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.

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. Photo: Dan O’Keefe, Michigan Sea Grant

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.