The cenotes and underwater cave systems of the Yucatan Peninsula are emerging as one of the most promising frontiers for Paleoamerican studies. Following the end of the last glacial maximum, rising sea levels flooded the region’s maze of underground passageways and preserved a diverse Late Pleistocene fossil assemblage. A female human skeleton, named "Naia," found in spatial association with the remains of now-extinct fauna in the submerged subterranean pit of Hoyo Negro presents a unique opportunity for interdisciplinary Paleoamerican and paleoenvironmental research in Quintana Roo, Mexico. At 13,000-12,000 years BP, the young woman’s skeleton represents the oldest nearly complete individual yet found in the Americas.

Investigations have thus far revealed a range of associated features and deposits, which make possible a multi-proxy approach to identifying and reconstructing the processes that have formed and transformed the site over millennia. Recent and ongoing studies involve osteological and taphonomic analyses; absolute dating of human and geological samples; human DNA analyses; and a consideration of site hydrogeology and sedimentological facies. Additionally, innovative recording and imaging techniques are enabling researchers to analyze deposits and their contexts with minimal impact to the site.

Recent research efforts have focused on detailed survey and mapping of the site (and associated submerged passageways and entrances) as well as detailed recording and initial sampling of cave deposits. In 2012, analyses of samples from the human skeleton and a gomphothere resulted in significant findings. Direct radiocarbon dating of human tooth enamel (via AMS) combined with indirect uranium-thorium dating of calcite formations on the human bones produced an age range of 13,000-12,000 calendar years ago. Analyses identified intact human mitochondrial DNA as belonging to D1 – a Beringian-derived sub-haplogroup.

One of the enduring mysteries of the First Americans is why, in terms of cranio-facial morphology, they look so different from modern Native Americans. This has led to the idea that perhaps the earliest Americans migrated into the New World from regions other than Siberia. Indeed, Naia shares much in common with the few Paleoamerican crania known to science. However, her Siberian/Beringian-derived mtDNA is shared by modern Native Americans. This link between a Paleoamerican (for whom we have a complete skull) and modern Native Americans suggests that the morphological differences we see between the two groups are the result of evolutionary changes that occurred within the Americas.