Otolith study confirms Harrison Chinook salmon rely on the Fraser River Estuary for early growth

New study reveals that juvenile Harrison Chinook salmon enter the Fraser River Estuary in a continuum from February through to May, and that the earlier they enter, the longer they stay and the more they grow in this estuarine habitat.

Lia Chalifour is the lead author of a recent study which reveals the early life histories of juvenile Chinook salmon in the Fraser River Estuary. It’s now published online and open access in the Canadian Journal of Fisheries and Aquatic Sciences. A version of this article was first published on Lia Chalifour’s personal site.


Juvenile Chinook salmon begin their lives in clear, cool streams in tributaries of the Fraser River. Anywhere from a month to more than a year later, they leave those streams to embark on a journey to the Pacific Ocean. Chinook salmon from the Harrison River, which was declared Canada’s first Salmon Stronghold, do something unique; rather than growing in their home lake and river system for the first year or more as many other salmon do, these fish go on a great adventure.

As early as newly emerged fry, with their egg yolk sack not fully absorbed, these little salmon will swim out into the surging, turbid waters of the Fraser River main stem, following it down into the backwater channels and marsh habitat of the Fraser Estuary.

This life history strategy is called ‘ocean type’, and those that migrate after growing for a year or more in fresh water are called ‘stream type’. Ocean type Harrison Chinook salmon also remain in the Salish Sea and British Columbia coastal waters as they mature and return to the river as adults later than other Fraser Chinook salmon populations, often bearing white flesh, making them an important cultural symbol and particularly prized by fishers.

If these fish rely on estuarine habitat for their early survival, how will they fare if further habitat is lost?  Tweet This!

The Harrison Chinook salmon once comprised about 80% of the total ocean type Chinook salmon in the Fraser, but were recently designated as Threatened by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC).

Our study revealed that juvenile Harrison Chinook salmon enter the Fraser River Estuary in a continuum from February through to May, and that the earlier they enter, the longer they stay and the more they grow in this estuarine habitat. On average, each fish spent 42 days in the estuary. This is important, because this habitat is a mere fraction of what it once was, and this population – Harrison River Chinook salmon – are in decline. 

If these fish rely on estuarine habitat for their early survival, how will they fare if further habitat is lost? How will they fare if the remaining marsh is swallowed by sea level rise? How much will they benefit from habitat restoration?

These are the key questions that myself and colleagues are using our findings to address. Here, I would like to share a bit more about the incredibly cool scientific methods that I used to determine just when these Chinook salmon entered the estuary, how long they were there before we caught them, and how much they grew in the meantime.

To uncover these secrets, I had the unique experience of examining the ear bones – otoliths – from Harrison Chinook salmon that we caught during our field season in 2016 to look at the growth and timing of their entry into the Fraser River Estuary. Similarly to the annual growth rings in trees, new bone material is deposited in the otoliths of fishes in regular increments, forming visible rings. The rings in juvenile salmon otoliths are proportional to about one day’s growth. This is fascinating, because we can extract the bones, polish them with diamond-coated lapping film (very fancy sandpaper), and measure the rings using a compound microscope.

Figure two images of the tiny ear bones and markers.
Otolith measurements taken under a microscope.

In addition to this visual check, the chemical composition of the bone material is influenced by the water and environment of the fish at the time that it is growing. In this way, it acts as a permanent time stamp of the daily environmental conditions that fish experienced as it grew up. For example, when a Harrison Chinook salmon leaves the clear, fresh water of its home stream and enters the brackish, turbid water of the Fraser Estuary, the chemicals in the water are etched in the signature of the bone in the otolith, sometimes seen as a clear dark growth ring, but often difficult to distinguish by eye. Cue the laser.

Understanding how important this estuarine habitat is to their early survival, it now seems vital to protect the remaining habitat in this heavily impacted system, and to work towards habitat restoration in the Lower Fraser River.  Tweet This!

I was fortunate to be trained by Jody Spence, an experienced technician in the School of Earth and Ocean Sciences at the University of Victoria, to wield a high-tech laser to carve a very thin line across these tiny otoliths. As the laser carves, or ‘ablates’, this path across the otolith, marking the time from the days before the fish was captured to the moment of its birth, the bone becomes aerosolized and the dust is sucked into an inductively coupled plasma mass spectrometer (ICP-MS).

The chemicals of the bone dust are then sorted by their mass and identified as specific elements – flashback to the periodic table on the wall of high school science classrooms.

Three elements in particular are of interest: strontium, barium, and calcium. Calcium is present at fairly consistent levels in all bones and acts as an internal standard, so the other elements are weighted by their proportion to the level of calcium present. This acts as a control for strange spikes or weird values in the elements, which can happen when the laser is slightly inconsistent in the amount of bone it zaps or the ICP-MS changes in its sensitivity for detecting the elements. After all, even machines are slightly imperfect.

Lia Chalifour and Misty MacDuffee in the Fraser River Estuary.
Lia Chalifour and Misty MacDuffee in the Fraser River Estuary.

The other two elements, strontium and barium, indicate opposite environments in what I like to think of as a beautiful ecological ballet. One is heavy, the other is light, and they vary in opposite ways in fresh vs saline waters.

When the fish are in fresh water they will take up and deposit lots of barium and very little strontium. When they switch to more marine-based saline water, they will take up far more strontium and very little barium. This translates to a sharp increase in strontium levels and an eventual decrease in barium within the otolith when the fish has moved into the estuary.

When I take these chemical results and line them up to the physical otolith, I can count the actual rings deposited from the point the fish entered the estuary, and get a time estimate of estuarine residency based on when I caught the fish.

This is important, because prior to this study, it was uncertain when juvenile Harrison Chinook salmon entered the estuary and exactly how long they stayed – we just knew, roughly, when they left the Harrison River. Several recent studies on Pacific salmon have focused on the documented decline of marine survival, particularly for Chinook salmon in the Salish Sea. Harrison River Chinook salmon are a part of this story, and their marine survival begins when they enter the Fraser River Estuary.

Research Assistant Danial Hunter hunches over the lab table, extracting otoliths.
Research Assistant Danial Hunter extracts otoliths (tiny ear bones). Photo by Lia Chalifour.

Understanding how important this estuarine habitat is to their early survival, it now seems vital to protect the remaining habitat in this heavily impacted system, and to work towards habitat restoration in the Lower Fraser River. In the face of broad scale threats such as climate change and declining marine survival, we must provide the best possible chance for salmon populations to adapt and persist.

We can do this by improving and restoring lost habitat, such as that in the Fraser River Estuary. Stay tuned for our recently accepted paper led by Riley Finn, documenting the barriers to salmon in the Lower Fraser River as an example of one of the many restoration strategies that we can take to benefit these populations.

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