A decade of research has revealed how the cognitive abilities of chickadees are shaped by their surroundings. Now scientists have begun to peer inside the black box of genetics, uncovering the variations in the birds’ DNA that made these adaptations possible.
From the Winter 2023 issue of Living Bird magazine. Subscribe now.
It’s January in California’s Sierra Nevada mountains, and scientist Carrie Branch is on snowshoes, trudging uphill through several feet of fresh powder. Her destination is a backcountry bird feeder in the Tahoe National Forest, accessible only by driving up six miles of forest roads and then bushwhacking in. Several inches of snow fell yesterday, but today the sky is clear, pure blue, and the quiet of the woods under the fresh blanket of white is broken only by the occasional croak of a raven. At 7,800 feet above sea level, the air is thin enough to make Branch pant a little.
It’s a lot of work for a birdseed refill, but it’s worth the effort—because this is no ordinary bird feeder. It’s part of an array of high-tech RFID-enabled feeders painstakingly designed to withstand winter weather and hungry bears. Branch and other scientists working with Vladimir Pravosudov’s ornithology lab at the University of Nevada have been conducting this backcountry birdfeeder research for nearly a decade now, using these RFID feeders to create puzzles for wild Mountain Chickadees and study their cognitive abilities.
For many animal species, “intelligence” (however one might choose to measure it) is meaningless; in whatever habitat, whatever lifestyle they find themselves adapted for, it doesn’t help them survive and reproduce, and so it’s irrelevant. “As humans, we think smarter is always better,” says Branch, “but it’s not.”
The Pravosudov lab’s growing body of research on Mountain Chickadees is showing, however, that when it comes to surviving the harshest of winters, spatial memory—the ability to store and recover food—is the crucial factor that decides whether a chickadee lives to raise babies and pass on their genes or perishes in the snow.
Now, they’ve even begun to reveal the genes underlying the variation in chickadee cognitive abilities. And by combining work in the genetics lab with ongoing observations in the field, they have an almost unprecedented opportunity to follow natural selection in real time, at the level of both genes and behavior.
Small but Smart
Mountain Chickadees are tiny conifer-loving birds with rakish white eyebrows that set them apart from most other members of the genus Poecile, a group of playful birds ranging from familiar North American species such as the Black-capped and Carolina Chickadees to Willow Tits in Europe and Sichuan Tits in China. Chickadees and tits have a habit of caching seeds, storing them away in nooks and crannies when food is plentiful and retrieving them later.
Vladimir Pravosudov arrived at the University of California Davis in 1999 as a postdoctoral researcher with an ambitious plan to study chickadees and their proclivity for caching. He had started his academic career 20 years earlier in what was then the Soviet Union with grand ambitions for a different study subject: eagles. But his advisor at Leningrad State University was unimpressed.
“My advisor said, ‘They’re cool birds, but what are you going to study?’” says Pravosudov. “And I said, ‘I don’t know, I’ll find something.’”
He spent a season observing White-tailed Eagles in northeastern Russia, enjoying himself immensely but not hitting upon a particular research idea. Finally, his Russian advisor gently suggested he consider studying another charismatic bird species: the Siberian Tit, or Gray-headed Chickadee.
“He said, ‘Did you know that they cache food?’” Pravosudov recalls his advisor asking him. “And that’s how it started.”
Soon Pravosudov was fascinated by these birds and their habitat of collecting seeds by the hundreds and storing them in hidden caches all over the forest, as insurance against a hard winter. Past researchers had primarily studied how natural selection might shape food caching by comparing behavior between species. Pravosudov, however, believed that the clearest results might come from comparing populations within a species.
Soon after making the move to UC Davis, Pravosudov proposed a study comparing the caching behavior and memory of Black-capped Chickadees from Alaska and Colorado, as well as the size of their hippocampi (brain regions associated with learning and memory) and how many neurons they contained. His hypothesis was that because Alaskan birds experienced harsher winters, they would need to be better at caching and recovering food.
“Initially reviewers didn’t like [the idea],” says Pravosudov. “They said no, it’s completely crazy, it cannot possibly work this way.”
But the results, published in the journal Behavioral Neuroscience in 2002, showed that in lab tests, the Alaskan chickadees indeed cached more food, recovered their caches more efficiently, performed better on spatial memory tests, and had bigger hippocampi with more neurons.
The study generated a small flurry of media coverage, and Pravosudov conducted a series of follow-ups that looked at chickadees from 10 locations from Kansas to Alaska and found similar results along a broad gradient of winter severity: the colder the winters in their home region, the better Black-capped Chickadees were at memory tests and the more neuron-dense their hippocampi were, even if they were reared in a lab from the time they were nestlings.
“We got full confirmation of everything,” says Pravosudov. “It was just amazing.”
In 2005, Pravosudov joined the faculty of the University of Nevada at Reno. There amid the Sierra Nevada, Mountain Chickadees, close cousins of Black-capped Chickadees, caught his attention. Mountain Chickadees live in high-elevation coniferous forests across western North America, usually between around 5,000 and 11,500 feet. Pravosudov suggested that a master’s student try the same cognitive comparisons he had conducted with Black-capped Chickadees on Mountain Chickadees. But this time instead of studying birds at different latitudes, the study would compare chickadees from different elevations in the same mountain range. The increasing severity of winter conditions as birds ranged farther up the slopes, Pravosudov reasoned, would mirror the difference between Colorado and Alaska.
Comparing chickadees from different habitats thousands of miles apart was one thing; could chickadees whose habitats were separated by only a few kilometers possibly be that different? As it turned out, they were, according to research published in the journal Animal Behaviour in 2012. Brought into the lab, Mountain Chickadees that lived at 8,000 feet performed better on tests of their caching behavior and spatial memory than chickadees that lived just a short distance downslope at 6,200 feet. Those higher-elevation Mountain Chickadees also tended to have larger hippocampi than their lower-elevation neighbors and had other variations in their brains similar to those between Alaska and Colorado Black-capped Chickadees.
Carrie Branch joined Pravosudov’s lab as a PhD student in 2012, with plans to take the Mountain Chickadee research outdoors. She too had fallen in love with chickadees and their relatives as an undergraduate at the University of Tennessee, where she studied communication in Carolina Chickadees and Tufted Titmice. After completing a master’s degree for which she studied cognition and episodic memory in lab rats, she was anxious to get back to the field.
For Branch, the close proximity of her new Mountain Chickadee study subjects—in the mountains just 40 miles from the University of Nevada campus—offered the opportunity to study animal cognition not in a lab, but in the wild. The problem was how exactly to test birds’ spatial memory in an unpredictable mountain environment. As luck would have it, an occasional collaborator with Pravosudov, the University of Oklahoma’s Eli Bridge, had been working on something that just might work: RFID-enabled bird feeders.
RFID stands for radio frequency identification. Birds are fitted with leg bands incorporating tiny transmitters, each of which beams out a code unique to its wearer. Feeders can then be equipped with receivers that detect and record the identity of each avian visitor. Pravosudov, Branch, and their colleagues devised a setup consisting of eight so-called smart feeders arranged in a square, each of which could be programmed to admit only specific chickadees. How quickly a chickadee learned which feeder in the array was programmed to open with its matching leg band, and how well it could recall this information later, provided a measure of its spatial memory abilities.
Branch, Pravosudov, and their colleagues first field-tested their RFID feeder array in 2014. Their initial plan was to place the feeders on individual wooden poles, allowing them to be rearranged into new configurations if necessary. But the black bears of the Sierra Nevada had other ideas. The bears, attracted by the prospect of a tasty birdseed snack, immediately pulled over and destroyed the feeders. The researchers tried putting barbed wire around the poles, but the bears were undeterred. Next, they switched to using thick poles of galvanized metal, but the bears could still pull them down with a single paw. Electric fences—nope. “Unwelcome mats” consisting of sheets of plywood studded with three-inch nails placed around the feeders—nope. Camera traps captured young bears playing on those.
“We joked that we were studying bear cognition for a while,” says Branch. Finally they found a way to keep the birdseed out of reach from bears, mounting the feeders onto a square frame and hanging it from tree branches using a system of pulleys.
The snow posed challenges to the scientists, too. Early on, they didn’t have snowmobiles well suited for traveling up steep mountains in the thick of winter, so they sometimes snowshoed a mile through snow up to 15 feet deep with all the gear to maintain the feeders. Dampness could be a problem, so they’d set up portable shelters to huddle under if it started snowing while they were programming the feeders and RFID chips.
“I grew up in northern Russia, and then I worked in Siberia,” says Pravosudov, “and I’ve never seen [snow] anything like this.”
Ultimately, the team finished troubleshooting and bear-proofing a field-study system for measuring cognition in wild Mountain Chickadees. Behavioral tests on captive birds in a lab can provide a snapshot of how birds from different groups differ in a single moment, or over a single season. But to study how natural selection acts on the particular traits of spatial-memory ability over time, over multiple generations, the tests must be conducted while following the lives of birds in the wild. The RFID tags deployed on the bird feeders and Mountain Chickadees in the snowy backcountry of the Sierra Nevada gave Branch, Pravosudov, and their colleagues a means to do that.
“It’s a very organic way of addressing spatial memory,” says Isabel Rojas-Ferrer, who studied songbird cognition for her PhD at the University of Ottawa. Rojas-Ferrer was not involved in the Pravosudov lab study, but she is familiar with the lab’s work, and she points out that it’s imperative studies like this be conducted in the wild.
“There are many questions that obviously require lab work,” says Rojas-Ferrer. “But especially when we’re talking about the evolution of cognition, the evolution of learning, we have to look in naturalistic environments because the noise [the variable conditions in which birds live their day-to-day lives] is very important for the development of this process. When you do lab work, it’s a measure of potential and not necessarily a measure of ability, of what is actually going on in the field.”
Beginning in 2014, Branch worked on a series of studies showing that high-elevation female Mountain Chickadees prefer high-elevation males; that high-elevation and low-elevation males sing different songs; and that females invest more resources in raising babies fathered by males with greater spatial memory abilities. The Pravosudov lab was creeping ever closer to showing that these differences in the birds’ brains and abilities were not rooted in their experiences, but hardwired by natural selection.
Then, in 2019, a study published in Current Biology and led by Pravosudov PhD student Ben Sonnenberg appeared to clinch it. By now, members of the Pravosudov lab had been able to follow the same individuals in the wild for several years, identifying them by their unique leg bands and assessing their performance on the feeder test multiple times, beginning when they were juveniles that had yet to experience winter on the mountain. Analyzing what was happening in the community over time led the scientists to an important conclusion. Adults had better spatial memory, on average, than first-year juveniles, but not because juvenile chickadees got better at the test as they grew up. Instead, the best performers among the juveniles were the ones most likely to survive to adulthood. Birds who couldn’t compete when it came to spatial memory were being weeded out by nature. It was, quite literally, survival of the fittest—with fitness in this case determined by a bird’s natural cognitive abilities.
The research had its skeptics, though. Upon publication of the Sonnenberg-led study, an animal-cognition scientist in the United Kingdom made a public call for further research, saying that the finding that superior spatial memory was inherent, not learned, needed to be proved by identifying the corresponding alleles (genetic variations).
The next step for the Mountain Chickadee research was clear: It was time to delve into their genes. And to do that, Branch and Pravosudov needed to find a geneticist.
The Genetics Behind Cognitive Abilities
Scott Taylor is a professor at the University of Colorado who made a name for himself studying the genetics of bird hybrids—including hybrids between Black-capped and Carolina Chickadees, work done during his postdoctoral research stint at the Cornell Lab of Ornithology. Branch invited him to come to Reno and give a talk about his genomics research on birds for the graduate students there.
“After my talk, Vladimir was like, ‘Do you think we could use some of the same techniques you’ve been using … to investigate the genetic basis of cognitive variation?’” says Taylor. “And my initial reaction was, ‘Probably not.’”
Much of Taylor’s work on the genetics of hybrid birds had focused on the colors of their feathers.
“[Plumage color] is a relatively simple trait,” he says. “You’re either black or you’re yellow.”
Cognitive abilities, on the other end, occur along a complex spectrum. Further complicating things, the numbers of study subjects in the Pravosudov lab’s chickadee research were relatively small, limiting the potential sample size for genetic analysis.
“But,” Taylor recalls telling Pravosudov, “we could try, right?”
Together, members of the Taylor and Pravosudov labs, led by Branch and postdoctoral fellow Georgy Semenov at the University of Colorado Boulder, selected the highest- and lowest-performing Mountain Chickadees on the spatial memory test from the research sites in the Sierra Nevada, a total of 42 birds. Using the closely related Black-capped Chickadee as a reference, they started with data on 41 million individual points on the genome for each bird, then used a series of analyses to narrow down which genetic variations appeared to be most strongly associated with the differences in the birds’ error rate on the RFID feeder test.
According to Taylor, they used methods typically applied in much larger studies, such as searching the genes of thousands of people for associations with a certain disease—not looking for links between the genomes of just 42 birds to a behavior measured in the uncontrolled environment of the field. But it worked.
“The results are really exciting,” says Taylor. In research published in Current Biology in 2022, he and the team identified a long list of genes tied to chickadees’ performance on the feeder test—genes that, in humans, chickens, and rodents, had previously been linked to characteristics such as neurogenesis (the process through which new neurons are formed), neuron growth and development, and learning and memory.
They already knew, thanks to Pravosudov’s past work, that chickadees’ ability to quickly recall which RFID feeder they could retrieve seeds from was linked to the size of their hippocampi and the number of neurons within them. But now they had evidence that these physical traits were tied to underlying genetic differences between the birds, rather than a product of their environment.
“Here we see the genetic signature of this trait,” says Taylor, “genes that could actually lead to that physical difference.”
Next up: Genetics, Cognitive Flexibility, and Climate Change
There are always more questions to explore. Pravosudov, for example, is interested to see how things change on the mountain as the environment shifts due to climate change. In particular, he wants to study any shifting in the relationships among high-elevation and low-elevation Mountain Chickadees.
Previous work in his lab has shown that high-elevation chickadees pay a price for their superior smarts, and that price is social subordination. When tested in a lab setting, high-elevation chickadees are slower to explore new environments than their low-elevation counterparts, and less aggressive toward their own reflections in mirrors. If a high-elevation and low-elevation chickadee are placed in the same room, the low-elevation bird consistently chases off the high-elevation bird and claims the best perches for itself, like a jock bullying a nerd.
“So hypothetically,” says Pravosudov, “there’s good reason to think that if everything’s going to get warmer and warmer and the snow’s going to melt, the smart birds will disappear.”
The chickadee research will continue, thanks in part to a new $2.7 million grant from the National Science Foundation to build on the results of this initial genetics study. But for Branch, who is now in a faculty position at the University of Western Ontario after completing a postdoctoral fellowship at the Cornell Lab, seeing genetic results that align with her team’s previous research findings was cause for reflection—a satisfying moment of validation after several years of hard work trudging through the snowy Sierra Nevada backcountry.
“It was so cool. It was like, see, we’re not crazy!” she says. “To see the genetic component back it up is really exciting.
“And, I think, pretty convincing.”
Rebecca Heisman is a freelance science writer based in Walla Walla, Washington. She is the author of the forthcoming book Flight Paths, about the history, science, and quirky personalities behind bird migration research.
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