ago. Food costs as a percentage of average incomes is much less, pesticide use is way down, the toxicity of pesticides used is much less and Skamania steelhead are now IDed as epigenetic.

Non-existant user wrote:

Hey Don. What about the genetically altered food we eat and not even aware of it? Scary

I helped build a turkey processing plant down here. I learned that growers can take a poult and in 6 months time turn it into a near 20 pound bird. Genetics and hormones can build birdzilla but there has to be a biological cost to the consumer when it is eaten. I am not sure of the consequences of farmed animals that are actually kept away from the wildlife, but I think impacts would be minimal to them. People however can choose or not choose to use altered foods. It is like most everything else, there is money to be made when people start paying genetic engineers to build super organisms.

Fun stuff! You are right! There is a cost to doing or not doing things the "old fashioned way." I bought $50 worth of groceries at Thanksgiving and the store gave me a turkey. I have a friend who raises "free-range, organic turkeys" and he charges $100 a bird at Thanksgiving. My son worked at an organic butcher shop in California. Hamburger was $12.00 a pound. More power to the Bloomington-ites who are willing to pay the freight for organic turkeys or the Californicators who pay 12 bucks for some burger.

Fact is, there are way more people studying the affects of GMO crops and factory-farmed animals than are checking the Great Lakes for micro-fibers, invasives and pollutants. The results of all the research is overwhelmingly the "modern" foods are as wholesome and usually offer better "wholesome-ness" than the organic versions.

Flavor-wise? No doubt a free-range turkey, a wild-grown apple or a wild caught Atlantic salmon has bolder flavors than the farmed versions. Of course the turkey is probably tougher, drier and may have parasitic roundworms called gapeworms. All those spots on the wild apples are from insect eggs and larva, rusts and fungus infections - sure to add to the flavor profile. Farmed salmon are fed special food additives to make their meat red. That's because they don't eat potentially "tainted" wild food that gives them a naturally occurring red meat.

About the only food-borne illness anyone ever hears about in the US is from veggies and meat tainted during harvesting (for veggies), improper processing for meat and vegetables or contamination after being purchased by improper storage or cooking. All human errors, not genetic errors.

Cool article Ed. Mike, I'm getting the impression that you may be sitting in front of your fireplace tossing books into it.

Thanks South Shore,

I thought it was a good read also. Pretty neat to see how fast things can change.

Look how fast a domestic hog changes if turned out into the wild.

What happens when a summer run skamania and a winter run skamania breed? Genectically they are still the same fish but there is a change. The winter run fish has the strongest genes, so the offspring are no longer summer run fish. How quick can that change take place?

There is always going to be new ways at looking at the same old stuff. Change is always taking place, just how fast?