We begin with a video of  juvenile Chinook salmon behavior.  It’s in high-definition, so watch it full-screen for best viewing.  We show a wide variety of behaviors here because they’re all very interesting, but the most common one in the Chena is drift-feeding, in which fish hold a fairly steady position in the river, facing upstream, and dart back and forth to intercept drifting prey as it passes.  You’ll also notice that these fish are often gathered into schools or shoals, because there are plenty of predators in the Chena and there’s safety in numbers.

It’s slightly unusual to see young-of-the-year salmonids grouped up like this, because normally they inhabit smaller streams, where it’s safe to spread out and defend larger individual feeding territories.  In this presentation, we looked at whether they are still territorial in a large-river setting.  This inquiry addresses a broader ecological question:  Can any schooling/shoaling fish also be territorial at the same time?

To answer that, we’re using 3-D video measurement technology introduced in this earlier post and updated in this poster (PDF download) at Luarca.  It allows us to do things like measure the 3-D configuration of the whole group of fish, and the distances between them (the green arrows):

We can also measure the habitat.  The video below shows prominent logs in brown, the boundary of dense cover in green, the surface in blue, the bottom in beige, and velocity vectors in yellow, which were calculated by tracking naturally drifting particles as they pass by the cameras.

We set out to use this system to detect territoriality in juvenile Chinook salmon.  We we found it, we hoped to learn something about the relative quality of each territory by seeing how much prey each fish catches.  However, when we started watching the feeding fish very closely, we noticed this happening a lot: the fish captures an item and spits it right back out.

Also, they often chase items they decide not to capture:

In fact, most times these fish chase a potential prey item, they get nothing for it.  About a third of the time, they decide not to even capture it.  Of the items they do capture, they spit more than half out.  The percentage of prey capture attempts that end with ingesting actual food is much lower for Chinook salmon in the Chena than for brook trout in still water, which were the subjects of the only other studies we found on this topic.  It makes sense that fish in a flowing river should feed less efficiently than those in still water, because there’s more suspended debris in a river, and because the fish have less time to identify moving objects before capturing them.

This principle may apply to juvenile salmonids in rivers in general, in which case ours is the first clear documentation of a pattern that could be very important for mathematical models of drift-feeding fish behavior.  Failing to account for the high debris error rate would lead current models to overestimate the amount of food these fish eat and underestimate the minimum size of suitable prey.  These errors would then influence predictions of growth, habitat suitability, and abundance.

The high debris error rate also means we can’t judge the relative quality of feeding territories by counting up the foraging attempts.  Two fish could be making the same number of attempts, while one gets mostly food and the other, positioned behind it, is stuck with nothing but debris to spit out.  That’s frustrating for our efforts to understand territoriality, but we can still tell a lot about territories even from failed attempts.  First and foremost, are these fish territorial in the first place?

Here’s the raw data to answer that question.  Each colored dot represents a foraging attempt, and each color represents a different fish.  The yellow arrow shows the direction of the water’s flow from the upstream end of the school.  These data cover 20 minutes of foraging by one school of juvenile Chinook salmon in the 70mm length range on August 14th, 2009.

You can tell there’s some exclusivity to the feeding areas of each fish, but it’s hard to judge exactly how much.  We can learn more by wrapping shapes called convex hulls around almost all the foraging attempts by each fish.  We use an objective algorithm to identify a few outlier points to exclude from these shapes, and the result is a very good representation of the core area each fish was using:

Now we can tell that these fish have very well-separated territories, but those territories look very different from the typical salmonid territories, which are spread across a large area of the stream in a 2-D mosaic.  All of these territories would fit within one typical territory for many other fish species of the same size.  Despite their close proximity, our calculations show that no fish performed more than 45% of its foraging attempts within the boundaries of another fish’s territory, and many had little overlap at all:

Summary statistics for a few territories. Click to view full-size.

This analysis highlights the exciting things we can do with the new 3-D video analysis program we developed, available at http://vidsync.sourceforge.net.  The first 20 minutes of video we’ve analyzed in detail have taught us some interesting things about juvenile Chinook salmon, and probably juvenile salmonids in general.  And that’s only the beginning — we have more than 12 hours to analyze, and will film many more this summer.  Stay tuned!

The village of Luarca, on the north coast of Spain. Photo by J. Neuswanger.

We presented both talks and posters.  Some materials from the talks (including high-definition fish video and 3-D animations of their feeding territories) will be available on this website within the next few weeks.  Click on the links below to download the posters as PDF files.

Wipfli et al 2010: Environmental processes affecting juvenile Chinook salmon in an interior Alaskan river – A summary of some key findings of the overall Chena project.

Neuswanger et al 2010: Improved 3-D video analysis methods, with applications to wild juvenile Chinook salmon behavior

Scientists interested in more information about these projects can email Mark Wipfli or Jason Neuswanger at our email addresses, mark.wipfli and jneuswanger, both @alaska.edu.  People interested in downloading the VidSync 3-D video analysis program, or its source code, can visit http://vidsync.sourceforge.net.  Help files and demonstration data for the program are coming soon.

Fish Video Highlights

These are some of the prettiest moments from my two years filming the foraging behavior of juvenile Chinook salmon.  They include a variety of revealing situations that show how the fish react to important elements of their environment such as food and predators.

Here’s a recording of the VidSync software, with a yellow arrow (part of VidSync’s built-in annotation features) following one fish through the course of a feeding maneuver.  It rises up from its “focal point” where it watches for prey, grabs something tasty, then sees a big piece of debris and scoots over to try it out.  It spits out the debris and goes back to its focal point.

Here’s the 3D digitization of that maneuver:

This is the same thing, viewed from 4 different angles:

Here’s a different prey capture maneuver, from the 2010 symposium on salmonids in Luarca, added to this post on 5/23/2010:

Of course, we don’t study maneuvers like that just to generate slick animations for PowerPoint shows.  The real point is to look at how far fish are moving for prey, which can be combined with information about water velocity and what the other fish are doing to help answer some important scientific questions.  For example, how much energy are they expending to capture prey — energy that could otherwise go toward growth?  Who gets more food for less energy, fish in fast water or fish in slow water?

Another important topic for our Chena research is territoriality.  The upper limit to how many fish a habitat can support depends on how much food there is and how the fish use that food.  When there’s a group of fish, there are millions of ways a limited supply of food could be divided between them.  Studying territoriality tells us something about how many fish are likely to do well in a given situation, and how many might be left out and risk starvation.

For a simple sense of territories, you can see the fairly uniform spacing among the fish in this 3D snapshot of a school of fish as the movie circles around it:

However, one moment in time can’t tell us much.  It gets much more interesting when we look at where the fish are relative to one another over a longer period of time.  The video below, from the VidSync software, shows part of 10 minutes of footage I analyzed to see the feeding territories of 4 fish in this video.  Each arrow marks a prey capture, and fish has different-colored arrows.

Here are the 3D territories.  At first glance on the original video it seems like the fish are just in sort of a mixed-up mess, chasing whatever tasty thing they see.  Watching them carefully and mapping their feeding in 3D immediately reveals some very interesting biological information: they’re respecting each other’s personal space remarkably well, with no intrusions during these 10 minutes.  It’s exciting to see a method reveal such interesting information even without the benefit of the large sample size and statistical rigor that will accompany this video method in practice.

FishDLT and VidSync Software for Scientists

This software is a work in progress: lots of work, and lots of progress.  It works well enough that we’re using it to process real data right now, but the current version of FishDLT has some personality (i.e. glitches) related to flaky behavior of Mathematica’s variable scoping in DynamicModules.  I’m planning to shift most if not all of the user interface stuff (buttons and picture-clicking) form FishDLT into VidSync, which will solve that problem and double (or better) the speed with which most things can be done.  That upgrade will probably be done by the time any other users begin to apply it to their data.  However, if you want to get started right away using the demo video, and you run into problems, contact me and I’ll be happy to help.

Hardware and Software Information/Downloads

Contact

Feel free to email me (Jason Neuswanger) about anything related to this method or these programs.  My address is my first initial dot my last name at sfos.uaf.edu, all lower-case.  (I can’t just write out my email address online, or spam robots will flood my inbox.)

We spent the long Fairbanks winter analyzing last year’s data and preparing results for several scientific conferences.  Most of us are beginning field work this week or next, so in recent weeks we’ve been purchasing, preparing, and organizing equipment at an ever-more-frantic pace.  In this picture, finishing touches are applied to a video calibration box that will help measure fish to millimeter-scale accuracy without even touching them.

Just like last year, Chena River users will notice mysterious contraptions up and down the river, collecting data for this project.  We’ll try to use this website to provide you with explanations of our more visible gadgets and the science they’re supporting.

First, here’s what one of our pools looked like in May during the peak of the spring snowmelt runoff:

And here’s the same spot during this flood:

Despite the high water, we managed to catch a few juvenile Chinook at the site above and gather information about their condition.  At least some of them have weathered the storm pretty well.  Some of our equipment (in this case, an insect trap tied to a log “above” the river) did not fare so well:

The water was beginning to creep out of its banks in places where the banks are a bit low:

Here’s the view downstream from the first bridge over the Chena on Chena Hot Springs Road, at what’s usually a popular gravel bar for camping and launching boats:

Even the eagles look bedraggled.

The North Fork is falling and clearing much faster than the main stem.  The high-water mark was about a foot higher than the level in the picture below.  The tree is new.