Sampling the WHOLE salmon!
The primary objective of the expedition is to document the abundance, ecology, and health of salmon across the northeast Pacific during the winter, a potentially critical period of the salmon life cycle that we know little about. To achieve our objective, in addition to counting the salmon, we take a wide range of tissue samples from outside and inside each fish. Some of these samples are processed on board the Professor Kaganovskiy within hours, while others require large (and often expensive) equipment and instead will be analyzed in laboratories around the Pacific Rim. By the time we’re done processing each fish in each haul, there isn’t much left except the head, skeleton, and a few bits of flesh.
Each tissue type we collect only tells us about a single aspect of the salmon, much like an individual jigsaw puzzle piece shows only a small fraction of the picture. By assembling the many pieces each analysis provides, we create the “big picture,” namely a comprehensive determination of how each fish is doing. Because so little salmon research has been conducted in this area at this time of year, our collective results fill an important gap in our knowledge of the salmon life cycle.
When the fish come on board the ship, the first thing we do is identify them to species: pink, chum, sockeye, coho, and Chinook salmon. We do this using a suite of characteristics, including body size and shape, the size of gill rakers and scales, and the shape and coloration of the tail, back, anal fin, and color inside the mouth. Distinguishing between species requires attention to detail, which can be hard when you’ve left your warm cozy bunk at 3 am to process the catch. Having several people--even sleepy ones--examine each fish ensures we get the species right, a critical first step in processing salmon.
We then examine the outside of the fish, noting whether the adipose fin has been clipped (indicating either a wild fish or the presence of an internal coded wire tag), any obvious scars or wounds, the presence of sea lice, and external signs of disease such as black spots (caused by an internal parasite). We secure a tag containing a unique number around the tail of each fish so we can trace all samples collected during processing back to each individual fish, or find the fish when we realize hours later that we forgot to take some tissue sample. Carefully recording the sample numbers that came from each fish is essential to fully assemble our jigsaw puzzle—if we don’t know which sample came from which fish, we lose a lot of information.
Next, we measure the length and weight of each fish, a deceptively simple procedure that provides extremely useful but rough information about approximate fish age, growth rate, and feeding success (skinny or fat). We also get detailed age and growth information from scales
and otoliths tissues we collect, but they take longer to process and will be analyzed back on shore. For example, we’ve been seeing several sizes of chum salmon (small, medium, and large), which we expect the scale data will show are fish that have spent 1, 2 and 3 winters in the ocean.
We then take several small fin clips that will be used to genetically determine where each fish originated from. Because salmon home to their natal streams, populations are genetically distinct and can be assigned to the geographic region or river of origin. For example, we can genetically distinguish between 24 populations of sockeye salmon in the Fraser River. Using the same methodology popular for human ancestry tests, we do this by comparing the genetic “finger print” of each fish to a baseline composed of genetic characterizations of hundreds of populations from rivers around the Pacific Rim.
We have the equipment and supplies on board the ship to make an initial genetic analysis for coho and Chinook salmon, a process that takes roughly two to three days to complete. The first batch of coho salmon was started yesterday and we eagerly await the results. Some of the questions the genetic data should answer are where each salmon came from, and whether the coho we’ve caught so far represent mixtures of stocks or largely come from a single population. If all goes well, we’ll have answers by dinner!
We can also learn where fish came from two “tags” we’re collecting: internal tags (coded wire and PIT tags) and otolith thermo-marks, or bar coding of the ear bones, which will be processed on shore. Both techniques are largely restricted to hatchery fish and applied while young fish are still in the hatchery. These are also important tools for salmon management, such as estimating harvest rates and catch distributions. However, we take advantage of the information they contain to tell us which specific hatchery each tagged fish comes from.
Once the external examination is complete, we put on the latex gloves and begin the dissections. Stomachs are removed and analyzed within hours of collection to determine both the amount and type of prey in their stomachs. Once the stomach is out of the way, we record whether the fish is male or female, and weigh the eggs or testes to document whether the fish will spawn in the coming year (maturing) or in will wait for future years (immature) before it returns to its home stream.
We also note the presence of large parasitic round worms, called nematodes, which inhabit the stomach, body cavity, and other parts of the body. These nematodes have complex life cycles that involve being passed from host to host, as the first animal they infect is eaten by the next host and the worm hitchhikes along. Most of the worms we’ve see use salmon as a temporary intermediate host; the worm’s ultimate host—where they complete their life cycle--is typically a marine mammal. At low abundances these nematodes probably don’t hurt the fish, but some of the high levels we’ve observed—up to thirty 4 cm-long worms in a single individual--probably have negative health effects.