Ancient Ecuadorian Genomes Show 1,500 Years of Continuity and a Baby With Tuberculosis DNA

A baby who died on the Ecuadorian coast about 2,300 years ago may have carried tuberculosis, centuries before Columbus. Researchers recovered DNA from the infant’s skull that points to the bacterial group behind the disease. The same study sequenced three more ancient people and suggests that one coastal population lived in the same place for roughly 1,500 years.

Four people from Salango

The study comes from a team led by John Lindo of UC Berkeley and Richard Lunniss of the Universidad Tecnica de Manabi, along with colleagues, and appears in PNAS Nexus. The researchers sequenced genomes from four people buried at Salango, a site on Ecuador’s central coast. Two belong to the Very Early Guangala phase, about 2,300 years ago. One belongs to the Early Guangala phase, about 1,900 years ago. One belongs to the Early Manteno phase, about 740 years ago.

The genomes have fairly low coverage, between about 0.5 and 2.3 times, so the team worked with limited data from each person. Even so, the four individuals looked genetically similar to one another.

A population that stayed through big changes

That similarity matters because Salango saw a lot of change over those centuries. Around 330 BCE, about 2,360 years ago, an eruption of the Pululahua volcano disrupted life in the region and, according to the paper, ended the Formative tradition. Later, chiefdoms rose and a maritime exchange network built around Spondylus shell connected coastal communities with distant partners.

One might expect such upheaval to bring new people. The genomes suggest otherwise. The results point to a mostly stable local population, so the cultural shifts likely happened within the same community instead of through large-scale replacement.

The team also estimates that the ancestors of these coastal people split from other southern Native American lineages about 9,800 years ago, with a confidence range of roughly 9,600 to 10,100 years. Estimates like this depend on modeling and on the limited data available, so readers should treat the figure as approximate.

An infant with signs of tuberculosis

The most striking individual is an infant, six to nine months old, from Burial 369. The baby’s skeleton shows lytic lesions, which are spots where bone has eroded. They appear on both shoulder blades, both forearms, the right hip, the right first rib and the ends of five left ribs. The skull is porous on the outside and grooved on the inside.

Those changes fit tuberculosis. DNA from the left petrous bone, a dense part of the skull, adds weight. A classification program assigned 8,367 DNA reads to the Mycobacterium tuberculosis group, the family of bacteria that includes the tuberculosis pathogen.

Why this matters

Genetic evidence of tuberculosis in the Americas before European contact is rare. If the result holds, it adds to the case that the disease circulated in South America long before ships arrived from Europe. It also shows that a baby on the Pacific coast lived and died with the illness more than two millennia ago.

The continuity result matters too. It gives archaeologists a clear genetic backdrop for Salango, a place where pottery styles, trade and politics changed while the people stayed.

Caveats and open questions

Four genomes cannot represent a whole region over 1,500 years. Low coverage limits how precisely the team can compare the individuals. Assigning reads to the tuberculosis group is also not the same as a confirmed diagnosis, and one commentator on the study called the 9,800-year split date its weakest number. Larger samples from more sites would test whether Salango’s pattern holds along the wider coast, and more complete bacterial data would show which tuberculosis lineage the baby carried.

For now, the study offers a rare look at one community’s long history and a very young child who may have been among the earliest known tuberculosis cases in the pre-Columbian Americas.

Sources

• John Lindo et al., “Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America,” PNAS Nexus (2026)
• Phys.org: Ancient Ecuadorian genomes reveal 1,500 years of genetic continuity along Pacific coast
• Anthropology.net: 4 Ancient Ecuador Genomes Hint at 1,500 Years of Continuity