Thursday, March 10, 2011

Blog Migration!

Hello, all:

I am extremely honored to announce a migration of this blog over to its adult habitat at the GAM at Southern Fried Science.

The new blog address is  Please join me in celebration of the move...and expect more awesome and informative salmon posts at the new address!



Wednesday, February 23, 2011

Embryos to Alevins

The fertilized eggs are safely in the gravel; their mother, Sally Salmon, has passed on; now what happens?  
Eggs in gravel.
Let’s talk about the development and survival of salmon embryos and the subsequent emergence of alevin.
The rate of development for an embryo is strongly controlled by temperature: embryos tend to develop faster in warmer temperatures (but not too warm!).  Variation in what we call Temperature Units (TUs, the number of days times the temperature) coordinates emergence.  There’s some heritability to emergence.  Spawning date is at least partially heritable and that affects emergence.  The physiological processes involved in development may also be somewhat heritable. 

Temperature is important to development and survival of an embryo.  So is substrate particle size.  There is a very rapid decline in survival of embryos with an increase in the percentage of fine material.  This is because, as we talked about earlier, the embryo is susceptible to being smothered.  Fine material also slows the water transport weight and reduces the amount of available dissolved oxygen (DO).  Dissolved oxygen is critical to the embryo and its importance increases as the embryo develops.  Embryos that are just about to hatch need the highest levels of dissolved oxygen.  Chronic low oxygen levels may not kill an embryo, but they would slow its development and the alevin that hatched would be quite small.  When DO levels are chronically low, the embryo is forced into less efficient use of the yolk; it cannot get the full benefit of the energy stored in the yolk sac.  A pulse event of low DO can trigger early hatching (the alevins will then try to move out of the low DO area and by moving, will increase air circulation).

Two other factors can affect embryo survival: flooding and embryo density.  When a stream floods, there is increased scour and gravel displacement.  Embryos may be dislodged and crushed or suffocated by sediment.  There is also a high degree of density-dependent survival in embryos.  Simply put, the more embryos there are in an area, the fewer will survive.
At this stage of embryonic development, eyes are clearly visible.
Okay, so say that you are one of the lucky embryos.  You had just the right temperature, substrate particle size, and amount of dissolved oxygen.  There wasn’t any flooding or overcrowding during your development.  And you’ve hatched into a healthy alevin.
Two alevins with attached yolk sacs.
Alevins go through three phases prior to emergence from the gravel.  The first phase is to GO DOWN.  The alevin displays negative phototaxis (i.e., it swims away from light) and moves with the gravitational pull of the earth.  At this stage, the alevin is still pretty small, it’s still mainly feeding off its remnant yolk sac, and it just wants to stay safe.  Getting deeper into the gravel will make the alevin safer from floods, droughts, and predation.  Alevins generally like to stay fairly still and “snuggle up” in the gravel matrix.  This behavior lets them save energy and keep their metabolism fairly low so that they can devote more energy to growth.
The second phase consists of lateral movement.  The alevin has gone as far down as it can get and it begins to move horizontally.  Larger gravel at this stage will promote greater amounts of movement; there is more space between the gravel for the alevin to wriggle around.  The alevin begins to develop positive rheotaxis (i.e., it swims against the flow of the stream).

Finally, the third phase consists of swimming up.  The negative phototaxis response is gone and a positive phototaxis takes its place—that is, the alevin begins to swim towards light.  Once it gets to the surface of the gravel, it emerges as a fry.  Emergence timing is variable.  Once again, temperature plays a large factor by increasing the rate of yolk absorption.  Warm water often stimulates emergence.  Alevins usually tend to emerge at night, though later in the season some will also emerge in the day.  Some still have a bit of yolk left at emergence and the fry combine endogenous feeding (getting nutrients from the yolk) and exogenous feeding (getting nutrients by eating zooplankton).
Coho salmon fry.
These gorgeous pictures can all be found on the Washington Department of Fish and Wildlife (WDFW) site.  They were taken through the WildWatchCam program and I highly recommend you check it out!  It's a great, non-intrusive way to see what's going on in nature.

Monday, February 21, 2011

Salmon Reproduction: the Spawning Process

Right, guys and gals, hold on to your hats!  Today we’re talking about sex.

When you’re a salmon, your spawning strategies pretty much depend on whether you’re male or female.  Females compete with other females to acquire, prepare, and defend nesting sites.  Males compete with other males for chances to spawn with females.  This type of competition is called intrasexual, meaning within the same sex.  But salmon also compete intersexually (between sexes).  They do what’s called “mate choice”, where one individual picks his/her mate based on traits such as phenotype (“Look at how big that guy’s hump is!”) and behavior (“Aw man, her tail waggle brings all the salmon to the yard”).

Females generally invest more in their offspring—they put more energy in gonads and produce fewer gametes (eggs).  In fact, 20-25% of the female’s energy is devoted to gonadal investment.  The relationship between body size and egg size varies a great deal.  The reason for this is an energy “cap”.  The female can’t afford to use too much of her energy for reproduction…otherwise she won’t have enough energy for herself (and remember, migration is energy-expensive!)  So there are two reproductive strategies here: devote your energy to making big eggs or devote your energy to making lots of eggs.  You can’t get the best of both worlds (big and many eggs)—you simply don’t have the energy!  So basically, the female salmon choice is: bigger but fewer eggs (big eggs are more likely to survive) or smaller but many more eggs (the more eggs, the more chances for offspring survival…sort of a “flooding the market” strategy).  In populations, if mortality is size-selective, bigger eggs tend to be favored; if it’s not, more eggs tend to be favored.

Biologists like to say, “Sperm are cheap, eggs are expensive.”   And because eggs are expensive (i.e., the female puts in a greater investment), females are often “choosier” than males.  Of course, in salmon, the female can’t do all the choosing.  Once she picks a nest site (redd), she won’t move too far away from it.  So she can only choose from the males in her vicinity.  Meanwhile, males don’t choose spots; they are free to wander among the different redds.  In this way, they have some choice in the matter as well.

So Sally Salmon is coming up the stream.  She’s exhausted after migrating 900 miles and she just wants to find a suitable place to nest.  What is she going to look for?  She’ll generally want a site with knee-deep water, water velocity from 0.1-0.7 m/sec, and substrate with less than 10% of the substrate material less than 1mm.  If the substrate material is too small, her eggs will be covered and will suffocate.  If water velocity is too slow, the same thing will happen because the water won’t be transporting enough oxygen to the eggs.  But if the water velocity is too fast, the eggs might get swept away.  Similarly, if the water is too shallow, the sunlight and heat will destroy the eggs; too deep and the eggs probably won’t get the nutrients and oxygen they need.

Generally, pool tailouts are favored spawning sites. 
I have mad MS Paint skillz.

Sally’s found a suitable site…now what?  She begins digging behavior—laying on her side and using her tail to dig a hole.  This winnows out the fine material which might suffocate eggs and also produces a bit of a tailspill (like what you get when your puppy digs a hole in the garden: a hole and a pile of dirt next to the hole).  Digging behavior is also a signal to male salmon: “Hey!  I’m ready to spawn!”.  Sammy Salmon sees this behavior, thinks Sally is a pretty cute (and fertile) salmon, and comes over to mate.  There’s some chemical and physical communication going on between Sammy and Sally at this point, and it’s critical.  If Sally’s eggs are exposed to water too long, they become unviable (i.e., no babies possible).  Sammy’s sperm must be released right with the eggs so that fertilization can happen right away.  Sally and Sammy do a “mating dance”.  They wriggle up together and at the exact moment (hopefully) release the eggs and sperm.  It all happens in just a couple quick seconds.  (check out this video of spawning coho salmon at the UW Big Beef Creek research station)

Sammy swims off.  But this is only one egg pocket!  Sally still has more eggs!  She moves a tiny bit upstream and creates a new egg pocket (and the tailspill from the new egg pocket hides the old one, which is a bit of defense against predators, scour, etc) and then repeats the process with Stanley Salmon.  Over the period of a day or two, Sally will make multiple egg pockets, each with a decreasing number of eggs.

Why does Sally need more than one egg pocket in her redd?  Well, she might be physically unable to squeeze out all her eggs at once.  But aside from that, high egg density likely reduces survival, so spreading the eggs out is beneficial.  She also doesn’t want to “put all her eggs in one basket”, if you’ll forgive the axiom.  She’s minimizing risk by producing several pockets—that way, if one pocket has bad luck, she’s still got others that might survive.  Finally, this strategy allows for multiple mates.  This promotes diversity and also minimizes risk.  For example, what if Sammy had bad sperm?  If she had only mated with him, none of her eggs would produce offspring.  But because she also mated with Stanley, then even if Sammy’s sperm were bad, she still has a chance at producing offspring with Stanley’s sperm.

Well, Sally’s all spawned out.  Most of her energy is gone and she is getting ready to die.  How does she spend the last days of her life?  Nest guarding from other females, of course.  She put so much effort into that redd that she doesn’t want any other salmon messing it up.  There’s been no quantitative study on the benefits of nest guarding (so far), but it’s likely that it serves some purpose.  All females do it, and those that arrive early actually do it longer—i.e., the females that arrive earlier to spawn specifically set aside some extra bodily energy so that they can survive longer and protect their eggs from the females that arrive later to spawn.

After guarding her eggs for a few more days, Sally’s done her duty.  She dies, and her carcass enriches the surrounding environment, contributing substantial amounts of nitrogen and phosphorous (which are often limiting nutrients) to the stream environment.  And Sally’s eggs lay buried safe in the gravel, slowly consuming their egg sacs and developing into alevin.

Monday, February 14, 2011

The Next GMO in Stores: Salmon?

My sincerest apologies for the recent dearth of's strongly correlated with the amount of statistics and oceanography classwork and thesis proposal writing I've been doing.  I won't promise regularly scheduled updates for this week either, as I anticipate it to be overwhelmingly hectic.  However, the M-W-F update schedule will resume in the near future.

In the meantime, here's some salmon in the news: controversy over genetically modified Atlantic salmon.

Wednesday, February 2, 2011

And this little salmon went whee whee whee, all the way home.

So we've talked a bit about migration.  And we know that salmon "home"--that is, they have some way of getting back to their natal stream to reproduce.

But how do they home?  Three hypothesized mechanisms are imprinting, genetics, and pheromones.

Imprinting can be described with four characteristics:
1.  it takes place as a developmental stage
2.  it requires no reinforcement (i.e., no rewards or punishment)
3.  it is remembered for a long period of time
4.  it creates a response to a specific stimulus

Salmon likely imprint to olfactory cues.  Basically, we think that as salmon transition from freshwater to saltwater in the early stages of their life that they imprint on the odors of their home stream and the odors encountered along the way to the ocean.  Salmon that have had their olfactory nerves cut or their nares (nostrils) plugged with cotton cannot find their way back to their home stream.

The obvious question here is: at what life stage do salmon imprint?  Fry?  Parr?  Smolt?  And do they imprint only once?  It's been found that when rearing location is farther away from release location, straying rates are higher, which suggests sequential imprinting during the juvenile migration to sea.  Solazzi et al. (1991) released coho smolts at their rearing site (Big Creek Hatchery near Bonneville Dam), downstream from their rearing site, and at sea.  They had a total of 6 release sites, each one progressively farther from the rearing site, and there was a corresponding decrease in the proportion of coho that returned.  37.5% of the coho released offshore (in water outside of the Columbia River plume) couldn't even find the Columbia River system, even though they spent a year at Big Creek Hatchery!

As salmon mature, sensory olfaction cells proliferate.  Water is funneled over the olfactory rosette as the fish moves.  This water carries chemical cues upon which the salmon imprints.  There is probably a relationship between thyroxine, a thyroid hormone, and imprinting.  At a certain stage of maturity, environmental factors (temperature, light-dark cycle, circannual rhythms) cue the production of increased thyroxine levels.  Thyroxine does two things in salmon: it increases the tendency to learn odors and it increases the tendency to migrate.  As a salmon migrates, it encounters new odors, which further stimulates the production of thyroxine in a classic positive feedback loop.
Figure 2. Scanning electron micrograph of an olfactory rosette from a nonbarged Chinook salmon smolt collected at Lower Granite Dam on the Snake River.
So it's probable that salmon imprint on olfactory cues and that they imprint sequentially throughout the migration to sea.  What about a genetic influence?

Salmon tend to stray more when they are released from a non-natal river.  There are some suggestions of a genetic component to homing, but at the moment we don't know how or why genetics fits into an explanation of homing.

One last hypothesis: pheromones.  What if salmon can detect population odors and that guides them back to their home stream?  Well, it turns out that salmon do have population-specific odors and they can distinguish their individual population odors from the odors of other populations.  They can even distinguish their siblings from other members of their populations!  However, they don't appear to be using those population-specific odors as a guide for homing migration.  Tests of the pheromone hypothesis have indicated that salmon will home to their natal site rather than to a non-natal site that has been infused with their population's pheromones.

And that's all for now, folks.  Here's the reference used above for the Big Creek Hatchery experiment, in case you want to go read more about it:

Solazzi, M. F., Nickelson, T. E. & Johnson, S. L. (1991).  Survival, contribution and return of hatchery coho salmon (Oncorhynchus kisutch) released into freshwater, estuarine and marine environments. Can. J. Fish. aquat. Sci. 48, 248–253.

Friday, January 28, 2011

I'm off at a 3-day Echoview training workshop which will, hopefully, teach me how to properly analyze the 3 years of acoustic data I have sitting on my laptop.

I work with split-beam hydroacoustic data, which produces images that look like this:

The colorful line is the bottom of Puget Sound.
For a summary of how we obtain these images, go to this post, in which I learn to collect data and am attacked by spiders.

But I haven't always worked with these kinds of acoustic systems.  A couple summers ago, I had an internship on the Hudson River which involved the use of a high-frequency system affectionately referred to as DIDSON (an acronym which stands for Dual-frequency IDentification SONar) and made by Sound Metrics.

The really cool thing about DIDSON?  You don't just get still 2D images like the one above.  Nope.  You get 3D VIDEO, baby.  Go to the image gallery on the Sound Metrics site and check it out!

(My favorite is the jellyfish, but I also like the alligator and the sharks.)

Wednesday, January 26, 2011

Obama, Fishing Closures, and Seattle Salmon

In this week's news:

If you missed President Obama's State of the Union address, you missed out on some salmon fun.  Here's a New York Times blog post about it.  And here's a YouTube video of the joke.

The Washington Department of Fish and Wildlife (WDFW) announced yesterday that fishing will close down early in Puget Sound rivers this year, for the second year in a row.  Why?  Conservation.  Wild steelhead are the primary concern, with several stocks listed as threatened under the Endangered Species Act.  Low numbers of steelhead are predicted this year and it's been decided that even catch-and-release is too risky.  Here's the WDFW news release.

On a lighter note, those of you who enjoy The Onion's offbeat humor should also check out The Seattle Salmon.