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In the young Jack Pine forests of northern Michigan, Nathan Cooper sometimes comes across an individual bird that he last saw weeks earlier in the Bahamas. The chance to have these repeat encounters is one advantage of studying the Kirtland’s Warbler, a species with a tiny population, hyper-specific breeding habitat, and a small wintering territory.

“It’s a very special situation to have this bird in your hand that you put a tag on two months ago,” says Cooper, a research ecologist at the Smithsonian Migratory Bird Center. “We both flew a couple thousand miles to Michigan. I took the easy way and took a plane, and it survived the gauntlet of dangers and the immense physiological challenge of flying 2,000 miles in 10 days.”

On top of those perils, the birds now face another, newly discovered threat. A by researchers at Penn State University found extensive but previously undetected signs of inbreeding in the genomes, or complete DNA sets, of Kirtland’s Warblers. The invisible effects of this inbreeding are potentially significant enough to complicate the species’ recovery after it was removed from the endangered species list, the researchers report. Worse, the findings arrive at a time when experts warn the birds are once again facing a sharp population drop.

The Kirtland’s Warbler, one of the rarest songbirds in North America, is bouncing back from decades of population decline driven by human changes to its habitat. To protect homes and other property, land managers adopted a policy of suppressing fires in the dry, sandy jack pine forests where the birds breed. But to reproduce naturally, jack pines need fire to pry their cones open, so preventing blazes stifled their regeneration. A landscape changed by farming also became more suitable for Brown-headed Cowbirds, brood parasites that hurt Kirtland’s Warbler nesting success. In 1971, a census of the species found that the population had fallen rapidly, with just 200 singing males left.

When the Endangered Species Act became law in 1973, the Kirtland’s Warbler was among the first species on the list. Decades of diligent conservation management—including tree planting and cowbird trapping—led to the species’ recovery, and it was delisted from federal protection in 2019. The last full census in 2021 counted 2,247 males—more than double the 1,000-pair federal recovery goal. Still the work isn’t done—and never will be, says Kylie McElrath, Michigan conservation manager at . “They are a conservation-reliant species, meaning that they do rely on human intervention, even beyond their delisting,” McElrath says.

The recent study suggests that genetic wear and tear from inbreeding could complicate those efforts, the authors say. It is not uncommon for species that experience a “bottleneck”—a period with very few breeding adults—to show signs of inbreeding, which can leave individual birds less fit for survival and reproduction. Given the harsh bottleneck the Kirtland’s Warbler went through, scientists suspected there might be some level of inbreeding, says Anna María Calderón, who led the study

To find out, Calderón and her colleagues turned to whole-genome sequencing, a method that until recently was prohibitively expensive. Past tests of genetic diversity in the Kirtland’s Warbler—including the studies that informed the decision to delist the species—used a small set of markers on the genome that the researchers compare to snapshots of a bird’s DNA. The newer technique, they say, offers something more like a high-definition film.

Their results showed a high frequency of potentially damaging genetic variants in the Kirtland’s Warbler, which could have ramifications across the bird’s development, migration, and reproductive success. “With this new analysis, it suggests there was probably much more inbreeding in Kirtland’s than was previously considered,” says co-author David Toews.

For comparison, the team also analyzed the full genomes of two closely related but much more abundant species. “We found no evidence of inbreeding whatsoever in Hooded Warblers or American Redstarts,” Toews announcing the findings. “In comparison, the level of inbreeding for the Kirtland’s Warblers is almost off the charts.” The findings raise an intriguing but ultimately unanswerable question, he says: If wildlife officials had known about the inbreeding, would they still have delisted the Kirtland’s Warbler?

The study joins a growing body of research using emerging genomic science to assess species health and applying those insights to guide management of vulnerable birds. For example, one study from Toews and his colleagues used whole-genome resequencing to determine that a small population of Black-throated Green Warblers found in wetland forests in Virginia and the Carolinas are in fact a distinct subspecies known as Wayne’s Warbler. The Center for Biological Diversity cited that study to the U.S. Fish and Wildlife Service to list the subspecies under the Endangered Species Act and protect its critical habitat of coastal wetlands. (To date the subspecies remains unlisted.)

Calderón says she plans to continue studying how inbreeding could affect the growing but still relatively small Kirtland’s Warbler population. For example, she may partner with Cooper from the Smithsonian to study egg viability since, at least based on Cooper’s anecdotal observations, there seem to be more unhatched eggs in Kirtland’s Warbler nests compared to other species.

Meanwhile, the species is facing other challenges. The birds have received less attention since they were delisted and, as a result, there’s been a lapse in habitat creation, says Bill Rapai, executive director of the nonprofit Kirtland’s Warbler Alliance. The birds need about 30,000 acres of jack pines that are between 5 and 20 feet tall, but the currently suitable habitat falls almost 10,000 acres short of that goal, he says.

Though the Fish and Wildlife Service and the Michigan Department of Natural Resources have made major commitments to correct that shortage, “it’s going to be until 2027 before we can reverse the absolute habitat decline,” Rapai says. A on Kirtland’s Warbler from the Committee on the Status of Endangered Wildlife in Canada warned that, in Michigan’s Lower Peninsula, “declines have occurred since 2021 due to decreased habitat availability, which is predicted to result in population declines of 20 to 50% within the next decade.” Rapai says he believes a new census of the species, which , could see the numbers dip below 1,000 pairs.

On the bright side, it’s possible to expand habitat in places that historically had young jack pine forests, McElrath says. That includes areas in Wisconsin, Ontario, and Michigan’s Upper Peninsula. And as climate change drives a northward range shift for jack pine and the Kirtland’s Warbler, she says, there are opportunities to conduct experimental plantings in other parts of the Great Lakes region.

Keeping the Kirtland’s Warbler viable long into the future may require not only plenty of habitat, but also a new approach to monitoring the health of the species, McElrath says. “It goes beyond just counting population or estimating population numbers,” she says. “Some of these genetic variables could be considered in future monitoring and measurements of success in the population.”

Advocating for the species—and continued collaboration from all involved—remains essential, Calderón says. “It’s amazing that the Kirtland’s Warblers were able to rebound as they have,” she says. Conservation efforts brought about that dramatic recovery, and now genomic science has a role to play in helping to sustain it. “We have this really awesome opportunity to merge both of them.”