Archaeology and palaeontology in underwater caves

Some of the most important evidence about the first people in the Americas and the animals they lived alongside lies in flooded caves. The reason is the same sea-level history that shaped the caves themselves: passages that were dry during the last glacial period served as shelters, water sources and traps, and were then sealed under water as the ice melted. Low oxygen, darkness and stable temperatures have preserved what was left behind.

Why flooded caves preserve so much

The team that described the Hoyo Negro skeleton in 2014 explained that cave systems in the Yucatán were reachable through sinkholes for much of the last glacial period, acted as natural traps for people and animals, and were flooded between about 10,000 and 4,000 years ago as glaciers melted ^[1]. In The Bahamas, a 2007 study of Sawmill Sink attributed its exceptional fossils to burial in anoxic salt water beneath a hydrogen sulfide layer ^[7]. Preservation does not mean that bones are robust. At Hoyo Negro, the project notes that the bones have kept their shape but lost almost all their protein, which makes direct radiocarbon dating difficult ^[4].

Hoyo Negro and Naia

In 2007 cave divers Alberto Nava Blank, Alex Alvarez and Franco Attolini, exploring an unmapped part of the Sac Actun system in Quintana Roo, found a pit up to 55 m deep that they named Hoyo Negro, Spanish for black hole ^[5]. It is a bell-shaped collapse chamber about 62 m across; the three passages that lead into it lie about 10 m below sea level, and animal bones rest on ledges and boulders between 40 and 43 m below sea level ^[1]. When the cave was dry, the skeletal material lay about 600 m from the nearest entrance, and today the site can be reached only by technical diving teams ^[1].

On the floor lay a nearly complete human skeleton, catalogued as HN5/48 and named Naia by the divers ^[5]. The 2014 study in Science described her as a slight young woman about 149 cm tall, aged 15 to 16, whose broken pubic bones are consistent with a fall into a shallow pool from one of the upper passages ^[1]. Two independent lines of dating were combined: radiocarbon dating of tooth enamel, and uranium-thorium dating of small calcite growths that had formed on her bones while the chamber was still air-filled. Together they placed her death between about 13,000 and 12,000 years ago ^[1]. Her mitochondrial DNA belonged to haplogroup D1, a lineage derived from Beringia that is shared with modern Native Americans; the authors concluded that differences in skull shape between the earliest Americans and later Native Americans probably arose through evolution within the Americas rather than separate ancestry ^[1][2].

The project, run under Mexico's national institute of anthropology and history (the INAH underwater archaeology branch) with the University of California San Diego, recovered accessible bones in 2014 and 2016 under permits from Mexico's archaeology council, and reports 98 bone elements and 30 teeth recovered so far ^[3]. Further study suggested Naia had given birth at least once and had healed fractures in her left forearm ^[3].

The animals around her are just as significant. As of December 2017 the project had recognised at least 34 individuals of 13 species on the pit floor and 8 more animals, including one additional species, in the connecting tunnels. Seven species, half of the assemblage, are extinct, among them a gomphothere (an elephant relative), three species of giant ground sloth, sabre-toothed cats, a short-faced bear and a wolf-like canid ^[4]. Dating so far puts one gomphothere at between 19,000 and 36,000 years and one bear at about 13,000 years ^[4]. Sediment cores from the connecting cenotes show that the pit floor was under water by at least 9,850 years ago and that the pit became inaccessible to people and animals from about 8,100 years ago ^[5].

Hoyo Negro is not isolated. The 2014 paper noted eight partial human skeletons found about 20 km to the south in the Tulum region, thought from their depth to predate 10,000 years but without reliable radiometric dates ^[1], and a 2020 study counted remains of at least ten individuals from the Pleistocene-Holocene transition in Quintana Roo's caves ^[6].

Ochre mines in the dark

Why did early people go deep into these caves? A 2020 study in Science Advances, involving members of the exploration group CINDAQ, reported the first Paleoindian-age underground ochre mine found in the Americas ^[6]. In three cave systems near the coast (Sagitario with its La Mina section, Sistema Camilo and Monkey Dust), divers and researchers documented extraction pits, digging tools made from broken speleothems, piles of shattered flowstone, stacked stones that appear to have marked routes, and hearths with charcoal from resinous wood. The activity spanned roughly 2,000 years, between about 12,000 and 10,000 years ago ^[6]. More than 7,000 m of the Sagitario system had been mapped, and the mined area of La Mina alone covers about 900 m of interconnected tunnels ^[6]. The authors concluded that red ochre was a valued resource worth prospecting for in complete darkness ^[6].

Work continues. CINDAQ's 2025 report describes an INAH project begun in 2024 on the prehistory of the Yucatán through evidence in caves and cenotes, studying ochre mining, calcite and charcoal, and a related project using mobile photogrammetry, ground-penetrating radar and satellite positioning to understand how people and animals entered caves that were then dry ^[13].

Sawmill Sink, The Bahamas

In 2004 diver Brian Kakuk found a complete tortoise skeleton on the peat-covered debris cone of Sawmill Sink, an inland blue hole on Great Abaco ^[7][8]. Excavation funded by the Antiquities, Monuments and Museums Corporation of The Bahamas followed ^[8]. The 2007 study in PNAS reported 38 non-fish vertebrate taxa, including a previously undescribed extinct tortoise, 42 individuals of the Cuban crocodile, 27 bird taxa and four bat species, together with plant fossils ^[7]. Radiocarbon dates on the peat span roughly 4,200 to 1,000 years ago, and a human tibia dated to about 1,050 to 920 years ago is the oldest directly dated human bone in the Bahamian archipelago ^[7]. The authors noted a gap of about 1,500 years between that human date and the youngest dates on extinct animals, which they expected further dating to narrow ^[7].

Florida springs

Florida's springs have yielded Ice Age bones for more than a century. A summary prepared for the 1998 Wakulla 2 expedition records that in 1930 mastodon bones were found in shallow water while a swimming area was being built at Wakulla Spring and that the Florida Geological Survey helped collect the skeleton ^[9]. In 1955 and 1956, dives by Wally Jenkins, Garry Salsman and companions found mastodon, mammoth, deer, camel, ground sloth and bear remains along with Paleo-Indian spear points, lifting heavy bones from depths of up to 60 m ^[9]. The State Archives of Florida hold photographs of divers recovering mastodon bones at Wakulla in the 1930s and 1950s, and note that stone tools from the time of mastodons and mammoths have been found in many large springs ^[10].

At Peacock Springs, the park's history mentions fossil evidence of giant sloths, camels, sabre-toothed cats and mastodons, and Paleo-Indian presence in the area by about 12,000 BCE ^[11]. One part of the cave, the Crypt, was named after the skeletal remains of a large turtle that Sheck Exley found there in 1975 ^[12].

Looking without touching

Most of this evidence is fragile and its scientific value depends on context: where a bone lies, what is around it and what has grown on it. The Hoyo Negro project has relied heavily on photography, video and three-dimensional models made from photographs, so that researchers can study and annotate the site remotely and sample only what is needed ^[14][1]. Florida's Peacock Springs park rules state that fossils and artefacts must not be disturbed or moved ^[12]. Researchers in Mexico work under permits from national authorities ^[3]. For recreational divers, the practical lesson is that archaeology in caves is a matter for permitted research teams, and that an unrecorded find moved by a visitor can lose most of its value.