What are Golden Eagles Eating? Swabbing May Have the Answers

13 December 2022

Why are Golden Eagles declining in the United States? HawkWatch International’s Conservation Science Director, Dr. Steve Slater, outlines a lot of the important drivers and the intensive monitoring we’re doing to support this species in his blog post here. But in addition to intensive monitoring efforts, we’re also doing some novel research on how diet may play a role in survivorship—that you can help with! I’ll explain…

During the data collection process for my dissertation, I collected oral and cloacal (the single opening for a bird’s digestive, urinary, and reproductive tracts) swab samples from eagle nestlings, in addition to whole blood, plasma, feathers, eggshell remnants, physical measurements, and time-lapse photos from motion-sensitive cameras to capture diet, behavior, and survival data. Initially, though, I wasn’t quite sure what to do with the swab samples.

Breeding Golden Eagles nest across the desert in very low densities. They nest on a variety of cliff types, from remote and rugged to urban and easy to access. It’s especially difficult to do this work when the nestling is nearing fledge age—not happy to see you and equipped with sharp talons and a beak to defend itself!

Before you finish the email that you are now surely writing, the answer is No. Adult Golden Eagles do not defend their nests from humans. As very long-lived, slow-reproducing birds, eagles play the long game when it comes to risk. Also, if these aerial apex predators did defend their nests, you would not be reading this right now because I would be studying something much less dangerous, like Frequentist mathematics or French literature.

So for three years, I collected the swab samples and kept them locked away at -80 Celsius. As I entered my fourth year of study, I started to read about advancements in environmental DNA (eDNA) and metabarcoding techniques. What caught my eye was that the science was now investigating a way to monitor carnivore diets by detecting prey DNA. Some of the new studies were even looking for prey information in waste and from remains on the beaks/talons of raptors.


Because Golden Eagles are generally territorial and have limited social interactions with other eagles, they are exposed to pathogens and contaminants primarily through ingestion. Pathogens such as Highly Pathogenic Avian Influenza (HPAI) or environmental contaminants such as lead or mercury can have negative health effects on adults and nestlings that are still developing both physiologically and neurologically. Consuming prey items that have previously been killed with lead shot (e.g., squirrels/rabbits) or switching to more avian prey that are reservoirs for HPAI when rabbit populations are low all increase the potential threats to nestling development and survival.

While the studies I came across were opening new doors in raptor research, the difficulties mentioned regarding researching eagles and other raptors (low sample sizes, difficulty in sampling, resource-intensive) still held true. Most of the work was observational in nature—trapping wild individuals while they were migrating (taking samples before release; without an unbiased understanding of their diet prior to capture). Or, the studies were experimental in nature—the work was done under controlled conditions (e.g., not real environmental conditions that may influence DNA detection and thus the scope of inference or utility of the current techniques).

The more I read, the more I realized we had an amazing opportunity! With the trail camera footage, I can validate the metabarcoding results from the DNA collected by my swabs. Our work validating this method may help future researchers, given that not everyone wants or is able to:

  • Purchase a $500 motion-activated trail camera (swabs are less than $1)
  • Spend several hours driving out to the desert
  • Rappel down a remote cliff-face, navigating loose rock
  • Then while hanging on a rope, place the camera, and in a month or two, do it all again to recover the camera.
  •  Catalog all the photos, which could range from 400 to 40,000, with some prey being very difficult to identify
  • Or do an entire dissertation investigating how Golden Eagle nestling immune function and survival are affected by disease, parasites, and contaminants…

To cap it off, we monitored environmental conditions with an iButton—a device the size of a nickel—buried in the center of the nest that recorded temperature and relative humidity on a half-hour basis. These provide some valuable environmental context for DNA/RNA detection. We were able to install them in most nests, but recovery has been a bit difficult due to rowdy youngsters!

My questions of interest evolved quickly from seeing if we detected the species the nestling ate on camera to:

  • Do detection rates vary depending on swabbing location (oral vs. cloacal)?
  • How long prior to swabbing the individual do we detect the DNA from a prey species captured on camera?
  • Is there a difference in the detection accuracy between or among taxa (think gopher snake vs. Great Basin rattlesnake and reptiles vs. mammals)?
  • Do detection rates vary depending on the size and age of the individual/prey and the environmental conditions leading up to and during the sampling event?

Since this project wasn’t part of my dissertation, I did not have funding allocated for this research. I secured funding through the Utah State University - Ecology Center to cover the wet lab costs for the work, but we are still short the funds we need to analyze the data.

If you are as excited as I am about the possibilities of this work, I could use your help taking this project to the finish line. With your gift, you can help us construct a genomic library of all the potential species Golden Eagle nestlings are eating and more safely and efficiently understand how diet impacts Golden Eagle’s health. Click here to contribute to this work: https://hawkwatch.org/savingeagles

Lastly, I want to thank my advisors—Dr. Kezia Manlove and Dr. Clark Rushing for providing assistance with the proposal and study design. Thank you as well to our partners, U.S. Army Dugway Proving Ground, National Fish and Wildlife Foundation, and Utah State University Ecology Center.




This blog was written by Dustin Maloney, HWI's Research Associate.
You can learn more about Dustin here.