Epigenetics

It has long been known that hatchery enhancement of wild salmon can lead to unexpected results. In the States, for many years, hatchery spring chinook were planted in many rivers in several states. This lead to obliterating natural genetics through inter-breeding between wild and hatchery fish. Diversity of natural genetics is key to survival of salmon, as they are adapted to the waters in which they were raised. Wipe out diversity and ability to adapt is also wiped out. Ditto for survival.

In Canada, we did not follow the same route. The intent was to use a raised stock in close-by waters that have similar genetics, rather than a generic fish for all rivers. For example, in the hatchery I know the most about, the Nitinat, chinook are used in that river, as well as Sarita, Sooke, Sooke Basin net pen and perhaps the San Juan, rivers that are close by and have similar genetics.

There are other approaches. Alaska, for example, does ‘ocean ranching’ which means pumping out billions of fry, most commonly, pink salmon, and reaping the abnormally high numbers of returning salmon to make the most money. Again, this wipes out genetic variation in wild stocks, but Alaska has chosen to make a commercial catch, in some basins, and ignore the genetic destruction. Catch results are impressive. Alaska’s catch of all species was 243 million in 2017.

In BC, right next door, the 2017 commercial catch was pretty much non-existent. A staggering comparison of side by side abundance and dearth. There are many reasons. The big four are: lack of adequate amounts of freshwater habitat restoration, DFO itself, fish farms and climate change. And factors like ‘the Blob’ offshore in rearing areas has lead to problems. As well, the PSF’s project for the Salish Sea is showing other effects, like seal predation of juvenile chinook to 40% and coho to 47%, phytoplankton differences in spring among other things. See the Salish Sea Marine Survival Project, 2016 Canadian Progress Report: https://marinesurvivalproject.com/wp-content/uploads/Canadian-SSMSP-Status-and-Findings-to-Date-2016.pdf. 

In recent years, the genetic considerations in enhanced fish has received more study. While genetics may be the same in a wild fish from the same river that a hatchery fish is produced, the expression of those genes may be different, and account for different outcomes, especially as the gene expression can begin and end in different periods of a salmon’s life cycle. Measuring those effects out in the ocean is difficult because it is difficult to find the fish. But the effects can be studied during raising of fry, and in mature fish when they return.

This field is known as epigenetics. See this article for a non-technical take on the issue: https://www.hakaimagazine.com/news/hatchery-fish-often-fail-in-the-wild-now-we-might-know-why/. Approaches to raising those fish are key. Here is a short quote: “Epigenetics is the physical and molecular processes that control how the instructions contained within DNA get expressed or turned into the proteins that affect day-to-day life. Often, epigenetics causes a gene to be expressed more or less frequently than it otherwise would. Everything from stress to chemicals to natural processes like puberty can cause epigenetic changes. Some of the changes are temporary or reversible, while others last forever.”

Louis Bernatchez, working at Laval University, has found that feeding and crowding in hatcheries accounts for much of the differences in gene expression. Perhaps surprisingly, this effect was consistent for fish of different stocks raised at different hatcheries. But, if you were brought up to gorge on brown pellets that nice people, or machines tossed at you, rather than be pretty hungry all the time, and have to hunt to find something to eat and stay out of the way of predators, the expression of some genes could dramatically differ. 

You will recall that evolution functions through ‘natural selection’ a concept that is the basis of all Darwinian thought. Do hatcheries ‘select’ gorgers, or is the food, temperature, relatively inactive life modifying gene expression? Regardless of the explanation, hatchery fish don’t always respond as well as wild fish. 

It is common, at least for chinook, for the fish to lose some or all of their ability to spawn in the wild. This may be good for wild genetics, but it suggests an important reason to rely more on habitat restoration than enhancement, something made all the more difficult in this time of climate warming, with its accompanying lower water flows, higher temperatures and lower oxygen in rivers. 

I think the time is coming where we will see convoys of trucks and helicopter buckets moving salmon above impassable river sections and depositing them in large pools to rest until the later rains of fall do the deed. This would serve the interests of chinook, coho and chum due to their October or later spawning pattern, when rain is more likely to be expected. I am not so sure about sockeye and pink, that can, due to their smaller size, navigate shallower water, and do spawn earlier, but sockeye have a problem with surviving in water above 20 degrees C. Coho are almost as temperature sensitive as well.

Spot fishing closures, as annoying as they are, to let wild fish through can make a lot of sense, as can producing hatchery fish that do not return migrate at the same time as their wild compatriots. But what about ‘fake’ food, couch potatoes and endlessly clicking iPhones?

The Nitinat Hatchery has been doing some interesting experiments in the past few years to try and find some answers. Researchers Kristi Miller and Sean Rogers are working with them. Miller you will know from the Cohen Commission presentation of her ‘Viral Signature’ work that showed sockeye dying at advanced rates of pre-spawn mortality in the Fraser. And she showed in 2017 that PRV causes HSMI, a serious problem for wild fish as up to 95% of farmed fish have PRV.

You may have had a serious laugh at the Jimmies, as one-year returnee hatchery male chinook salmon have been dubbed – Sarita, Nitinat. Take a six-weight rod and plop a generic Tom Thumb dry fly where they are snapping away and you can pretty much ding every one in the pool. They look like pink salmon, but have long sharp teeth, and that unmistakeable smell of a chinook. Presumably these, along with Jacks, sexually mature two-year-old males, that no one really wants - except in very low water - are the result of epigenetic changes in hatchery chinook.

The Nitinat has, with both coho and chinook, found interesting things by varying food, lifestyle, size of smolt at release and so on. They do both small and large chinook smolts and yearlings. They also compare standard raceway fry with others that have an ‘enriched’ lifestyle, such as putting objects, bushes, flotsam in their water to explore, hide in, feed on those mayflies, stoneflies and caddis flies that show up on high algae objects, rather than solely pellets.

There is also putting fry into local lakes to bring themselves up, particularly with coho. The aim is to produce fish with more wild behaviour, fish that have a greater chance of wild spawning, and reduced percentage of young, sexually mature males. The more the epigenetics are right, the better the fish; and the more that enhancement becomes a better option for increasing salmon spawner numbers of wilder fish; in other words, a true companion to the over arching need for freshwater habitat restoration, the crux of the other half of the story.

Some experiments of smaller fitter fish lead to larger adults, and for chinook, the larger fish are typically female, the sex we want to return, not to mention that more five-year fish are returning as, yes, larger fish. Current experiments suggest that environment enrichment doubles smolt to adult survival, an important consideration when wild return is about 1% to maintain a run. So, we may be heading to lower density, lower growth rates and enriching environment more consistently across the Salmon Enhancement Program.