Unpacking new research on the Fraser Estuary’s importance to Chinook salmon

Lia Chalifour and Misty MacDuffee tell us about their work to better understand juvenile salmon in the Fraser Estuary and the need to safeguard and restore their habitat.

A new paper, “Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary,” has highlighted the importance of the Fraser estuary as critical habitat for Chinook salmon.

The researchers used salmon ear bones, or otoliths, to study how juvenile salmon were using the Fraser estuary, and found evidence that Chinook salmon from the Harrison River rely on the estuary for one to two months while they feed and grow. 

We sat down with Lia Chalifour, lead author of the paper, as well as co-author and Raincoast biologist Misty MacDuffee to discuss the new findings and their importance.

How did you first become interested in studying salmon?

Chalifour: I’ve always been passionate about our coastal ecosystems in the Pacific Northwest, and I’ve mostly been interested in things that eat salmon, as well as the ecosystem as a whole. But I actually was starting a masters with Julia Baum at UVic, and we were going to look at the resilience of fish communities in eelgrass meadows to things like climate change and human disturbance and Misty came in and told us about the Fraser Estuary and how no one was really looking at how salmon were using that habitat and meanwhile that habitat was being destroyed. 

This was a big concern, and the Fraser also has huge eelgrass meadows. So it was a really good fit to look at those various habitats within the estuary and what fish are there, including salmon. And then the more I was learning about salmon and their declines, the more I got interested and was pulled further and further down the salmon train.

MacDuffee: And mine was very similar. I started off more enamored with all the furred and the feathered and the finned creatures that ate the salmon. And it was really working in the watersheds on the central and north coast of the Great Bear Rainforest that you really get a firsthand sense of just how important salmon are as a driver to these coastal ecosystems.

My fascination shifted and it really became all about salmon. That ultimately led me to the Fraser. That and the fact that Southern Resident killer whales are very dependent on Chinook salmon coming from the Fraser, and the importance of the whole Salish Sea in terms of food supply to Southern Resident killer whales.

And with this particular new study, why did you want to focus the research on this estuary habitat?

Chalifour: Well, this study built off of our first study that we published in 2019, where we looked at the different fish communities in three different habitat types in the estuary. And during the course of that study, we found that there were a lot of salmon hanging out in the brackish marsh in particular, throughout the out-migration season. And so it really seems like the estuary, and the marsh in particular, was important for the early marine survival of some of these salmon. 

Different methods look at different timestamps, essentially, and otoliths provided the longest time frame for us to look back at the life history of these fish. They basically act like a time capsule for every moment of that fish’s life.  Tweet This!

And when we started to dig further into the genetics, which led into the paper that was recently published, we realized that most of these juvenile salmon we were catching, especially early on in the season, were juvenile Harrison River Chinook, an ocean-type Chinook salmon population with juveniles that hatch and very quickly move down from the Harrison into the estuary and actually rear in the estuary. And so that organically struck our interests as we’re examining the estuary and the health of the habitat and the health of the fish communities. We’re finding these little fish are clearly relying on this habitat for their early life history.

So we then looked into the otoliths, found that they were actually spending months growing in the estuary, essentially getting ready for their big marine migration. So it was kind of a feedback loop of looking, doing the fieldwork, being interested in salmon, interested in who’s using the habitat, and then that unfolded this picture of Harrison Chinook that are really heavily relying on it.

Misty MacDuffee and the field team assess salmon in the Fraser Estuary.
Raincoast field team assesses juvenile salmon in the Fraser Estuary. Identification, measurements and genetic sampling of juvenile Chinook salmon has been part of the Fraser estuary study since 2016. Photo by Alex Harris / Raincoast Conservation Foundation.

MacDuffee: The cool thing is that we’ve been able to do what researchers didn’t have the technology to do 30 years ago when they were studying the movements of juvenile Chinook, or all salmon into the estuary; they didn’t have the power of genetics and the power of otolith analysis and microchemistry. So even though they could characterize these patterns of seeing salmon using and moving into these areas, the ability to say where these salmon were coming from within the Fraser watershed just wasn’t available to them. 

And that’s the really cool thing that this study has been able to do: utilize the genetic technology, and all the other technology, that has developed in the 30 years since these fish were studied in the estuary.

Why did you choose to study the ear bones and how did that research work?

Chalifour: When we were thinking about trying to quantify when these fish are entering and how they’re using the habitat, we thought about a few options that are common in modern science. And so one of those options are otoliths, and they’re really great because they basically act like a time capsule for every moment of that fish’s life. 

When they’re growing in fresh water they’re consistently laying down bone material onto this otolith and that freshwater signature is trapped in that bone. And then when they move into brackish water that water signature changes in the bone. So you can really easily detect their movements over periods of a week or two. And then you can directly measure the width of each increment, just like a tree, and correlate that back to the growth of the fish. So it’s a really nice way to look at migration and growth. 

Another common practice is to look at stable isotope analysis. And so for that, you actually look at different fatty tissues of the fish and you can get an idea of what they’ve recently been eating. You can sometimes correlate that as well with different environmental signatures to look at movement, but it seemed like that might not get that migration piece as clearly. And another method is looking at the other metrics of growth, so looking at growth hormones, for example, in their tissues and their muscles, to see how quickly they’re growing. 

But all of these different methods look at different timestamps, essentially, and otoliths provided the longest time frame for us to look back at the life history of these fish. So by sampling regularly throughout the season, catching and releasing these fish and measuring them, and then combining that with the otoliths, it just gave us a really good picture of how they were moving in the estuary and how they were growing there.

In terms of the actual results you found about how much time the Harrison River Chinook spend in the estuaries, were they surprising to you at all?

MacDuffee: So the cool thing is that when we’re collecting these fish, or the thing that we always have to keep in mind, is that we’ve intercepted their life. So in the sampling that we’re doing, we’re only getting a piece of how long that fish has been in the estuary up until we sampled it. And so we know that this is the minimum period of time that they would spend there. And that even though the average is one to two months, there were these outliers where we sampled fish that had been in the estuary already up to 90 days. So it gives us a spectrum of just how important this estuary is until we interrupted them.

I think that there had been studies in the literature generally that alluded to these time periods where they’re relying on the estuary, but to actually see it really solidified that they are relying on these habitats, and then how much they grew on average in the period of time that they were in the estuary. So, we had some idea that it might be these results, but to actually see how important the estuary is was really important and reaffirming.

Chalifour: We really didn’t know what to expect, and so every time we found data that confirmed what people had guessed from 20 or 30 years earlier, based on just looking at the size of these fish, that was exciting. And when we found data that contradicted it that was also exciting. 

They didn’t have DNA analysis, as Misty mentioned, and so as they were catching larger and larger Chinook in the estuary, they assumed they were still all the same population and growing and that was probably mostly true for the first several months. But then what we found in June, you really start to get a drop-off of the Harrison Chinook as they’re moving out to the ocean and you get other populations coming through later on. And so those bigger fish are not actually the same fish anymore. 

The cool thing is that we’ve been able to do what researchers didn’t have the technology to do 30 years ago when they were studying the movements of juvenile Chinook, or all salmon into the estuary; they didn’t have the power of genetics and the power of otolith analysis and microchemistry.  Tweet This!

There also had been reports of juvenile salmon being in the estuary into the fall. And we really didn’t find that in the sampling that we did in 2016. It doesn’t mean they’re not there, it just means they are probably not there in very high attendance. So that was interesting. 

It was also interesting to see that there were Harrison fish coming in on a continuum. So either they were hatching at slightly different times and coming down right away or some might’ve just been choosing to hang out in the freshwater for a bit longer before moving down. But some of them entered as early as the beginning of March, and some actually entered in May. And then all of them hung out and grew while they were in the estuary at a pretty consistent rate.

So you would think maybe there’s a strategy to entering really early or entering really late, but it doesn’t really look like there’s a big difference there. It’s just the earlier the entry, the smaller you are and the more growth you do in the estuary, but the daily growth was pretty similar across all those fish.

Lia Chalifour holds up a tubesnout on the Fraser Estuary.
Lia Chalifour holds a tubesnout, a cousin to sticklebacks, and one of dozens of fish species that inhabit the Fraser Estuary. Photo by Misty MacDuffee.

Having now more concretely confirmed that the Chinook are spending a lot of time in the estuary, what do you hope this will mean for the broader context of the Lower Fraser River and the threats that it faces?

Chalifour: Well, I really hope that it serves as another wake up call. I think that salmon biologists, and a number of different types of biologists who work in the Lower Fraser, are well aware of the many different pressures here; the heavy human footprint on this area, not to mention the looming threat of climate impact. And so I think that when you go from thinking the estuary is probably important for a population to knowing that it’s a key part of the survival of this population, that it’s just that much stronger to say, okay, we really need to evaluate what we’re doing with this remaining habitat, because that habitat is directly supporting this population of fish. 

And we hope it will influence environmental assessment decisions for different development projects, as well as restoration initiatives and maybe even some protection initiatives, although there’s not much left to protect.

MacDuffee: The big threat that is looming over the Fraser is the expansion of Terminal Two. Some of our earlier research, before it was published, was presented to the panel in different formats and the panel made their decision about significant adverse impacts on juvenile Chinook, mainly from the Lower Fraser and the South Thompson, before we even published those papers and before the other work that Lia’s been part of, which is the priority threat management assessment, all of that came out after the panel had already concluded significant adverse effects on these juvenile Chinook populations. So hopefully that awareness will trickle up and influence the kind of decisions about more development within the estuary. 

Has this research led to more questions or things to investigate next?

Chalifour: Always. That’s the way of science. I think we could continue to do otolith analyses and just assess the variation across years. Dave Scott is looking more closely at the other ocean-type Chinook populations, such as South Thompson Chinook, that use the estuary but appear to move through a lot faster than the Harrison Chinook population. 

We know inherently that how they do in the estuary is tied to their overall survival, but we could quantify that by looking at the adult returns and comparing them back to those juvenile life histories.

And then, of course, where we’re really heading right now is looking at the applied research. So we’re looking at management strategies that we can take in the Lower Fraser to benefit salmon, and figuring out what are the best strategies to take. We’re looking at issues of governance in the Lower Fraser because it’s a very complex region. So there are endless, endless, further directions to go.

MacDuffee: And then the other thing that has always interested me, is that there’s another type of Chinook that moves through the Fraser estuary, that uses it more as a migration corridor than rearing habitat, but that we never caught very many of, and that is the stream-type Chinook that spend a year in freshwater before heading down to the estuary.

But in the last couple of years, as Dave Scott has shifted sites and we’re sampling in different areas, we’ve been catching a lot more of these stream-type Chinook, and it’s the stream-types that are the most endangered Chinook in the Fraser. If we could learn more about where these fish go and how they use the estuary, and their movement patterns through it, it would be really cool. And even if we could understand the health of these fish by the time they reached the estuary it would shed light on how they’re doing in freshwater. Because we don’t even know, in assessing the status of these fish, whether it’s the fresh water or the marine environment that is driving their problem. So it’s definitely a curiosity of mine to better understand the stream types.

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