A close-up image shows a Yellow Warbler’s feather in great detail: yellow barbs photographed against a black background, with a brownish shaft running through the center of the feather.

A single feather, such as this one from a male Yellow Warbler, contains enough DNA to sequence a bird’s entire genome. Photo: Noppadol Paothong

Science

The Bird Genoscape Project Aims to Unlock the Secrets in Birds’ Feathers

Recent breakthroughs have allowed researchers from across the Western Hemisphere to begin building a library of avian DNA filled with insights about where birds migrate and their resilience to mounting pressures.

A burst of whistles pierced the foggy morning in the Missouri Ozarks. It came from Marina Rodriguez’s Bluetooth speaker but sounded enough like a Yellow Warbler’s song to catch the attention of two males. They swooped down from the high canopy and landed simultaneously in a mist net that Rodriguez and her team had erected alongside the Current River.

Netting two birds at once is a rarity. “Kind of like Christmas,” said Rodriguez, a Ph.D. student at Colorado State University. “I think we got two because they were fighting over territory. Each thought the other was making the sound.”

It was a promising start to the final stop in a two-week springtime tour. Rodriguez and three other students had been roaming the Midwest in a white Ram 1500 in search of breeding Yellow Warblers. In mosquito-thick Kansas, they had encountered tornadoes, hail, and long, unproductive stretches. Here they hoped for less drama and more birds.

The sky brightened over the coneflower- and moss-covered landscape. Rodriguez and an undergraduate popped the warblers into cloth bags and carried them to a makeshift research station on the truck bed. They banded the birds, measured their beaks, and took blood samples. Then they plucked two feathers from each.

It might not look like cutting-edge science, but the feathers Rodriguez collected would provide enough DNA to scan the warblers’ entire genome, a complete set of genetic material. The scientists could then translate that vast data source into a “genoscape,” a map of genetic variations across the species’ geographic range. That map, in turn, would offer insights into the birds’ migratory paths and their ability to adapt to threats along the way. Such detailed information was out of reach even five years ago.

As part of the Bird Genoscape Project, Rodriguez is collaborating with scientists across the Western Hemisphere. They are building on human genome research to create maps for what will ultimately be dozens of songbird species. This resource could prove essential at a time when—for a gaggle of reasons, including climate change—half the migratory species in North America are declining, according to Breeding Bird Survey data. Long-distance neotropical migrants like the Yellow Warbler are suffering the most.

After recording the measurements and dropping the feathers into envelopes, the team released the two birds. The data extracted from their DNA, Rodriguez hopes, will unlock information about the birds’ resilience, or lack thereof, at a time of unprecedented global climate disruption. That knowledge could yield precise new strategies for conserving the most vulnerable populations. By the time the first two warblers disappeared into the trees, a third male had flown into the net. It was just shy of seven o’clock.

In a lush, green forest, four researchers look skyward with binoculars in hand.
Marina Rodriguez, left, and her crew scout the Missouri Ozarks for Yellow Warblers. Photo: Noppadol Paothong

M

ore than three decades earlier, evolutionary biologist Thomas Smith was working on his dissertation in the Cameroon rainforest, studying bill size variation in African finches. As he measured and sampled the birds, he sometimes noticed feathers falling out. He taped these feathers into a small black notebook—a gesture that baffled his field assistant. Why not just throw them away? But Smith had in mind the writings of Aldo Leopold, the early-20th-century wildlife ecologist and champion of the conservation long game. “To keep every cog and wheel,” Leopold wrote, “is the first precaution of intelligent tinkering.”

“You know, there’s DNA in those feathers that could be useful someday,” Smith, the founding director of the Center for Tropical Research at the University of California, Los Angeles, recalls saying.

Smith’s ambition outstripped the existing technology. Still, as a new professor in the 1990s, he asked bird banders to send him loose feathers, and he also collected many himself. A colleague discovered that pulling a couple of outer tail feathers did not harm the bird, so he added that to his request. Smith stored the samples in a freezer, then several freezers, in his lab. Graduates tapped some feathers for research using the genetic tools available at the time. Meanwhile, Smith looked forward to the breakthrough that would unlock all the information they contained.

That breakthrough came in 2003 with the completion of the Human Genome Project, the global effort to map the three billion pairs of chemicals that form the DNA molecule—life’s genetic building block. The advance enabled researchers to take an unprecedented look into our cellular architecture, allowing them to find tiny variations in people who share a disease, physical trait, or ancestral migration route. In the years that followed, intense competition and new technology drove down the cost of sequencing a genome, from hundreds of millions of dollars to less than a thousand. This put the technique within reach of scientists studying all sorts of animals, including birds.

Among those scientists was Kristen Ruegg, an evolutionary biologist at Colorado State University and a former graduate student of Smith’s. Ruegg was attuned to the cutting edge of genomics, and she shared Smith’s mission of pushing the bounds of migration science.

In the top image, a creek flows through Echo Bluff State Park in southern Missouri. A cliff hovers above the rippling water, as the sun peeks over a forest in the background. In the bottom image, a researcher extends a mesh net for catching Yellow Warblers, while two colleagues stand in the background, one holding the other end of the net.
Sinking Creek flows through Echo Bluff State Park in southern Missouri (top), where Colorado State University professor Kristen Ruegg (bottom) and colleagues set up a mist net to catch Yellow Warblers on their breeding grounds. Photos: Noppadol Paothong

Researchers know, broadly, why so many migratory bird species are declining: climate change, pesticides, and the conversion of native habitats, such as grasslands, for agriculture and other human uses. Pinpointing the causes of any particular decline, with enough precision to address them, is trickier. That’s because migration is a complicated matrix. Two birds might look alike but come from separate populations, with different breeding and wintering grounds, different flight paths, and different perils along the way. They might have genetic distinctions, too, that make them well- or ill-suited to environmental changes.

Traditional research tools provide limited data. Metal bands and most electronic tracking devices require capturing the same bird twice, which doesn’t happen very often. (For small, banded birds, just one in 2,000 are reencountered more than 15 miles from the original site, according to U.S. Geological Survey records of 14 species; most of those are found dead.) GPS trackers remain expensive and heavy. Ruegg’s idea was novel: She wanted to take the Human Genome Project’s big-data approach and apply it to birds.

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Migration is a complicated matrix. Two birds might look alike but come from separate populations, with different flight paths.

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Using DNA from feathers, Ruegg hoped to generate entire genomes, then find small variations within a species that distinguished one population from another. Because each feather came from a known location, she and her colleagues could then draw migration maps with more specificity than in the past. They no longer needed to recapture a bird with a metal band or a geolocator; they could track entire populations based on the shared genetic information in their feathers.

The plan, which Ruegg hatched with Smith, seemed audacious. “Up to that point, the best we could do was something really crude,” says Irby Lovette, who heads the evolutionary biology program at the Cornell Lab of Ornithology. “I’m not sure if I want to admit this, but I remember back in the beginning of this endeavor being quite skeptical about it actually working.” Since then, he says, “she completely proved me wrong.”

For her test case Ruegg chose the Wilson’s Warbler, a black-capped yellow songbird that is declining in some places and relatively stable in others. Out of 320,000 banded Wilson’s Warblers, zero have been captured on both ends of their migration.

Ruegg examined more than 1,600 feather samples from monitoring stations across North and Central America. She noted how they varied at 96 key genetic locations, narrowed down from 450,000 candidates, then sorted the species into six populations. Her paper, published in the journal Molecular Ecology in 2014, included a map of overlapping migratory routes, along with timetables showing when each population traveled. Ruegg and her coauthors even suggested where the biggest geographic trouble spot might be.

“That was the proof of concept,” Ruegg says. “Once we had done that, Tom and I were like, ‘This is cool. We can do it. Now we need to go out and facilitate this work in as many species as possible.’ ” The following year Ruegg and Smith launched the Bird Genoscape Project. They had raised almost $1 million and sought enough funding to map 50 to 100 species.

From the get-go the duo wanted to ensure their research didn’t languish in academic journals. So they built partnerships with conservation groups and government agencies, and they asked those partners to list their priority birds. One of the first they heard about was a drab, little songbird with a buzzy voice that had generated more than its share of conflict.

T

he Southwestern subspecies of the Willow Flycatcher once flourished on breeding grounds stretching from California to Texas. But its numbers plummeted throughout the 20th century as the dense streamside forests where the birds nest and forage disappeared. Water diversions, cattle grazing, and urbanization all contributed to their decline. So did Brown-headed Cowbirds, which laid eggs in their nests.

The U.S. Fish and Wildlife Service listed the subspecies as endangered in 1995. Ranchers worried the designation could prevent grazing animals in the birds’ habitat. “They’re not looking to save that bird,” C.B. “Doc” Lane of the Arizona Cattle Growers Association told a reporter at the time. “They’re looking to control that land, and the bird is a handy way of doing it.”

The debate kicked back up in 2013, when the agency added protections to more than 200,000 acres of habitat. Critics said the protections would cost hundreds of millions of dollars in unnecessary land-use restrictions. Ranching and real estate interests formed a coalition and petitioned to delist the Southwestern Willow Flycatcher in 2015, just a month before the Bird Genoscape Project’s public launch. Represented by the Pacific Legal Foundation, a property-rights group, they argued the Southwestern population wasn’t a subspecies at all, and therefore didn’t merit protection.

Scientists had initially used differences in color and wing structure as evidence that Southwestern birds were their own subspecies. To back up its challenge, the Pacific Legal Foundation offered a 2015 study by evolutionary biologist Robert Zink that relied in part on mitochondrial DNA. Passed down by females, this type of genetic material offers a glimpse up the bird’s maternal line. Ruegg, who worked with mitochondrial DNA in graduate school, describes it as a low-resolution tool that’s useful primarily in studying species with deep and ancient evolutionary splits. The Willow Flycatcher, she says, is not such a species.

In the top image of a diptych, a manila envelope labeled with data sits on top of a white paper filled with handwritten data. Two yellow feathers sit on top of the envelope. In the bottom image, several plastic tubs filled with manila envelopes are stacked in a refrigerator, with frost accumulated on the bottom tubs.
Feathers from a bird collected in Current River State Park in Missouri (top) will be stored in an envelope in a box with hundreds of others for later analysis. Altogether the boxes fill 15 freezers. Photos: Noppadol Paothong

For his part, Zink, who is now at the University of Nebraska-Lincoln, says that, while imperfect, mitochondrial DNA evidence is powerful enough that the USFWS has used it in close to 100 decisions.

Ruegg and her husband, geneticist Eric Anderson, along with evolutionary biologist Rachael Bay, set out to settle the debate using the tools of the Bird Genoscape Project. They analyzed 105,000 genetic markers and found not only that the Southwestern subspecies was distinct, but also that it was the most distinct of the three subspecies that breed in the American West. “So if anybody was concerned if there’s any legal argument over that,” Ruegg says, “we now have the data.”

Ruegg says she kept USFWS scientists abreast of her findings, which wouldn’t be published in time for the agency’s decision. In 2017, the USFWS announced it would keep the bird on its endangered list.

With DNA, scientists could answer another critical question: Where do Southwestern Willow Flycatchers winter? Until then, they didn’t know with precision. “We didn’t have the right glasses prescription,” Ruegg says. “We could maybe hand-wave: ‘We think, with some weak probability, that it might be somewhere here.’ ” Using genetic sequencing was like putting on “glasses with the perfect prescription.”

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With DNA, scientists could answer another critical question: Where do Southwestern Willow Flycatchers winter?

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By looking at feathers collected in Latin America and comparing them to the Southwestern birds’ DNA signature, the researchers narrowed the subspecies’ wintering range to parts of Costa Rica and Nicaragua. This will help conservationists pinpoint where to preserve habitats, says Mary Whitfield, research director at the Southern Sierra Research Station in California, and engage local residents and stakeholders in that effort.

In February 2020, a team led by Whitfield visited a Nicaraguan reserve that the Bird Genoscape Project had identified as a subspecies wintering site. There, they recaptured a Southwestern Willow Flycatcher that had been banded as a nestling in San Diego almost three years earlier. When biologists from the biodiversity group Paso Pacífico returned the following month, they found the land cleared by neighboring farmers and the bird gone. Since then, Paso Pacífico has paid growers to protect the habitat while the flycatchers are using it, leveraging money raised specifically for the subspecies’ conservation.

O

n their second morning in the Ozarks, Rodriguez and her team shunpiked to the rocky edge of Sinking Creek, across from a sheer dolomite cliff. Immediately they heard a Yellow Warbler: Sweet sweet sweet, I’m so sweet! It appeared to be coming from a nearby branch, so they unfurled the net, positioned the speaker, and waited.

It was an efficient morning. The students caught three birds in as many hours, including one they nicknamed “Scarface” for the missing feathers near his beak. “When you hit the territory, they fly right in,” said Ruegg, who is Rodriguez’s Ph.D. adviser and had joined for the end of the tour. “It’s always nice when there are a lot of birds and it’s beautiful.”

The two-day total was now 10 warblers. Through her binoculars, Rodriguez spotted a female. She had already been banded, so Rodriguez called it a wrap. “I feel good,” she said. “Ten is a lot.”

Yellow Warblers are not threatened like Southwestern Willow Flycatchers. But some populations are faring better than others. The birds’ very ubiquity makes them important to study, says Rachael Bay, who did some of the Bird Genoscape Project’s early research on the species.

“North America has a lot of different climates during the breeding season,” says Bay, now at the University of California, Davis. “So from an evolutionary biologist’s standpoint, there must be something different between the birds that are in the Central Valley where I live, which is over 100 degrees Fahrenheit and extremely dry during the summer, and birds that are living in Atlantic Canada or New England.”

Bay wanted to know how specific populations would adapt to climate change. First, she had to define the term. “What component of climate matters?” she says. Is it temperature? Is it rain and snow? Using DNA samples from the Bird Genoscape Project, museum collections, and researchers, she found markers in a cross-section of the bird’s genome associated with hot and cool climates and various levels of rainfall.

“What we find is that precipitation is really important,” Bay says. Warblers living in wet and dry regions had different genetic variants. “Temperature,” she says, “is not that important.”

Bay then looked at climate projections for 2050 to figure out which populations will have the biggest mismatch between their genes and the changing environment. The Yellow Warblers least poised to adapt, she found, are the ones that breed from the southern Rockies to Alaska, along with some East Coast populations. Those groups have already experienced the heaviest losses. Midwestern birds are hardier.

Bay published her findings in the journal Science in 2018. Since then, the technology has gotten so inexpensive that Rodriguez can afford to scan an individual bird’s entire genome, whereas Bay had to make do with just 5 percent. Using whole-genome sequencing, Rodriguez found even more climate-related genetic markers that varied between different Yellow Warbler populations.

Rodriguez is advancing the science in another way, too. She’s using blood samples, including those from the Midwestern road trip, to examine telomeres, the protective caps at the ends of chromosomes. Birds and humans both have telomeres, and they shorten as we get older. The faster they shorten, the sooner we die.

Stress speeds up the process. “Predator pressure, food availability, human disturbance, urban environments—there are a ton of examples in different populations that cause telomere shortening,” Rodriguez says.

Birds that die younger reproduce less. If an entire population has shorter telomeres, its overall numbers could suffer. Scientists therefore use telomere length as a proxy for the health of a population.

Rodriguez is exploring whether Yellow Warblers from regions where the climate is changing quickly are already feeling the effects. She is looking at weather records from the 1970s to the present and correlating the amount of change with telomere length. “Then we can make that connection and say, OK, these birds aren’t just vulnerable in the future. These birds are hurting right now.”

T

he Bird Genoscape Project has so far mapped about 20 species, Ruegg says, and has enough funding to bring that total to 50. Hundreds of collaborators, working at nonprofits, universities, and government agencies, contribute to the feather collection, which has now grown to about 260,000 feathers from throughout the Western Hemisphere. They fill 15 freezers.

A researcher’s gloved hands hold a clear plastic plate containing samples of genetic material.
A lab assistant at Colorado State University holds a plate containing 94 samples of genetic material that will be loaded into a genotyping machine for analysis. Photo: Noppadol Paothong

Ruegg continues to consult with agencies, academics, and conservation groups about which species are most in need of study. High on the list are Loggerhead Shrikes, Canada Warblers, and Burrowing Owls, all of which are experiencing population declines.

The DNA extracted from feather samples doesn’t replace old-school tracking methods. In fact, they complement each other. Researchers at banding stations, where most feathers are collected, record a lot of information about the birds they capture: the creatures’ physical condition, their fat reserves, how often they return to the same location. These details, when combined with a more granular understanding of the birds’ migratory paths, are critical to understanding which populations are most at risk.

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The feather collection has now grown to about 260,000 feathers from throughout the Western Hemisphere. They fill 15 freezers.

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Ruegg and Smith know the urgency of their work. “We have to move very fast,” she says. “And we have to work together. Because we’re not going to get there if we don’t.” To that end, Ruegg also contributes data to Audubon’s Migratory Bird Initiative, which the organization’s scientists launched in 2019 to consolidate migration data and prioritize critical sites for conservation.

Still, Ruegg would like the Bird Genoscape Project to have more partners—in particular in Latin America and the Caribbean. Most conservation efforts in this hemisphere focus on birds’ breeding grounds, typically in the United States and Canada. This neglects their winter habitat and all points in between, notes Whitfield. “If you don’t protect them through their whole life cycle,” she says, “then we’re likely going to see more declines.” Mobilizing scientists and bird banders on a much larger scale would give agencies and conservation groups even more high-quality data. “Then hopefully they’re using that to do the on-the­ground conservation,” Ruegg says, as in the Nicaraguan flycatcher reserve.

Birds can also serve as a model for other animals. “We have a lot of information on birds that we don’t have for other species,” Ruegg says, which makes the initiative she has led all the more valuable. The feather collection that has been growing since the 1990s, in her vision, could help us understand more than a few dozen migratory species. It might help us understand how climate change, and the other stresses we’ve placed on the world, is affecting life itself.

This story originally ran in the Spring 2022 issue as “Birds of a Feather.” To receive our print magazine, become a member by making a donation today.

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