Alaska Fish & Wildlife News
March 2025
Stalking Shorebirds on Alaska’s Remote Outer Coast
Researching Elusive Red Knots Part 3
The pilot season was featured in January and the first season in February
Jenell Larsen Tempel picks up the story as the project progresses
We saw dribs and drabs of one to five Red Knots during most of our surveys in our assigned polygons (study areas) during the 2022 pilot season, but the real numbers tended to show up at low tide far out from camp. It seemed like the mud in that area contained a good deal of Limecola balthica, a small clam that is a favorite of Red Knots. At low tide we would look for leg flagged birds and do scat sampling as well as our benthic surveys. The benthic surveys were conducted on randomly selected plots of the intertidal and the goal was to determine the different potential prey items in the bay. Within the plot we conducted four transects, which are straight lines that run parallel to each other. Then at set distances from the shore, along that transect line, we pushed a PVC pipe sediment corer into the mud and pulled it back up. We used a spatula to keep the tube of mud and sand from falling out of the pipe, placed the sediment core in a sieve and then walked to the nearest trickle of water or edge of the tide to wash out the mud. We would be left with tiny clams and marine worms.
Each organism was placed carefully in a Whirl-Pak (a small plastic baggie) with a label including the date, exact location, sediment type and organisms present. Once back at camp we would fill these baggies with ethanol to preserve the organisms. Much later the organisms would be sorted in the lab to understand the types of prey that dominate Controller Bay and are available as shorebird dietary items.
The Song of Knots
The list of challenges was long, but the rewards were also high. We did eventually get to see knots. They showed up a week after us and were generally only in very small numbers, nothing like that flock of 300 that I saw on Okalee Spit the year before. One of the really cool things we got to experience was Red Knots singing. Usually, shorebirds are only heard singing on their breeding grounds. They are absolutely vocal during other times of the year, having their own repertoire of calls when they are flying in a flock, calling out an alarm to others, or squabbling amongst themselves to better their positions while foraging. But the distinct courtship call that Red Knots make is beautiful. It is often described as flute-like. It starts off with see-saw notes low-high, low-high, low-high and then they raise the pitch completely and sing a series of notes that become more rapid and fluid. I could image them on the tundra singing the same song and dipping their tails up and down in courtship 10,000 years ago. To be able to experience what few people ever see or hear, because it takes place on their dispersed Arctic breeding grounds, was really special. They must have been practicing their dances and getting their voices ready, bobbing their tails up and down as they sang circling one another. On one occasion I even woke in my tent to the sound of them streaming overhead while singing their courtship song, the sunlight streaming through the alder branches above me. It is my most peaceful memory of my time out there that year.
Lessons learned
I probably don’t have to tell you that we didn’t return to the bear infested Edwardes Camp the following year in 2023. We also never set up another camp on Kanak Island and in fact I had that crew move locations completely during the 2022 field season because again, there were no knots over there, and the weather made surveying by boat to the other side of the bay impossible. The Kanak crew moved to the mouth of the Bering River, which turned out to have promising Red Knot habitat and a few days with flocks numbering 300-500 and one as great as 1,000! The crew camped out on Okalee Spit had the most success, saw consistently more birds, and recorded the most leg flags. In 2022 we recorded a total of 13 flags, but only nine were legible. The number of resights was too low to conduct the mark-resight methods I 
planned to employ for estimating population size. Moreover, the leg flags that observers in the field recorded did not match the records of bands put out, resulting in a big issue of not knowing if these reports were the result of observer error, or if folks doing the banding were not submitting the band data to the federal Bird Banding Lab. This was problematic because we needed to be certain that the flags recorded were correct and could be correctly re-identified by another observer in the field. Our methods relied on that.
Although we could not obtain an abundance estimate in 2022, we gained a slew of valuable information. We found that only working to survey birds bracketing the high tide wasn’t working. Sometimes it was beneficial to work them from the waterside when the tide was falling as they moved closer to you, sometimes you had to factor in the wind. Sometimes the ideal tide was very late or very early and didn’t allow for enough daylight or a long enough survey. We loosened up our survey timing. As long as each polygon was surveyed with the same amount of effort daily, the timing was a bit arbitrary. I
took the count data we collected throughout the bay and worked with a GIS analyst to map out the Red Knot hot spots. Clearly there was a pattern that observers noticed in the field about where the knots liked to forage and areas where we never saw them. We mapped out the habitat use from these surveys and three obvious hot spots jumped out at us: the western half of Okalee Spit, the mouth of the Campbell River, and the mouth of the Bering River along the eastern edge. It was easy to decide where to put in camps for next year. We would focus on having larger crews at these frequently used locations. We would scrap the middle of the bay completely. The other decision I made that was a game changer, was to hire on dedicated photographers.
In 2022 a Ducks Unlimited Intern, named Blake, was working for the summer with my Forest Service collaborator. He came out to participate in the Red Knot work and was stationed out at the Bering Camp for 10 days. Photo: From left, Fernando Angulo, Blake Richard, Aaron Bowman and Lyda Rees at the edge of the frame taking the photo.
He happened to be a professional photographer and took beautiful pictures of Red Knots foraging in the intertidal and even captured some crystal clear images of leg flagged birds. Unfortunately, some of these leg flags were completely blank (had no 
alphanumerics or the ink was worn off), or so they appeared while in the field. But using the amazing photographs that Blake took, we could zoom in on the images and actually make out the engraved letters and numbers and determine that the ink had washed away. Having the photographs converted the flagged bird from being a useless but unique sighting to a now-useful piece of data and a bird that could be identified and resighted again so long as we had a decent photo of it. This completely changed my thinking about what type of people I should recruit for my field season next year -photographers. My hope was that by having permanent photographic evidence of the leg flag alphanumerics it would eliminate any observer error issues.
Lastly, we adjusted our season to be one week later to better capture the peak migration. This decision was the toughest to make. Migratory shorebirds are notoriously difficult to study because they are inconsistent. They can 
arrive weeks earlier or later in some years, and while some species have high site fidelity, others appear to use a variety of sites without any particular pattern, skipping some sites altogether in some years. I spent weeks trying to gather any data I could on historical peak migration dates of Red Knots in the general area of the Copper River Delta. I spoke with local birders, used data from eBird and worked with other biologists that had done GPS tracking on the species or recorded peak numbers in coastal Washington, the nearest known large stopover site. Using these bits of information across multiple years, I determined that the peak migration could be as early May 8, or as late as May 23. I decided on a season spanning May 4-27. We could always pull camp early, but we couldn’t do anything about arriving too late and missing them.
A knock-out year
Armed with a season of experience and a year of reflection we began again. I had many returning crew members, 
and a few new faces joined us. One of those new faces was Fernando Angulo, who is a professional ornithologist from Peru sponsored by International Programs under the US Forest Service to collaborate on several avian projects occurring in the Copper River Delta, including my Red Knot project. Having spent most of his fieldwork in places that were hot, humid, and close to the equator, I was nervous how Fernando would fair in the cold, wet, windy environment of the Lost Coast. My worries dissipated in a matter of days. Fernando was an excellent photographer, amazing birder, and a very motivated individual. In the field he would often jest our other photographer Blake saying, “No time for rest Blake,” as the two moved from flock to flock photographing flagged birds, tag teaming different angles, and either chasing or running from the tide. He also taught us how to make proper rice back at the cook tent. Dr. Julie Schram was another new member on our 
crew. Dr. Schram is a professor at the University of Alaska Southeast and specializes in a variety of techniques that assess prey quality, including lipid and fatty acid analysis and other measurements used in the laboratory to determine the caloric value of organisms. Together we wrote a grant that could support her coming out into the field and support student involvement in the lab. Last but not least, we had the pleasure of having Alan Kneidel join our team (shown below, collecting scat). Alan is a Conservation Biologist with Manomet, a 
conservation organization on the east coast. His expertise was brought onboard to assist with the eDNA fecal sampling as he started doing this work with rufa Red Knots on the east coast and he perfected the very niche job of scat sampling for a single species, where chaos abounds. He also happened to be an excellent birder and photographer.
We kicked off our work right at the start of the annual Copper River Delta Shorebird Festival. I had many returning crew members, and as it turned out, 2023 proved to be a knock-out year. Between the two camps we recorded 45 leg-flagged individuals and nine of them were seen across multiple days. Thanks to our amazing photographers, we had photographic evidence of every single one! We had just enough data to run our abundance estimate model. The results are still preliminary but suggest 
that in 2023, approximately 9,000 knots stopped over in Controller Bay. This is approximately 42% of the population (based on the most recent population estimate which used and pioneered the same methods we employed and was estimated from data in 2009 in Washington state). We timed the migration well and stayed several days after peak migration occurred. The last four days of the field season, the Okalee Crew didn’t even see another Red Knot. This gave us high confidence that we were not missing large flocks of birds, though there will always be late arrivals, some are recorded as late as June along the Copper River Delta. Having dedicated photographers turned out to be just the sort of adjustment we needed to make the methods work in this remote and challenging place. Additionally, the two base camps made surveys much more reasonable and focused our efforts. I was happy to assign myself to the Okalee Spit Camp, a location with more sand and sun, far fewer bears and a lot more knots! The information we gathered told us just how important this bay is for Red Knots to stop and refuel on their way to the Arctic, but still I wanted another year of data to see if the numbers varied. The next question was what were they using as fuel?
Back at the lab
During the off-season I worked with two University of Alaska Southeast college students that were interested in 
volunteering on the prey availability project (the author, photo right, in the Douglas office). We worked together to go through all the little baggies of invertebrates and identify them under a dissecting microscope. Bivalves in Alaska have been well-studied, and several field guides are dedicated to their identification. Most of these were easy to determine to the species level due to their differences in shape (round vs oblong or with a pointed end), color, or texture (ridges or no ridges and the number of them). However, marine worms are lesser known, and we required more expertise to determine the species or even genus level. For polychaete worms, which are segmented marine worms, you need to be able to dissect and identify the jaw parts in order to differentiate them at the species level. We did not have the tools or expertise to do this on fragile, tiny worms that were tissue paper thin after sitting in ethanol, and so all polychaete worms were lumped together. What we ended up finding was that the bay offered low benthic diversity for shorebirds. In our samples, 89% of all organisms belonged to the bivalve Limecola balthica (the Red Knot favorite, a knot is eating one in the photo below), 6% were 
polychaete worms, and 4% were the bivalve Mya arenaria which is an invasive species but has been recorded in Alaska since the 1950s and likely made their way from the Atlantic to the Pacific coast due to commercial oyster farming. The remaining 1% were a hodge podge of other bivalves, amphipods, and a lone sand flea (a small crustacean).
The results were not entirely surprising. Other studies that looked at the benthic community further north of Controller Bay, along the mouth of the Copper River also found low species diversity, though their numbers were higher for polychaete worms and amphipods. While we saw most species of shorebirds in the field pulling up polychaete worms (especially the black-bellied plovers and dunlin), none of our observers saw Red Knots physically eating polychaete worms. (Photo of a dowitcher flying with a polychaete worm in bill) Additionally, there was an event in 2022 when many shrimp washed up. It created a buffet for shorebirds, gulls and terns, however, the Red Knots did not seem be partaking in the feast. It 
appeared that they feed exclusively on bivalves in the bay. Still, I knew that they could certainly be eating other things we were not seeing or swallowing them while their beaks were partly submerged, keeping us from viewing their prey. So now that we knew what was available to them based on our prey availability analysis, I wanted to determine what they were choosing to eat. Were they truly bivalve specialists or did they also forage on other species like polychaete worms and amphipods that we could not see or perhaps were too small and were washed out of our sieve when sampling? The question has important implications from a conservation perspective. Species that are specialists may lack the adaptive capacity to switch to alternative food sources. Should there be a collapse in the bivalve prey base due to environmental conditions or anthropogenic ones, would these birds be able to switch to something else, even if it wasn’t their preferred prey?
Shorebird foraging strategies
Part of this could have less to do with the bird’s preference and more to do with their foraging strategy or how they
find food. One of the fascinating things about shorebirds is the varied approach they have in foraging strategies. Given that over 20 species of shorebirds have been recorded along this region of Alaska’s coast and an estimated five million come through the Copper River Delta each spring, it makes sense that they don’t all have to compete for the same prey and within the same terrain. Dunlin foraging, above.
Have you ever noticed that the bigger birds with long legs and long beaks are usually seen foraging in deeper water, while the birds with shorter legs and shorter bills are moving quickly across the sand pecking at things rather than 
probing for them like their long-billed counterparts? Take for example the godwit (Marbled Godwit, pictured left) which wades in water belly deep, often submerging its whole head and long bill, to probe for its prey by feel, pulling up marine worms and mollusks. Then conversely there is the ruddy turnstone (pictured below) with comparatively short legs and stubby bills. Turnstones are aptly named for their foraging technique of flipping over stones and seaweed on the shore to look for small invertebrates hiding under them. Plovers (solo, below left) are known to have large eyes compared to other shorebirds and they feed primarily by using their keen 
eyesight. And then there are Red Knots. They don’t have the long legs of a godwit, but also do not have stubby bills and legs, they are in the medium category. You will see that they mostly like to forage just where the water washes over the sand, so that the sediment is wet.
Scientists did experiments with Red Knots in captivity and discovered that in wet sand they can successfully find stones, buried centimeters under the surface. This was surprising. Unlike living animals, the stones are the same temperature as the sediment, do not move, produce no smell and have no electromagnetic field. This indicated that knots were not using any of the senses or mechanisms known in 
other birds or animals for detecting prey. Instead, scientists determined they must be responding to some sort of physical interaction between the water, sand, and stone. Further investigation found that the bill tips of Red Knots have little divots on the bone, not unlike a golf ball in appearance. These little pits in the bone contain “Herbst corpuscles.” These act as organs that are responsible for detecting changes in water pressure as the bird probes in wet sediment!
Given all this information, it makes sense that knots specialize on bivalves, it is what they have evolved to locate, but we know that they are capable of eating other prey and taking advantage of locally abundant prey. Red Knots on the east coast of the US are famous for eating horseshoe crab eggs, which are soft and squishy and are found on top of the sand not buried under it. Researchers in Mexico have reported that Red Knots there may feed 
on fish eggs belonging to grunion. And those that stop over at the Salton Sea (a salt lake in California) have been reported to feed on brine shrimp. We know that on the breeding grounds knots switch to eating terrestrial invertebrates (insects) as they feed on the tundra far from marine resources. So, although they are considered bivalve specialists, it stands to reason that they have the ability to switch prey seasonally or locationally as needed. In order to determine what birds are actually consuming at our study site, we began collecting scat with the goal of using eDNA techniques to determine prey.
Environmental DNA
eDNA has been employed for a great variety of uses. You may have heard of it being used to determine the species that are found in a certain body of water, or you may have read a previous Alaska Fish and Wildlife News article on how some of our biologists are using it to study harbor porpoises. Although it is often thought of as being used for water or sediment, it can likewise be applied to fecal matter. However, it is important to note that eDNA is not a silver bullet. It often requires having known prey items for the species in question and can be prone to issues like cross-contamination. As with everything else in 2022 we had some issues with our eDNA analysis. In order to save costs and increase the amount of samples we could collect we attempted to sample five Red Knot poops per vial. To do this, two observers went out together outside of the survey time and watched a small flock until one bird deposited a scat on the mudflats. One person kept the little bird scat in view of their scope. Once the birds moved on, or before the tide washed away the scat, the other observer went out to retrieve it taking directions from their partner at the scope. This was not as straightforward as it should have been. For one thing the bay is a shorebird mecca. There are bird poops everywhere. For another, the scale can be quite hard to judge. For example, it might appear to the person at the spotting scope that you are standing right on top of the scat, but you are looking down seeing no scat. In fact, you are 3 feet or 6 feet away 
from where the scat was deposited. Most challenging was the wind. Even as your partner yelled at you and waved their arms wildly to the left or right it was hopeless to locate a pinky nail sized bird scat among dozens of others without the radios in the wind. And sometimes you were so focused on collecting the scats before an incoming tide, that by the time you turned back to where you left your gear and bike, it was all underwater. Above, the author recovers her bike and gear after it is swamped by the incoming tide.
Although we did our absolute best to select only Red Knot fecal samples, about half of our samples came back indicating that there was also DNA present from other shorebird species (i.e., the sample was 50% REKN, 25% Dunlin and 25% Black-bellied Plover). These samples (the whole vial) had to be discarded because we could not differentiate what proportion of the prey these other species ate versus the knot. Some of our samples also contained contamination from the lab as species appeared in the results that were not even present in the area. And then for the ones that were ok, the lab didn’t have a prey library that was comprehensive enough to match any of the DNA in the fecal matter to prey species. This was 
unforeseen, even by the lab manager. This meant we would need to physically collect the potential prey items from the bay. Something we didn’t do. It was disappointing. As with everything else, we made some changes for 2023. I found a new laboratory at a university that had experience extracting fecal DNA from Red Knots on the east coast and switched labs. I also found a biologist that was an expert in shorebird fecal collection methods. Alan could look at a bird track in the mud and tell you what species made the track and follow the tracks to identify scats. He was a one man show. No spotter, no shouting into the wind. While we focused on perfecting the survey protocol, getting those leg flag shots, he dedicated part of each day to carefully observing and tracking Red Knots and doing scat sampling.
Next month: The Big Picture – the final installment brings the entire project together with an overview of what was learned.
More on eDNA, AFWN article from 2024 Harbor Porpoises Highlighted for Surveys - New tools aid study of secretive marine mammals
Crew members returning to camp on a rare sunny day in Contoller Bay.
All photos ADF&G, by Jenell Larsen Tempel, Blake Richard, Fernando Angulo, Ria Smyke, Tory Rhodes, Nick Docken, Arin Underwood, Evan Ward and Lyda Rees.
The Institutional Animal Care and Use Committee (IACUC) reviews programs and projects to ensure animal welfare. IACUC protocol numbers for work done for 2022: 0107-2022-25, for 2023: 0107-2022-25
Red Knot calls and sounds (The second-to-last song in the list, recorded in Alaska on June 22, 2014, by Andrew Spencer, is particularly cool.)
More on the Threatened, Endangered and Diversity Program at ADF&G
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