Deep beneath the tropical forests of the Yucatán Peninsula lies a vast subterranean domain few people can explore. Accessible by sinkholes known as “cenotes” and potentially stretching across thousands of kilometers underground, these are the world’s most extensive underwater cave systems.
Their tunnels are dark and flooded now, but they were dry at times during the Late Pleistocene, a period approximately 126,000 to 11,700 years ago. Proof that humans and animals once roamed deep within these tunnels rests in fossils and traces of human activity that have been undisturbed for millennia. That we know of them at all is thanks to the work of highly specialized divers and their collaboration with teams of international scientists.
One particular part of these caves made headlines in 2014. Hoyo Negro (or “Black Hole”) is an enormous bell-shaped pit in Sac Actun, the second largest cave system in the Mexican state of Quintana Roo. Numerous fossils were found in its depths, including Naia, one of the three oldest human skeletons from the Americas known to date.
Three divers—Alejandro Alvarez, Franco Attolini, and Alberto Nava Blank—discovered the pit in 2007. Three years later, Mexico’s National Institute of Anthropology and History (INAH) created the Hoyo Negro Underwater Archaeological Project (Proyecto Arqueológico Subacático Hoyo Negro of the Instituto Nacional de Antropología e Historia), a team made up of paleontologists, archaeologists, and divers from Mexico, Canada, and the U.S.
Diving into the unknown
Roberto Chávez Arce has been exploring those tunnels since 2011, when he was invited to be a part of the project. He is a project co-director and diver, and his phenomenal photography within Sac Actun was one of the windows that enabled scientists above ground to view its contents.
He described the marvels of being able to witness that subterranean world firsthand in video interviews with Gizmodo. But entering that realm is dangerous, not least of which because when they first began, Sac Actun’s tunnels were largely unknown, unmapped, and in total darkness underwater.
Alberto Nava retrieving one of the last vertebrae of Naia in Hoyo Negro. © Roberto Chávez Arce
To explore the tunnels leading to and around Hoyo Negro, divers have to carry all of the mechanisms that keep them safe, including breathing gear, spools of lines to prevent them from getting lost, and lights to see where they’re going. This is on top of the cameras and video equipment they use to document everything.
For added protection, Chávez Arce explained, they carry “spares of the spares. We need redundant gear in case [anything] fails” while they’re in the depths of the cave system.
Getting to Hoyo Negro isn’t a quick journey, depending on where divers enter the cave system. Initially, Chávez Arce and his fellow divers—usually in groups of two or three—would enter Sac Actun from a cenote that was 3,000 feet (914 kilometers) from Hoyo Negro. Simply swimming from that entrance to the pit would take a little under an hour, an important detail when one is dependent upon the limited oxygen of diving gear.
But that changed over time. Accessing Hoyo Negro is currently much faster for two reasons. They have since discovered another cenote that is about 250 to 300 feet (76 to 91 meters) from the pit, and the divers are now propelled through the water by motorized scooters that look like torpedoes.
At first, mapping the cave system meant using rudimentary implements, including “a compass and lines and counting distances with a tape measure,” Chávez Arce said. Eventually, however, they transitioned to structure-from-motion (SfM) photogrammetry. He explained this as taking “pictures that overlap,” then feeding those pictures into software, which creates a 3D point cloud. “That,” he noted, “took us a long time,” requiring “many, many hours of diving.” But what it created is an astounding virtual model of Hoyo Negro and parts of Sac Actun, one that brings the underwater world to scientists who wouldn’t be able to access it otherwise.
One of his photos is enough to show the scale of Hoyo Negro. In it, artificial light illuminates the walls of the pit and the jumble of rocks at its base. The two divers, shown swimming midway to its ceiling, are dwarfed by its dimensions. At its rim, Hoyo Negro has a diameter of over 120 feet (32 meters); the bottom of the pit expands to a diameter of over 203 feet (67 meters); and it is almost 200 feet (60 meters) deep. It’s huge.
When the caves were dry, accessible and possibly inviting
Studying sediment cores and ancient bat guano deposits and seeds helped the team determine that the water level in this chamber, and in the three tunnels that connect to it, fluctuated over time. They found that water reached the bottom of Hoyo Negro at least 9,850 years ago. Water in the cave system continued to rise in step with sea level increases, so that by approximately 8,100 years ago, Hoyo Negro and its upper passages were flooded, and by about 6,000 years ago, the entire cave system was underwater.
This is significant because it indicates when people and animals could access the cave, as well as providing a clue as to why they would do so. Notably, the Pleistocene ecosystem of Quintana Roo was a lot different than what it is now. Instead of a lush jungle, the area was more of a savanna. The drinking water available within the caves would have been a powerful draw. So, too, the cooler temperatures in the heat.
But a dry cave still has dangers, as demonstrated by the fossils that remain within it. Falling 10 stories into this pit meant perilous injury, if not immediate death, and its high walls prevented escape. The bones of the lone human among the many mammal fossils found at the bottom of Hoyo Negro are a case in point.
The same three divers who discovered Hoyo Negro also found Naia, who was named by team member and diver Susan Bird. Bird was responsible for carefully handling Naia’s remains underwater for measurements before eventually transporting them to safety in Mexico, after signs that outside divers were disturbing the site. Naia is neither the first nor the only human found in these cave systems, but, dated to approximately 12,970 to 12,770 years, she is the most complete human skeleton of the three oldest known to date in the Americas.
Sadly, her short life ended in tragedy. Her adult teeth hadn’t fully developed, and tell-tale signs in her limbs indicate that she was not yet 20. Based on these factors, the team estimates that she died when she was approximately 15 to 17 years old and suffered a broken pelvis that occurred at or around the time she died by falling into the pit.
“She landed right on her pubic bone,” Dr. James Chatters explained in a phone interview with Gizmodo. “That’s what broke on both sides.”
Chatters is another co-director of the project who, like Chávez Arce, has been on the team since 2011. In 2012, he was asked to be the scientific lead by the then-principal director Pilar Luna Erreguerena, who has since passed away. He added that the unhealed injury on the pubic bone suggests it happened around the time of death. Healed spiral fractures in one of her forearms, however, “suggests rough handling either as a teenage girl or as a child. Because it’s healed, it’s hard to know when” those injuries occurred, he explained.
Analysis of her bones, scattered throughout the bottom of the pit, offers more insight about this young woman. She was “very slightly built,” Chatters said, at about 4 feet and 8 and a half inches tall (about 1.5 meters). Her pelvic bones reveal that she gave birth at least once. But dental wear and other analyses offer a startling insight into her diet, suggesting “she was not getting her food from the sea,” Chatters said, which is surprising since Hoyo Negro is only a little more than 4 miles (7 km) from the coast.
Their research indicates that she experienced seasonal protein deficiency throughout her life, “which would not have been the case had she been using the sea as a source of protein,” he explained, as marine life would have been plentiful year-round. And this, he said, indicates that “her people weren’t marine-adapted. They weren’t using the shoreline as a food source. Which argues against the idea that the earliest people came in by the Pacific coast,” as they would be expected to have a marine-based diet.
Why Naia was in the cave, or for that matter, any of the other humans found in neighboring cave systems, continues to mystify the team.
“Were they in there getting clay?” Chatters wondered, suggesting that clay provides minerals needed during pregnancy, for example. Or, he mused, could they have been hunting hibernating ground sloths or bears? “Or were they in there for water? We don’t know.”
What they do know, however, is that all of them accessed the caves at a time when the sea level was much lower. So “either they got lost and died in there, or they were taken in there as a mortuary practice,” he said. Or, in Naia’s case, died as a result of a terrible accident.
Remnants of human activity
But the traces humans left—versus the bones of those who died—indicate exactly why those particular people ventured underground.
In other Yucatán cave systems, there is widespread evidence people were mining ochre, a mineral that, in this case, produces a red pigment. “Red ochre is the most commonly identified inorganic paint used throughout history worldwide,” wrote a team in a 2020 paper detailing the evidence of mining in those caves. They explain that its use includes decoration, burial practices, and rock paintings. But why people in the Yucatán valued it is yet another mystery, according to Chatters, who is a co-author on that paper. “This particular ochre has a fairly high arsenic content,” he said, suggesting that “it would be good for killing lice.”
Evidence of human activity is abundantly visible in cairns, or piles of stones, that they left as markers along the way. It can be seen in the profuse amount of broken stalactites and stalagmites they removed to get through passageways or used as digging implements. Their digging efforts left extensive trenches or pits made when removing ochre from the ground, many of which extend from about 246 feet (75 meters) to about 328 feet (100 meters). “Fire-reddened stones and earth” and charcoal suggest the use of fire to combat the darkness. “[T]he ceiling above these charcoal-bearing features is still visibly blackened, evidently by the soot” from fires they constructed, according to the paper.
And “there is some [evidence of ochre mining] in Sac Actun,” Chatters explained, “but it hasn’t been reported yet.” Just one aspect of exciting research yet to be published from that cave system.
What entered didn’t always exit
Humans, however, weren’t the only ones to leave traces in Sac Actun. Divers found fossil footprints in one of the tunnels leading from Hoyo Negro that paleontologists on the team have attributed to animals we associate with caves today: bears.
Among the many large fossil mammals found in Hoyo Negro, most are of an extinct type of short-faced bear known as Arctotherium wingei.
“We have at least nine individual bears from the Hoyo Negro pit, and most of them are adults,” explained Blaine Schubert in an email to Gizmodo. Schubert is a professor and museum director at East Tennessee State University who is also a member of this project. There is “at least one individual that was a younger subadult,” he added.
Although the size of these bears is estimated at a hefty 330 pounds (150 kilograms), the bears in Hoyo Negro were among the smallest of the extinct short-faced bears previously known only from South America. The largest of the South American short-faced bears (Arctotherium angustidens) may have weighed more than 2,200 pounds (1,000 kg).
Hoyo Negro is the first to reveal fossils of Arctotherium wingei outside of South America. They are the best preserved from any fossil site to date, and, Schubert notes, if further research into the fossil footprints within the tunnel indicates that “they do represent Arctotherium, then they [will also] represent the first record of their tracks.”
Among the other “firsts” from Hoyo Negro is the discovery of Protocyon troglodytes—a “wolf-like canid” according to Schubert—among the fossils in the pit. Protocyon was also previously thought to be endemic to South America.
“This,” he said, “is a dramatic expansion in their distributions and has interesting biogeographic implications. In addition, whereas we had fossils of these animals from South America before, we didn’t have a great fossil record.” Hoyo Negro, he continued, offers “complete skeletons, which allows us to learn a lot more about the animals.”
Protocyon and saber-toothed cat fossils are among the extinct carnivores found in the pit, but some fossils are of species that continue to exist today, even if no longer in the Yucatán. These include the puma and ocelot, he said, along with the omnivorous coati and skunk.
“All the animals would have been attracted to the cave (and probably the pit) by the smell of fresh water, which would have been really limited at the surface,” he explained. “In addition, carnivores would have been attracted by the smell of dead animals floating” at the bottom of Hoyo Negro.
A new giant ground sloth revealed
Another animal associated with caves—at least during the Pleistocene—is the ground sloth, and Hoyo Negro has its share. These include fossils of Shasta ground sloth (Nothrotheriops shastensis) and Xibalbaonyx exinferis—a species of ground sloth initially discovered by a separate team in a neighboring cave system and described in 2020. The team also discovered an entirely new genus and species, which they named Nohochichak xibalbahkah, meaning “the great claw that dwells in the underworld.” It is a combination of the Mayan word “Nohoch,” which means “great,” and “ich’ak,” which means “claw.” “Xibalba” references the underworld of the K’iche Maya, people that originate both today and in the deep past in Guatemala. “Ahkah” means “dweller.”
Greg McDonald is a former BLM paleontologist and the sloth expert for the Hoyo Negro project. Nohochichak, he explained in a phone interview with Gizmodo, has huge hip bones. “If you look at the body, it’s sort of pear-shaped. The center of gravity is shifted towards the back of the animal.” That indicates that they would be able to “sit upright while they were feeding,” using “their arms and their claws to hook branches to bring them down to their mouths to bite off leaves and twigs and fruit.”
The size of this sloth is comparable to the enormous Jefferson’s ground sloth (Megalonyx jeffersonii) which is estimated to have been more than 2,200 pounds (997 kg).
The discovery of this new sloth, as well as the existence of Arctotherium wingei and Protocyon troglodytes, sheds new light on our understanding of the Great American Biotic Interchange, or GABI, a series of migrations between the northern and southern continents that occurred at various points depending upon land access and sea levels. Based on the fossil record, for example, ground sloths originated in South America. Unraveling the timing and reasons behind their migrations could help to shed light on evolution and the impacts of Pleistocene climate change.
“Our understanding of North American sloths has been heavily biased by all of the fieldwork done in the U.S. and northern Mexico,” McDonald said. “That is changing, and we are finding different sloths in tropical environments,” thanks to work at Sac Actun and other extensive cave systems in the Yucatán and in Belize. “In a rainforest,” he added, “everything gets recycled” very quickly. “There are very few spots where organic material can be preserved.” Which is one of the many reasons Sac Actun is so unique and important.
The gomphothere in the room
Something the size of an elephant might not immediately come to mind when thinking of caves. And yet, fossils of gomphotheres—extinct elephant-like animals with long tusks—have been found in Hoyo Negro and nearby tunnels, proving that these giant beasts also explored Sac Actun perhaps in search of fresh water.
Roberto and Gomphothere in Hoyo Negro. © Alberto Nava
Joaquin Arroyo-Cabrales, a senior scientist at Mexico’s National Institute of Anthropology and History (INAH) and an expert in proboscideans—the order to which gomphotheres, mammoths, and elephants belong—is also a member of the project. At the time of an email exchange with Gizmodo, he said that they were still studying the gomphothere fossils in Hoyo Negro and other sites within the Yucatán to better understand the gomphothere that roamed these underground caves (Cuvieronius hyodon).
He described these gomphotheres as “smaller proboscideans,” comparing them to today’s Asian elephants, rather than the enormous Pleistocene Columbian mammoth. And he hoped their research might provide insight into why gomphotheres lived in the Yucatán and why the Columbian mammoth—which is known from other parts of Mexico—apparently did not.
It’s yet another hint of the exciting research yet to come. Thus far, 14 years of study within Hoyo Negro is adding more complex threads to the tapestry of evidence life left behind. Researchers presented much of that work last year at the 12th North American Paleontological Convention at the University of Michigan. More research was discussed at this year’s annual meeting of the Society of Vertebrate Paleontology. But, Schubert said, “we still have a tremendous amount to learn about the paleobiology and evolution of America’s fauna, and caves will continue to be a primary resource for these discoveries.”
“Like no other setting,” he continued, “caves allow us to travel back in time and more fully experience the environment in which past organisms lived and died.”
Jeanne Timmons is a freelance writer who rediscovered her passion for paleontology later in life. Her work has also appeared in Ars Technica, The New York Times, Scientific American and Live Science.
