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An American symbol: The bald eagle and its complex DNA

The bald eagle has bounced back from its 20th-century population free fall—but does its DNA suffer from a genetic bottleneck? Our blog explains.
An American symbol: The bald eagle and its complex DNA hero image

The takeaway: That iconic ruler of America’s skies, the bald eagle, has had a tough go of it lately. While its breeding numbers have risen in the Lower 48, questions about its genetic lineage remain.

The bald eagle, Haliaeetus leucocephalus, is more than just a big bird and an apex predator—its symbolism means a lot to Americans in particular, with the bird adorning everything from coins to flags.

The eagle, of course, is to a large extent such a notable predator thanks to its ariel acrobatics—these birds can soar to great heights with barely a flap of their wings, spotting prey from dozens of feet above the ground, and dive-bombing not just to prairies and grasslands but even into lakes and rivers to snag sizeable fish. But its role in American consciousness is much more complex than simply killing fish—it symbolizes freedom and independence. Despite that, this bird was pushed close to extinction not that long ago, and it may not be out of the woods just yet.

Evolutionary history of the bald eagle

Studies over the years have answered the question of where bald eagles are descended from. The eagle is no newcomer to its role near the top of the food chain. Evolutionary biologists suspect the bald eagle evolved from a reptile, and that it owes much of its hunting agility to that evolution. Birds began to evolve around 144 million years ago, and early versions likely had teeth. Their feathers were presumed to be an evolution of reptilian scales, and the earliest birds scavenged and hunted fish.

Eagles appeared on the scene around 36 million years ago, descending from a group of birds known as kites. The first were sea eagles, which had no feathers on their feet, followed by booted eagles, which had feathers below the knee. The bald eagle evolved around 1 million years ago, and while these hunters have featherless feet, they do have a number of specialized adaptations that helped them to thrive today: powerful toes and sharp talons, spicules on the bottom of their feet that allow them to grasp prey, special pigments on their feathers that prevent breakage when they dive into water, and serrations on the roof of their mouth that make it easier for them to hold on to slimy fish as they soar to a snack spot.

DDT nearly killed off bald eagles in some areas

All has not been rosy in the recent history of bald eagles, however. DDT, the infamous insecticide, resulted in severely shrinking population through the middle of the 1900s, and this led to a severe population bottleneck. Genetic bottlenecks can affect the distribution of genetic variation among species. This can lead to genetic drift and change the proportional random distribution of alleles and even lead to a loss of alleles—and it can lead, down the road, to a population that is at a greater chance of inbreeding and genetic similarity. Without genetic variability, a species may be more susceptible to extinction due to factors that otherwise would only impact a small portion of the population—for example, losing the ability for a species as a whole to overcome a disease. This can happen to eagles as easily as it can happen to soybeans.

According to a 2011 study, the bird’s population had plummeted to less than 450 pairs in the Lower 48 states—perhaps hitting a low of 417 nesting pairs in 1963. DDT played a big role in this. According to the U.S. Fish and Wildlife Service, DDT washed into rivers and lakes and was absorbed into fish, and when the eagles ate fish, the DDT was passed on to them. The main result of DDT in eagles was that the birds lost the ability to produce strong eggshells, and the eggs were likely to break during incubation or simply would not hatch.

Bald eagle conservation ensued. Bald eagle conservation status saw the birds listed as endangered in 1967, with the listing changing somewhat in 1978. The listing, however, allowed the federal government to partake in captive breeding programs, reintroduction efforts, and law enforcement-led nest protection during the breeding season. Recovery was steady, and in 1995 the birds were moved from endangered to threatened status—a less dire situation—and removed from the list altogether in 2007.

Bald eagle DNA: With bald eagle studies, what do we know?

Although the bald eagle is an important predator within the North American food chain, and although the bird plays a massive role in the founding of the United States—psychologically at least—there has been little investigation into the animal’s genetic makeup, and that research in the past decade concerning bald eagle studies has been shockingly sparse.

In the previously mentioned 2011 study, a researcher compared mitochondrial and nuclear DNA loci to compare local population in Alaska and two spots in Florida to the broader population. The researcher performed DNA extraction and PCR amplification and sequencing.

“Mitochondrial DNA showed significant evidence of population differentiation between populations with highly significant FST values between Alaska and Florida Bay and Alaska and North Florida,” the report states. “There were no significant differences between the Florida Bay and North Florida populations. The Florida Bay population is more depauperate for both haplotype and nucleotide diversity as compared to Alaska and North Florida. The differences between Alaska and Florida Bay populations indicate that there is little gene flow between the two populations and may be attributed to isolation by distance.”

The report theorized that isolated populations of bald eagles could suffer from genetic similarities yet also possess unique traits to the species that could better position them to adapt to changing environments.

The theory was further tested in a 2020 article in Conservation Genetics. That study used a custom single nucleotide polymorphism (SNP) array and conducted initial population genomic analysis on geographically distinct bald eagle populations in order to assess generic variation among populations—the understanding of which is key for developing smart conservation management plans.

“Results from all of these analyses indicate that despite the significant population bottleneck, sufficient genetic variation is detectable within the bald eagle gene pool.” The authors wrote. “Moreover, based on our disparate geographic sampling of bald eagles, our preliminary analyses indicate statistically significant partitioning of the genetic variation among broad sampling areas.”

In 2016, PCR technology was used to learn more about a sick bald eagle in Florida and to analyze a gene that was later found to be a poxvirus. A new sequencing technique called shotgun sequencing, meanwhile, has helped researchers in the United States learn more about previously unidentified viruses that are impacting the eagles. In the upper Midwest, in the 1990s, bald eagles started showing strange symptoms—they were weak, stumbling, vomiting, and experiencing seizures. Vet hospitals were unable to save them. Researchers studying Wisconsin River Eagle Syndrome used shotgun sequencing to identify a new virus, bald eagle hepacivirus, or BeHV, which was later determined to infect eagles nationwide.

The future of bald eagles: Despite setbacks, a promising future

Are bald eagles endangered? Today, thankfully, no. Studies like those that used NGS to identify BeHV, and efforts at the federal level to protect habitat and reduce toxins, are helping to protect bald eagles in the United States and beyond today. Populations of the bald eagle have quadrupled just since 2009, according to the U.S. Department of the Interior, the federal agency that manages many of the public lands that eagles use for critical habitat.

“The recovery of the bald eagle is one of the most well-known conservation success stories of all time,” said Service Principal Deputy Director Martha Williams in a press release. “The Service continues to work with our partners in state and federal agencies, tribes, non-government organizations and with private landowners to ensure that our nation’s symbol continues to flourish.”

Where will bald eagle research head from here?

Bald eagle genetics research, and research into other critical animal species, is made possible through IDT products such as PrimeTime™ Assays, PrimeTime Probes, and PrimeTime Master Mixes.

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