WE MIGHT BE UP A TREE

W‌hen Spanish explorer Francisco Vázquez de Coronado and his men traveled north from Mexico in 1540 into what would later be called Arizona, they were searching for fabled cities of gold. But accounts from the expedition also noted they were on the lookout for a different kind of treasure: los álamos, the cottonwoods. The towering canopies of green signaled that life-sustaining water and abundant shade were near.

Today, los álamos are as treasured as ever in Arizona for their beauty, their cooling canopies and the biological diversity they support. But scientists say that compared with when Europeans first set foot in the Southwest nearly five centuries ago, 95 percent of cottonwood habitat in Arizona has disappeared. The most precipitous decline has come in the past 200 years, as the result of overgrazing from cattle, the damming of rivers and groundwater pumping to support development. And then there’s climate change, which has subjected Arizona’s cottonwoods to record heat waves along with record drought.

There still are spectacular cottonwood groves across the state, ranging from Sabino Canyon in Southern Arizona, to Sedona’s Oak Creek, to Phantom Ranch at the bottom of the Grand Canyon. But ecologist and retired Northern Arizona University professor Tom Whitham says

the groves we marvel at today represent just small remnants of what once were abundant riparian oases across the Southwest. And Whitham warns the continued degradation of cottonwoods poses an existential ecological threat that extends well beyond the loss of the trees themselves.

“Cottonwoods play a very outsize role in the biology and biodiversity of the American Southwest,” he says. “They basically define riparian habitats.”

A leading authority in cottonwood research, Whitham has been studying the trees for more than four decades and has documented their role as a “foundation species” that determines the overall health of riparian ecosystems. According to Whitham, more than 1,000 different species — from beavers and birds to insects and fungi — depend on the trees, in one way or another, for their survival. “If the trees die, then the habitat that all these other organisms depend on is just gone,” he says.

Yet there is hope. Whitham and a cohort of more than a dozen scientists — from Northern Arizona University, Phoenix’s Desert Botanical Garden and other institutions — have demonstrated that cottonwoods in Arizona are evolving to endure increasingly harsh environmental conditions. And the scientists are trying to help the trees in this fight through a novel application of genetics in cottonwood ecology.

But climate change shows no signs of slowing down. And the clock is ticking on how much longer the cottonwoods and their riparian habitats in the desert Southwest can hold on. Whitham and his colleagues are determined to crack the genetic code in time.
 

IN AUGUST, I join four DBG scientists who collaborate with Whitham as they take their high-tech genetic research into the field. We gather at the Walnut Creek Center for Education and Research in the Prescott National Forest, where the scientists pitch their tents near a drainage that’s lined with towering cottonwoods. Some of the trees along the creek are around 100 feet tall and perhaps up to 200 years old. Like all mature cottonwood groves, the canopies of the trees form a protective dome over the creek drainage, allowing species that rely on shade and lower temperatures to thrive.

But rather than study the well-established grove, the scientists have come to research what they call a “common garden” that contains dozens of young cottonwoods planted three years ago, primarily for the purposes of genetic research. While the trees were watered for two years through an irrigation system, the moisture was cut off to some of the plants earlier in the summer as a way to mimic drought conditions.

The scientists want to analyze how different species of cottonwoods respond to heat and drought — and perhaps discover how their specific genetic traits could better endure climate change. The common garden contains the two species of cottonwoods found in Arizona — Fremont (Populus fremontii) and narrowleaf (Populus angustifolia) — along with their naturally occurring hybrids. The latter are unique in their genetic makeup for having inherited traits of both the Fremont and the narrowleaf species.

The Fremont cottonwood, with its broad, heart-shaped leaves, is adapted to desert heat and found in riparian areas throughout the Southwest, at elevations ranging from near sea level to about 6,000 feet. The appropriately named narrowleaf cottonwood, which has elongated leaves shaped more like a surfboard, is adapted to cooler climates and grows at elevations from around 5,000 to 8,000 feet. In regions where their habitat overlaps, it’s common for Fremonts and narrowleafs to naturally hybridize as male pollen fertilizes female flowers to produce millions of cottony tufts of airborne seeds.

Located in Central Arizona at an elevation just above 5,000 feet, the Walnut Creek Center is a natural cottonwood hybrid zone where both cottonwood species and their hybrids could potentially thrive. And by subjecting all the trees in the common garden to the same conditions, the DBG scientists are able to attribute different responses in the cottonwoods to genetic traits, rather than environmental factors.

“I am interested in figuring out how cottonwoods can survive during climate change and where they can survive,” says DBG plant researcher and laboratory manager Alexandra Schuessler.

“The fact that cottonwoods span diverse environments in Arizona, from low desert to mountain forests, allows us to study their adaptations,” adds Brad Posch, a postdoctoral research scientist at the DBG. “We are trying to find out how hot or dry it can get before the trees can no longer handle it.”
 

Schuessler, Posch and I sit under a large oak tree, taking a break in the shade before returning to the common garden to collect more data. The two researchers are weary after rising in the middle of the night to study the cottonwoods when the temperature was lowest. Soon, they’ll venture out under the blazing sun, when the daytime temperature is at its highest, to see how things have changed for their study specimens.

In 2023, Posch and his colleagues at the DBG conducted a study that evaluated the ability of Fremont cottonwoods to endure intense heat. The trees were located in a common garden at the DBG facility in Phoenix, and the study fortuitously coincided with a record-setting heat wave in the Phoenix metro area. The temperature climbed above 113 degrees for 17 consecutive days during the hottest summer on record. (That record would be broken in 2024, along with many other heat-related records for the region.)

The 2-year-old cottonwood saplings in the 2023 study were well watered during the heat wave, and researchers were impressed by how the trees efficiently cooled their leaves through a process called transpiration. As long as there was ample soil moisture, the saplings pulled water through their roots and sent it to the leaves, where it exited through pores called stomata. That cooling system is similar to the way humans bring their body temperature down by sweating. And even though the average air temperature during the study was higher than what Fremont cottonwoods were historically used to, the trees managed to cool themselves as long as the water supply remained constant.

However, when researchers cut off the water to mimic drought conditions, the plants began to wither in just a few days. They dropped leaves and would have eventually died if the water had not been turned back on. The study, then, showed that the key to cottonwood survival is making sure their long roots stay tapped into a constant water source, such as a perennial stream or underground aquifer.

Unfortunately, long-term drought caused by climate change is robbing cottonwoods of the predictable precipitation that keeps streams flowing and aquifers recharged. And making matters worse is an increase in groundwater pumping. According to a May 2025 study by Arizona State University and NASA, the amount of groundwater pumped in Arizona has been steadily increasing and depleting underground aquifers faster than nature can refill them. The study noted that over the past two decades, the amount of water taken from Arizona’s aquifers is nearly equal to the total storage capacity of Lake Mead.

The corridor of stately cottonwoods at the Walnut Creek Center is among the many groves across the Southwest showing signs of strain. During my August visit, the rocky creek bed is dry and some leaves are turning yellow six to eight weeks earlier than normal. Even if cottonwoods survive shedding their leaves due to extreme heat or drought, other species — the ones depending on the trees’ shade — may not.

“When we were here last year at this time, the creek was flowing,” Schuessler says. “The leaves are turning from water stress.” She attributes the stress to multiple factors: weak precipitation the previous winter, nonexistent monsoon rains (as of mid-August) and a nearby farmer who’s pumping groundwater to grow alfalfa.
 

Once the temperature reaches the low 90s, Posch and Schuessler gather their instruments and head back into the garden, where rows of shoulder-high cottonwoods grow like corn. They measure the moisture levels on leaves to gauge stomatal conductance, an indicator of how hard the trees are fighting to stay cool.

Meanwhile, I duck beneath the domed canopy of a giant juniper where DBG scientist Susan Bush has set up a makeshift lab. She’s measuring water potential in leaf samples, another indicator of how drought might be affecting the trees in the garden. As classical music plays from her phone, she places freshly cut leaf samples into the chamber of a device she calls “the bomb.” Pressure in the chamber pushes water vapor out of the leaf, giving Bush a moisture reading that she writes down in a journal. Later, she’ll compare the daytime and nighttime readings and calculate how each genotype in the study stacks up when it comes to handling drought.

While Bush continues her work, I venture back out into the afternoon heat, where scientist Dan Koepke is gathering more leaves to put in the pressure device. We walk up and down the rows of trees tagged to identify their species and the location from which they came. There are Fremonts, narrowleafs and a range of hybrids, including the F1, a first-generation hybrid descended from Fremont and narrowleaf parents.

The home territories of the common garden specimens encompass Arizona’s varied terrain, from the lower Colorado River near Yuma to the White Mountains in Eastern Arizona to Jacks Canyon near Sedona. The trees are genetically unique in terms of being evolutionarily adapted to specific geographic locations. The researchers have discovered, for example, that a Fremont growing near sea level has a different genetic makeup than a Fremont found at 5,000 feet.

The DBG study seeks not only to understand how cottonwoods could improve their drought and heat tolerance, but also to build evidence for carrying out “assisted migration.” Results from the Walnut Creek common garden experiment will eventually show that the heat-adapted Fremonts and Fremont-dominated hybrids did better during drought conditions than the narrowleaf plants. As the environment changes and higher elevations become more like lower elevations, in an assisted-migration scenario, such results could support moving Fremont or Fremont-hybrid trees to higher elevations where they’re more likely to survive than narrowleaf trees that can no longer endure increasing temperatures.

And when it comes to restoring cottonwoods to damaged riparian areas, Whitham and the DBG scientists generally believe the most successful strategy is to plant a heat-adapted hybrid, rather than a genetic duplicate of the tree species that’s been there for hundreds or thousands of years.

“We know humans are changing the climate and temperatures are getting hotter,” Koepke says as he stares down at two cottonwoods among the garden’s rows of trees — one with brown leaves, the other appearing healthy. “Do we wait for plant mortality? Or do we try to plan ahead and relocate some of these trees now, to elevations where they will hopefully have a better survival rate in the future?”
 

TWO MONTHS after my visit with the DBG researchers, I meet Whitham at his home in Flagstaff, where he’s nurtured a personal grove of cottonwoods for more than 40 years. The trees are on the banks of the Rio de Flag and just on the other side of his backyard fence.

Whitham planted his first common garden of cottonwoods along Utah’s Weber River in 1982, soon after he earned his doctorate at the University of Utah. He has since authored or co-authored more than 300 peer-reviewed articles on plant genetics and restoration ecology, with much of his research focused on cottonwoods in the Southwest.

“All these trees have been DNA fingerprinted,” Whitham says as he stands amid 20 cottonwoods behind his house. The trees constitute one of the research group’s many common gardens across the state, and Whitham and his colleagues have used these sites over the decades to study genetic traits among cottonwoods.

The climate was cooler and wetter when Whitham moved into his Flagstaff home in the mid-1970s. Back then, it was a rarity for any homes in the mountain town to have air conditioning, and in late spring, the Rio de Flag was a rushing stream filled with snowmelt. Whitham planted both cottonwood species and their hybrids along the stream to see which would fare better. It didn’t take long for the Fremonts to succumb to harsh spring frosts. And over the decades, the narrowleaf trees haven’t done well, either, due to warming temperatures and a decrease in precipitation that leaves the Rio de Flag bone dry most years. But the F1 hybrids, now up to 60 feet tall, are thriving.

“The F1 is succeeding here because it is adapted to greater extremes,” Whitham says. “It has the genes from its parents to survive both low-elevation climates and high-elevation conditions.”

It’s the third week in October, and the leaves in Whitham’s grove are turning bright gold amid unseasonably high autumn temperatures. He picks up an F1 leaf from the ground and shows me that the shape looks like that of a Fremont, but more elongated. “I expect the narrowleaf to eventually disappear from here as they are overtopped by the F1 hybrids,” he adds.

But all the cottonwoods in the Rio de Flag are living on a razor’s edge. Whitham says he thinks the grove is tapped into groundwater about 15 feet below the surface. More dry winters, combined with future development in the area, could drop the water table below the reach of the trees’ roots, ensuring the grove’s demise.

Whitham speaks wistfully of historical records he’s read about the 16th century Spanish explorers who encountered a Southwestern landscape laced with ribbons of green, now long gone. But he’s also convinced that Arizona’s cottonwood groves can be both preserved and restored through a combination of cutting-edge genetic research and water conservation.

“Hybrids may be the future,” he says. “They hold the key to maintaining genetic diversity as climate change pulls the rug out from thousands of years of evolutionary history.”

A gentle breeze drifts overhead as golden leaves of various shapes and genetic traits flutter in the wind. The sound coming from the cottonwood canopy is just like that made by flowing water — an uncanny echo of what keeps the trees and their web of connected species alive.