Duck, Duck, Whitewater

When you picture waterfowl, whitewater isn’t often the first thing that comes to mind. But for biologists studying harlequin ducks, rapids are a rite of passage—and a challenge.

Just ask Holli Holmes, a graduate student at the University of Montana (UM) and a Boone and Crockett University Fellow. Her master’s project focuses on finding new, more efficient ways to detect these often hard-to-reach and hard-to-find birds. Her work helps build a stronger foundation for a regional monitoring program

As sea ducks, harlequins spend most of the year along the rocky shorelines of the Pacific, from Oregon to the Arctic. When other birds head north in spring, harlequins head inland, breeding and raising chicks along fast, whitewater streams. “They’re just the most hardcore species,” says Holmes. “They’re incredibly hardy."

Harlequins—perhaps best known for the males’ striking burgundy, blue and white appearance—are only present in Montana for about four months, from May to mid-September. Males are around for even less time. By early June, they’ve bred and moved back to the coast, leaving females to raise chicks solo. Harlequins experience highly irregular levels of reproductive success, Holmes says. Since the males leave early, there’s no chance to try again if a nest fails. The dynamic becomes exceptionally tricky when paired with threats like development, river-based recreation, or changing stream flow patterns exacerbated by climate change, which can flood nests or dry up breeding streams. 

“The significance of Holli’s research is we now have a better sense of where [harlequin ducks] are and how to find them."

 -Hannah Specht, Montana Fish, Wildlife and Parks biometrician 

Indicators suggest harlequin populations are declining in the Northern Rockies. The ducks are a Species of Concern in Montana and are designated similarly in several Western states and Canadian provinces. To better manage the species, federal and state agencies and NGOs in the Northern Rockies collaborate as part of a regional working group. The group conducts broad-scale surveys for regional harlequin ducks every five years. The next is slated for 2026.

Historically, the working group has relied on ground surveys, where observers hike upstream and look for ducks. The group wondered if there was a better way to conduct surveys and whether additional areas should be included in their efforts. “Because they’re in such rugged places, we don’t really have an amazing sense of where they are, and because it’s hard to access them, we don’t even have a great sense of how efficient our survey methods are,” says Hannah Specht, Montana Department of Fish, Wildlife and Parks biometrician and Holmes’ co-advisor.

It’s an animal people are interested in and a conservation concern we can act on if we have the correct information, Specht says. It was pretty clear what information we needed. That’s where Holmes comes in. 

University Fellow Holli Holmes takes samples to detect harlequin duck e-DNA (left). A black bear is just one of the perks/hazards of field work. 

Utilizing e-DNA

Holmes’ master’s project investigated non-invasive methods to survey harlequin ducks on their breeding streams in Montana and Idaho. First, she quantified the effectiveness of traditional ground surveys. She then explored new alternatives, including game cameras and environmental DNA (e-DNA), which worked exceptionally well.

Ground surveys alone had a 50 percent detection probability. In other words, when harlequin ducks were present in a stream, observers conducting ground surveys detected the ducks half of the time. When foot surveys were combined with e-DNA sampling, the detection rate jumped to 98 percent.

E-DNA is a newer science that involves collecting and testing environmental samples for genetic material left behind. Finding DNA in the samples can indicate an animal’s presence. According to Holmes, DNA is in all our cells and present in the environment from dander, saliva, or feathers. Environmental samples could include water or snow samples, or even swabbing a plant. Because harlequins are confined to streams, e-DNA sampling involves collecting water samples and looking for any cells containing DNA in that water. 

Holmes tested 50 locations using the new method and found harlequins on 12 new streams where they hadn’t been documented in at least 15 years, if ever. As a result, the working group will implement Holmes’ method for future surveys.

Mapping Harlequins

Specht says that even the most refined survey methods won’t work correctly if you’re looking in the wrong places, though, and harlequins are good at hiding, making them easy to miss. That elusivity, combined with gaps in historical survey data, made it challenging for managers to pinpoint all of the locations across the harlequin's breeding range.

The working group wondered if they should conduct surveys in additional areas. To help answer the question and refine the search area, Holmes built a predictive occupancy model to predict where else harlequin ducks might be hiding. This research, a second component of Holmes’ master’s project, filled in gaps in historical survey data and will further streamline the data collection process for future surveys.

She combined a wide array of data to build the model, including 15 years of ground survey information, the e-DNA samples from her master's work, fisheries datasets, and citizen science input. The result was a map of streams in Montana and northern Idaho likely to hold harlequins, providing managers with a list of possible new locations for research and management.

“The significance of Holli’s research is we now have a better sense of where [harlequin ducks] are and how to find them,” Specht says.

From Field to Lab

As part of her master’s work, Holmes worked in Glacier National Park for the last three summers, working on harlequin surveys. Her field work involved memorable moments, from run-ins with moose to seeing grizzly bears. Research sites sometimes took a full day of backpacking to reach. One site required travel across the U.S.-Canadian border. 

During the school year, Holmes is in Missoula at UM, where she’s a student in the wildlife biology program and a member of a lab group led by her other co-advisor, Joshua Millspaugh, Boone and Crockett Professor of Wildlife Conservation. As a University Fellow in the Boone and Crockett Club’s University Programs, Holmes says the Club helped fill monetary gaps for her project when other funding sources stalled, allowing her to complete her research without interruption. She also enjoyed being part of the lab and counts working with the other members, including other University Fellows, as one of her most positive grad school experiences.

“Really lean into that community,” Holmes advises future graduate students. “Your peers are going to be your greatest support system.”

Bushwacking and Beyond

Originally from Estes Park, Colorado, Holmes earned a B.S. in wildlife biology from Colorado State University and then worked on research projects across the Western U.S. studying fisheries, birds, small mammals, ungulates, and reptiles. 

She worked in Glacier in 2019 and then returned in 2020, eventually joining the park’s birds and bats team, where her supervisor approached her with a master’s project involving harlequin ducks.

Holmes graduated in spring 2025 and will continue working through the summer, aiming to publish her research in a scientific journal. She hopes to continue her education this fall and pursue a master’s of public administration in New York.

In the long term, Holmes hopes to return to Montana, which feels like home. She’s inspired by community-based conservation—people coming together to identify and solve local conservation concerns. She’ll bring her can-do attitude and willingness to tackle tough questions wherever she goes.

“Holli learns quickly, and then she implements that learning really fast,” Specht says. “It’s been a particular asset for a project like this, which requires such a wide variety of skills from becoming the world’s foremost expert bushwhacker to organizing hundreds of volunteers to doing technical data analysis.”

Boone and Crockett Fellows Program

Through its Fellows Program, the Boone and Crockett Wildlife Conservation Program supports graduate students in wildlife conservation and related fields. A Boone and Crockett Fellow is an undergraduate, graduate, or postdoctoral student supported by Boone and Crockett funding and/or advised by a Boone and Crockett professor or professional member. In addition to displaying academic excellence, Boone and Crockett Fellows are committed to scholarship that:

1. Promotes effective conservation policy through dedication to research, education, outreach, and service.
2. Exhibits leadership in wildlife conservation.
3. Helps others understand the mission of the Boone and Crockett Club and the evolution of conservation in America.
4. Recognizes and appreciates the values of hunting and fishing and the principles of Fair Chase.

For more information about Boone and Crockett Club Fellows or its University Programs, please contact Luke Coccoli, Director of Conservation Research and Education, at [email protected].