What’s in a packrat’s petrified pee? Just a few thousand years of secrets.

YOU’VE LIKELY BEEN TOLD that a packrat is a thief. A selfish collector. A taker of things in the night. Common wisdom holds that this long-tailed rodent will snatch your diamond rings and gold watches, your loose change and car keys, and hoard them in glistening stockpiles like some miniature, beady-eyed dragon.

Some of that is true. Scientists aren’t entirely sure why, but the rodents in genus Neotoma do seem to possess an instinctual drive toward curation. Even when packrats aren’t living near humans and pocketing our treasures, they gather plant clippings and seeds, which they store in great mounds for future use. Part living quarters, part larder, these so-called middens can also include sticks, stones, bones, and animal dung—the packrat’s own, but also patties and hairy turds discovered out in the world and hauled back for safekeeping. What business do they have with sun-bleached bear femurs and ringtail scat? We know not. 

This obsessive stockpiling of brick-a-brack, however, is excellent news for an array of researchers hoping to study shifting climates, evolving flora and fauna, and even mysterious human treks across ancient deserts. As successive generations of packrats add layer after layer to a midden, they slowly build boulder-sized masses in caves, cliff faces, and other nooks and crannies that can persist for millennia. 

This is where the packrat’s story takes a turn. If you could add up the value of all the trinkets these animals have been accused of filching over the years, the sum would pale in comparison to what scientists say the rodents and their kin have started to give back—one sticky, stinky midden at a time. For around half a century, paleoecologists have been working on using their collections as miniature time capsules to tease out ecosystems long past. Arid regions like the North American Southwest are finally yielding data on ancient plants previously only accessible in areas with ice cores and lake sediments to sample. More recently, the discovery of middens outside of North America has kicked off a new wave of research, especially in places like South America’s bone-dry Atacama Desert. 

More than 20 different kinds of packrat exist across North America alone, and each has its own collecting preferences. N. stephensi specializes in juniper, while N. lepida is more interested in rocks than flora. 

[Related: These insects preserved in amber are still glowing 99 million years later]

But no matter how an individual decides to furnish its midden, it’s its pee that really ties everything together. Literally. To conserve liquid in arid climates, packrat urine is thicker, stickier, and less watery than that of most animals. When they take a leak—as they have a habit of doing all over their constructions—what liquid there is evaporates nearly instantly, leaving behind only waste-products like calcite and calcium oxalates, which are well-known as the building blocks of human kidney stones. These crystallize rapidly in the heat, forming a shiny, viscous shellac known as amberat. Sort of like tree sap mixed with asphalt, the substance solidifies and fossilizes everything it touches. 

Surveying the plunders of rodents who nested with or near ancient humans can uncover truths about where and how our ancestors lived, as well as what environmental forces drove them. Now, with technological advances in DNA analysis, packrats are poised to provide countless new insights into the past of our species and planet.  

Packrat time machine

In 1961, a plant ecologist and an entomologist went on a hike in the mountains above Las Vegas. This is not the beginning of an obscure joke, but rather one of hundreds of ecological surveys conducted around the Nevada Test Site, a 1,360-square-mile tract of land where the US Government detonated around a thousand nuclear devices beginning in 1951. That day, the scientists—Phil Wells, then a post-doctoral researcher of plants at New Mexico Highlands University, and Clive Jorgensen, field director of a team studying insects at Brigham Young University—simply wanted to catalogue what the flora and fauna of a mountain called Aysees Peak. In particular, the young researchers found it strange that there were no stands of juniper trees at its summit, despite the fact that the hardy conifers thrived at similar elevations nearby.

Giving up for the day, the men stopped for a breather on the way back down the mountain, whereupon Jorgensen happened to notice a glob of dark resin beneath a cliff face. Curious, the entomologist broke off a chunk, surveyed its contents, and gave a yelp. He’d found the missing juniper. At first, his discovery made no sense. How could this piece of gunk hold fresh-looking needles when the pair had failed to find juniper trees growing anywhere on the mountain? 

It was only after the duo sent a few samples off to a lab that the mystery began to unravel. Scientists there used radiocarbon dating—a then-newly-discovered technique that measures the age of an organic object based on the levels of naturally occurring carbon isotopes within it—to determine that the needles Jorgenson plucked off Aysees Peak were just short of 10,000 years old. Under normal circumstances, they would have surely decayed and disappeared into the ages, leaving no hint that the trees had ever grown there. Instead, a packrat had collected them, and sealed them with a piss.  

It was in that moment that a new field of study was born, says Julio Betancourt, a retired senior scientist for the US Geological Survey and co-author of Packrat Middens: The Last 40,000 Years of Biotic Change. Up until this point, Betancourt explains, most of what scientists knew about past flora came from pollen deposits. But that field of study, known as palynology, had a blindspot: Pollen is most reliably extracted by coring lake sediments and ice sheets, which are two things you don’t typically find in the arid American Southwest. This made the ancient flora of modern deserts relatively unknowable. But by meticulously sampling the world around them, packrats had quietly and inadvertently been building their own hardy museums of long-lost plant and animal species.

[Related: Millennium- old poop reveals the surprising diversity of our ancestors’ microbiomes]

For more than 40 years, Betancourt has pioneered new ways to use piles of packrat trash as proxies for the past. He’s scaled mountains, accidentally grabbed rattlesnakes, and once stumbled upon a sleeping mountain lion all in the pursuit of rodent piss. He nearly lost a limb in 2000, when a particularly tricky hunt sent him toppling off an Australian cliff. “That leg got pretty trashed,” he says. “It broke 90 degrees to normal.” 

Over the years, he’s handled hundreds of middens—and smelled them, too. At this point, he says, he can give a rough age estimate just by taking a whiff. The youngest ones sock you in the nose with their pungency. But the older they get, he says, the less they offend. He claims some of them can even develop pleasant odors of Pine-Sol and pipe tobacco. 

Of course, to render a midden scientifically valuable, you need more than a sensitive nose. First, researchers must use hammers and chisels to break off pieces of packrat tar. After hauling backpacks full of brick-sized chunks back to the lab, they plunk them into buckets of water and let them stew for a few weeks. This dissolves the amberat that holds the midden matrix together. After a good soak, researchers can pour the resulting slush through a series of ever-smaller screens, like panhandlers searching for gold.

“We’re like forensic scientists, in the sense that we pull these things apart and identify little bitty pieces of flowers and seeds and things like that,” says Claudio Latorre, a paleoecologist at the Pontifical Catholic University of Chile, a new epicenter for midden research in South America. “And then we try to relate those to the plants that are living on the landscape today.”

By comparing data from middens of varying ages, locations, and elevations, paleoecologists can look back in time and track specific species as they migrate through pre-history. For instance, Betancourt stalked ponderosa pine as it lurched northward from Arizona to Montana over the course of a few thousand years after the ice sheets receded. A bit to the south, he and his colleagues upended a long-standing belief that the Sonoran Desert’s assemblage of lifeforms has been virtually unchanged for tens of millions of years or more. In fact, packrat middens confirmed that saguaro, organ pipe cacti, and the other flora that make the Sonoran unique came together just over 11,000 years ago, making this desert extremely young by ecological standards.

Middens have also revealed the histories of other critters. In a study of the Chihuahuan Desert in the American Southwest and northern Mexico, ancient packrats were found to have collected remains of everything from 9,000-year-old pocket gophers to 12,000-year-old pallid bats. The rodents’ leavings have also helped scientists expand the known range for several species, including the eastern cottontail and Gunnison’s prairie dog. 

There’s even more to learn on the miniature scale. Almost all middens contain insects, arachnids, and other creepy crawlies unlucky enough to become trapped in the amberat. This can lead to the description of new species, as happened with Ptinus priminidi, a never-before-seen spider beetle plucked out of a midden in modern-day Arizona in 1976. 

Even the packrats’ poo is precious. Fecal pellet diameter tracks closely with body size, and body size decreases with climatic warming, says Betancourt. In this way, the scientists have actually used rodent droppings to reconstruct temperature changes over thousands of years.   

There is, however, a limit to these gunky time machines. Because radiocarbon isotopes decay to the point of near disappearance around the 50,000 year mark, packrats can’t help us pin dates to organisms that existed before that threshold—say, dinosaurs. But 50,000 years worth of data is treasure trove enough, says Betancourt. And scientists keep finding new ways to make use of the capsules packrats have left behind. These piles of piss may even uncover a few secrets about our own species’ history. 

The cave of wonders

In Argentinian Patagonia, there sits a wide-mouthed grotto known as Cueva Huenul. Formed by eons of erosion between two different kinds of igneous rock, the cave sits right in the middle of where weather from the Pacific Ocean meets weather from the Atlantic Ocean. The site has also served as a crossroads of sorts for ancient humans. Hunter-gatherers have been coming to this place for around 12,000 years, according to radiocarbon dating of sediments on the cave floor. 

As Huenul holds some of the oldest known evidence for the presence of people in South America, scientists have been eager to discover its secrets. Initial results were intruiging: Radiocarbon dating tells paleontologists that the first art appeared smack in the middle of an 8,000-year period where humans seem to have mostly abandoned the McMansion-sized cave. 

Why go to the trouble of posting ancient billboards in the middle of the desert and then hardly ever return?  Best as anyone could tell, the people of this area had succumbed to a more general population decline that was happening throughout the region, says Guadalupe Romero Villanueva, an archaeologist specializing in rock art for the National Scientific and Technical Research Council—Argentina (CONICET) and National Institute of Anthropology and Latin American Thought—Argentina (INAPL).

And so it may have stayed, if it weren’t for a set of midden-making inhabitants taking refuge in the cave over the millennia and lately revealing its secrets: fluffy, bunny-eared cousins to the chinchilla known as viscachas. 

In a study published in Palaeogeography, Palaeoclimatology, Palaeoecology in 2020, scientists sampled fecal pellets and vegetation from 16 vizcacha middens in and around Huenul. Bits of plants and pollen were then used to reconstruct fluctuations of the local climate for the first time. To chase down such patterns, experts must stare through microscopes and count hundreds of individual grains of pollen per sample, some of them no bigger than a white blood cell. It’s painstaking work, says María Eugenia de Porras, co-author of the study and a palynologist at the Center for Advanced Studies in Arid Zones in Chile. But when you start to notice, say, one species associated with wetter climates declining in number and another one associated with dryness rising, it can also be really exciting. “You know that there is a change,” she says. “You can picture a brand-new story based on what the pollen record is telling you.” 

[Related: Ancient dental plaque shows humans have always loved carbs]

In this case, the middens show that the desert surrounding Huenul peaked in aridity in the mid-Holocene, between 9,200 and 5,500 years ago. Importantly, this period also syncs up with that long stretch of time when evidence of human presence in the caves dwindled. It’s also when the first rock art images appeared.

By putting all of these pieces together, the paleontologists have arrived at a new hypothesis about the cave’s role in the lives of the hunter-gatherers. It makes sense that the rock art appeared during such challenging times, says Romero Villanueva, because it’s a device humans created to communicate and share information. These people were frequently on the move, and the drawings would have “released them from the need of face-to-face interaction.” Perhaps the artworks explained where to find resources or provided information about which nearby groups were friendly or dangerous, she says. The more information you have, the less prone you are to failure, because you can make better decisions. 

What’s more, knowing that they still visited Huenul even when the world was drier and more forbidding than ever before suggests that the site might have been of great significance. “Maybe they just went there to do something special, some kind of celebration or something mystical,” says de Porras.  

Romero Villanueva adds that the ancients might have been in search of obsidian. Or perhaps the journey itself was a ritual of some sort. With no passed down oral history or other frame of reference, we may never fully interpret Huenul’s drawings, or learn for whom such messages were meant, she says. 

But the middens, and the climate data they record, add context to the clues the ancient people left behind. “It’s a huge insight about how important it is to be flexible,” says Romero Villanueva. “They were reorganizing their behavior.” That’s insight we’d do well to remember in light of our current climate crisis, she says. 

This would not be the first time middens added nuance to an ancient mystery. Back in the 1980s, Betancourt used them to weigh in on the question of what happened to the Ancient Puebloans of the North American Southwest. Packrat leavings showed what trees had flourished at various points in time, revealing that the once-great civilization cut down forests faster than the landscape could replenish. This resource overuse, perhaps combined with drought and failing agriculture, may well have been the society’s undoing. 

They can also shed light on more recent history. In 2018, a group discovered rodent nests hidden inside the walls of a well-preserved slave trader’s house in South Carolina. Not only did the rats provide a rich source of buttons, stockings, marbles, and other artifacts that date back to the early 1800s, but a small piece of paper torn out of a reading primer suggests that one enslaved individual may have been learning to read. “A compelling thought,” wrote one of the historians in a blog post, “when you consider that reading and writing was illegal for enslaved people in South Carolina at the time.”

Nuggets of information such as these would otherwise have been lost to time, and researchers never know what scraps a midden might be harboring. But soon, finding treasure in these troves of trash could be easier than ever. 

Hitting the jackpot with desert DNA

As illuminating as midden research has been over the last half-century, experts in the field have their eyes on the horizon. The advancement and increasing affordability of technologies like DNA analysis and machine learning mean that in the near future, scientists will be able to wring even more information from the globs of plants, poop, and pee.  

A paper published in 2018 by Latorre, South America’s leading midden pioneer, used DNA analysis of rodent leavings from Chile’s Atacama Desert to show that plant pathogens such as rust fungi have thrived during periods when precipitation spiked over the last 49,000 years. “When you look at the DNA, you not only have the composition of the plants, not only the composition of the insects, but also the bacteria, parasites, and pathogens,” says Latorre. “You can pull apart the entire ecosystem.” The findings provide critical evidence for how wetter weather spurred by climate change could fuel outbreaks of crop-killing pathogens in the years to come. 

Betancourt, meanwhile, is using DNA to look at the bigger ecological picture. In a study published in Ecology and Evolution in 2020 he and a team of researchers used an approach known as shotgun metagenomics to compare DNA extracted from packrat middens dating back as far as 32,000 years ago to known sequences in a database. The experiment revealed traces of bacteria, plants, arthropods, nematodes, fungi, and chordates, showing that under the right conditions, middens may be storehouses of information from across the tree of life. Studies like this hint at the tantalizing possibilities of advancing technology. Because as scientists build out these databases with more and more genomes, from creatures both living and extinct, the number of organisms we can identify from a scattershot examination of a single sample just keeps going up. 

[Related: Humans started transforming Earth a lot earlier than we thought]

Factor in the potential for machine learning—where a computer program learns to scrutinize images of midden contents in place of a human hunched over a compound microscope—and Betancourt says future findings could be “totally revolutionary.” 

It’s even possible that bits of human DNA will emerge in the form of shed hair and scavenged bone. “We probably have lots of stuff that we don’t even know what we have,” says Betancourt. 

Consider a sample Betancourt collected in 2003 that’s been in limbo ever since. A roughly 14,000-year-old midden made by vizcachas in southwestern Argentina yielded a turd from an extinct species of ground sloth. The problem? There were no other records of such creatures inhabiting that particular place.  

Perhaps it’s evidence of a range extension for a known ground sloth species for which we have no DNA. But it could also be a new species entirely. To know for sure, we need more fossils preserved under the Goldilocks-like circumstances that preserve strands of DNA despite the dry heat that fights to destroy them. Middens tend to do the trick, and there are many more to be found. 

While scientists have scoured North America for middens, and efforts to do the same in South America are now kicking into overdrive, the rest of the world lies relatively unexplored. On the southwestern coastal deserts of Africa, dassie rats create abodes not all that unlike those of the packrats or vizcachas. Hyraxes native to much of Africa and the Middle East even produce an amberat-like substance with their urine, called hyracium. In Australia, where Betancourt busted his leg, it’s the stick-nest rat that shows promise.  

“There are probably three or four animals that make these deposits in South America and certainly in other parts of the world that we don’t even know,” says Betancourt. “Central Asia, for example, is a frontier.”

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