The Secret to Song Sparrows’ Extraordinary Success Lies in Their Genome

This ordinary-seeming songbird species is teeming with subtle genetic diversity, which allows local populations to respond in various ways to a changing world.

From the Summer 2025 issue of Living Bird magazine. Subscribe now.

If you’re a birder in North America, you’re almost certainly familiar with Song Sparrows. Because they’re found everywhere—from the deserts and volcanoes of Mexico to the outlying islands of Alaska.

That’s exactly what makes them so interesting to some researchers: How did these little brown birds conquer the continent?

The answer, at least in part, is local adaptation. Ornithologists have recognized no fewer than 25 distinct subspecies of Song Sparrow, each with its own suite of traits that help it thrive in the specific place it calls home. Song Sparrows in cold climates—like Melospiza melodia maxima, the so-called “Giant Song Sparrow” of the Aleutian Islands—have large bodies (compared to Song Sparrows elsewhere) that reduce heat loss; Song Sparrows in deserts—like Melospiza melodia fallax, the “Desert Song Sparrow” of the Mojave and Sonoran Deserts—have pale plumage that may make them less visible to predatory hawks; Song Sparrows in wet habitats, like Melospiza melodia caurina of the Pacific Northwest, have darker plumage to harden feathers against degradation by moisture-loving microbes.

In 2022, scientists from the Cornell Lab of Ornithology and University of British Columbia in Canada sequenced the entire genomes of 316 individual Song Sparrows spanning almost every subspecies, allowing the researchers to identify the genes underlying regional sparrow adaptations. Now they’re digging into this DNA to explore the varying ways evolution is finely tuning each subspecies for its local environs.

“People are usually pretty underwhelmed by sparrows, because they think they’re all the same,” says Jen Walsh, a research associate at the Cornell Lab who specializes in avian genomics. “But there’s this cryptic diversity there that I think we’re starting to understand more and more.”

Twenty-Five Kinds of Song Sparrows

In biology, a subspecies is a group or population within a species that has some unique identifying traits, but isn’t so different that its members can’t interbreed with other members of the same species. About 46% of bird species worldwide have recognized subspecies, but the Song Sparrow has perhaps the most of any songbird in North America.

Working before the advent of genomic sequencing technology, ornithologists originally identified bird subspecies according only to the physical characteristics observable by the human eye—noting, for example, that Song Sparrows in one area were smaller and paler than those in another area. It could be a “slippery concept,” admits Peter Arcese, an emeritus faculty member at the University of British Columbia, who started studying Song Sparrows in 1981. Sometimes, Arcese says, the differences are subtle enough that it’s hard to tell where one subspecies ends and another begins. But the subspecies concept is useful, he says, for giving bird scientists a framework to study these variations across the landscape.

Beginning in the 2010s, new techniques emerged that made genetic analysis faster and cheaper, and today it’s possible to sequence a bird’s entire genome in just a day or two, with the genomes of many individual birds being analyzed simultaneously. Getting to this level of detail with a manageable amount of effort means that scientists can now start looking for the genes that underlie the differences between subspecies. That’s what Arcese and collaborators Jen Walsh and Katherine Carbeck—a former PhD student of Arcese’s who’s now working as a postdoctoral researcher at the Cornell Lab with Walsh—have been working on. Together, they’ve overseen a massive project to unravel the entire genomes of representatives of 21 out of the 25 identified Song Sparrow subspecies.

Arcese and Walsh first began collaborating in 2016, after meeting through scientific conferences and realizing how well their research interests complemented each other—while Arcese had been studying Song Sparrows in the field, Walsh had been examining the genomes of other sparrow species such as Saltmarsh Sparrow. Arcese’s decades of research experience helped him build a vast network of collaborators and former students across the continent, from whom he could obtain the samples needed for this research: 316 bits of blood and tissue from 29 sparrow populations spanning 21 different subspecies, taken from a mix of live birds and museum specimens. Hundreds of vials of blood and feathers from across North America were shipped to the Cornell Lab’s Fuller Evolutionary Biology Laboratory in Ithaca, New York, where Carbeck set to work preparing them for genetic sequencing.

“When I started this project, I came from an ecophysiology background,” says Carbeck—she’d previously focused on interactions between birds’ physiological processes and their environment. “I actually didn’t have much experience with genetics at all.” She says that Walsh spent a lot of time showing her the ropes. “I think it was actually good that I didn’t know what I was getting myself into,” says Carbeck, who would ultimately oversee the sequencing of around 4.5 trillion base pairs of DNA. “I was like, yeah, that sounds possible, I’ll do it!”

The result was almost five terabytes of data (an “insane amount” of data, as Carbeck put it) stored on a server, which the team analyzed over the course of a month using a Cornell-owned supercomputer. Once the research team had the fully sequenced genomes in hand, they began digging into the genes underlying the differences among Song Sparrow subspecies from different parts of the continent, starting with an obvious difference: size.

The Song Sparrows that live on Alaska’s Aleutian Islands, strung between Russia and mainland Alaska in the northern Pacific Ocean, are, astoundingly, almost three times the size of the sparrows found around California’s San Francisco Bay. This is an extreme example of a pattern that scientists have been aware of for more than 150 years, named “Bergmann’s Rule” after Carl Bergmann, the German biologist who first described this relationship between temperatures and bird body sizes and wing lengths. According to Bergmann’s Rule, related animals will be larger in colder environments and smaller in warmer environments. Larger bodies help animals in cold climates better retain precious body heat, while smaller bodies in warm climates have the opposite effect, helping animals cool off.

Carbeck, Walsh, Arcese, and their colleagues began by identifying genes that appeared to be connected to size in the hefty Alaskan sparrows as well as medium-sized Song Sparrow subspecies in British Columbia and the Pacific Northwest. Then, they checked their work by using related genetic variants carried by the San Francisco birds to predict how big they should be based on their DNA. It worked—their predictions lined up with reality, a clear example of the links between physical traits, genes, and the environment.

These variations among subspecies, calibrated to differences in habitat, seem to be a key reason why Song Sparrows are common in ecosystems ranging from the boreal forest to deserts to coastal tidal wetlands. But the research is also showing how fine-tuning by evolution to fit into a very specific environment can backfire, when that environment begins to rapidly change.

Localized Adaptations: The Song Sparrow Secret to Success

A New Concept: “Genomic Offset”

Scientists have come up with a name for this mismatch between genes and environment: genomic offset. It’s a way of measuring how far off the habitat that an animal is optimally adapted for is from the habitat in which it actually finds itself.

Song Sparrows Get Bigger as Latitudes Get Higher

Research led by Katherine Carbeck—a former PhD student at the University of British Columbia, now a postdoctoral researcher at the Cornell Lab of Ornithology—found that Song Sparrows in the Aleutian Islands are twice as big as Song Sparrows farther south in the Pacific Northwest.

Using the terabytes of genomic data stewarded by Carbeck, the team has been able to calculate genomic offsets for various Song Sparrow subspecies. First, they identified Song Sparrow genes linked with adaptations for certain temperature ranges and moisture levels. With this information, they can then look at the specific genetic variants carried by any group of birds and figure out their ideal climate—and see how well it matches, or doesn’t, the real place where they live.

“Basically,” says Walsh, “you can take all this genomic data from across all of North America and you can correlate the genomes with the environment. Then you have an idea what regions of the genome are locally adapted, and what parts of the environment are driving that selection.”

This approach works across time and space. Arcese, who recently retired, spent most of his career leading research on the Song Sparrow population on British Columbia’s Mandarte Island, with the permission of the local Indigenous Tsawout and Tseycum tribal bands (who call the island X̱ O¸X̱ DEȽ). On this small scrap of rock and brush near Vancouver, biologists have been recording the birth, life, and death of every single sparrow for nearly 50 years.

Arcese, Walsh, and Carbeck checked the Mandarte Island sparrows’ DNA to determine their perfect environment, then compared that to actual conditions on the island across five decades, looking to see if periods of high mismatch between the birds’ genes and the island’s climate coincided with any dips in their reproductive success.

As conditions cycled back and forth between El Niño and La Niña years, the island sometimes experienced conditions far from the birds’ optimum. And it was in the years following these extremes—once in the 1980s when the island experienced an extreme cold snap, and a few more recent years that were wetter and hotter than usual—that the researchers found effects on the population. The year after each of these periods of high genomic offset, the birds were less successful at reproducing. Two years after, juvenile survival was lower and population growth slowed. In the third year after extreme weather and high genomic offset, adult survival was lower. Ecologists refer to these as “carry-over effects,” the ripple effects that environmental conditions experienced by an animal at one point in its life can have through the rest of its life cycle.

After identifying the drivers of genomic offsets on Mandarte Island, the scientists set out to look for more such offsets across the rest of the continent. The team determined the degree of genomic offset that each of the 21 subspecies whose DNA they’d sequenced currently experiences in the environment it lives.

Thanks to data that birders have submitted to eBird over the past two decades, scientists (and anybody with access to eBird on the web) can know whether local populations of Song Sparrows have been increasing, declining, or holding steady. During the decade from 2012 to 2022, Arcese, Walsh, and Carbeck found that genomic offset accounted for almost 60% of the variation in Song Sparrow subpopulation trajectories. Birds that were still tightly matched with their local environmental conditions were doing okay. But where climate change was causing conditions to move away from what the local birds were adapted for, their numbers were more likely to be dropping.

The researchers were surprised by just how strong the correlation was. The link between genomic offset and population declines is “really tight,” says Walsh. “If you’re mismatched from your environment, you’re not doing well.”

“I did expect some relationship between climate and rate of change and population,” says Arcese, “but the relationship there is just massive.”

However, the data included a surprising twist: the effect was not equally strong across all subspecies. Some Song Sparrow subspecies are migratory, making medium- to long-distance journeys between seasons (for example, sparrows that breed in the Northeast might fly to Kentucky or Virginia for the winter, while others are homebodies that remain in the same area year-round). The researchers found that migratory subspecies were less affected by genomic offset than year-round residents, apparently buffered from the impacts of their genome-environment mismatch by their ability to move around.

“Resident populations have adapted to that local optimum enough that if the climate is changing a lot and they’re not changing with it, they’re going to have more severe consequences,” says Walsh. Migratory subspecies, on the other hand, are more flexible. Moving from place to place means they need to deal with different local environments over the course of the year—and that could translate to being better able to handle changing environments over time.

One Species, Many Forms

Rescued By Their Own Diversity?

For Jen Walsh, Song Sparrows are far from just a boring, brown backyard bird.

“I think Song Sparrows are really interesting. They’re a super broadly distributed, super common species that we don’t really think about,” she says, “but [like many species], they’re in decline.”

Both Christmas Bird Counts and Breeding Bird Surveys have recorded gradual declines in Song Sparrow populations across much of North America since the 1960s. Data from eBird Trends agrees, showing the total population of Song Sparrows in North America dropped by around 2.4% between 2012 and 2022. That’s a subtle drop compared to the steep declines of other bird species, but as Walsh and her colleagues’ work demonstrates, those numbers don’t tell the entire story.

Song Sparrow population trends vary quite a bit from one place to another. At northern latitudes, for example, where migratory Song Sparrows are more common, population declines are less pronounced.

“What our work is showing is that there is a remarkable amount of diversity across their range, which is really important,” says Walsh. “We know that diversity provides the building blocks for evolutionary change and for responding and adapting to future environmental conditions.”

Genomic offset data, Walsh explains, can help “predict how these populations might change in the next 10, 20, 30 years.” It’s even possible, she says, that as migratory sparrows move across the landscape, they could interbreed with sparrows from struggling subspecies and spread helpful genetic variants to new places.

Each new research insight, says Walsh, reveals just a little bit more about this seemingly ordinary, little brown bird that harbors tremendous hidden diversity—and the capacity to respond to changing conditions across the continent in myriad ways.