Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America

Abstract

The demographic history of pre-Columbian South American populations remains poorly understood, particularly along the Pacific coast where ancient genomic data are scarce. Here, we present the first whole genomes from ancient individuals buried at Salango, Ecuador, spanning ∼2,300 to ∼740 years before present and representing 3 distinct cultural phases. Despite major environmental disruption following the Pululahua volcanic eruption and substantial sociopolitical change, these individuals exhibit remarkable genetic continuity across nearly 2 millennia. Population genetic analyses consistently support long-term continuity at Salango, while demographic modeling suggests that the Ecuadorian coastal lineage diverged from other Southern Native American (SNA) lineages approximately 9,800 years ago (95% CI: 9.6–10.1 ka). Together, these findings are consistent with coastal Ecuador representing a long-standing component of early South American population structure while maintaining connections with neighboring Andean populations through time. In addition, we recovered authentic Mycobacterium tuberculosis complex (MTBC) DNA from an infant dated to ∼2,300 BP with skeletal lesions consistent with tuberculosis, providing molecular evidence for one of the earliest documented cases of MTBC infection in pre-contact South America. Although the moderate pathogen genome coverage precludes detailed phylogenetic interpretation, the combined osteological and molecular evidence expands the record of tuberculosis in ancient South America. Overall, our study provides the first ancient genomic data from Ecuador, establishing an important geographic reference for investigating the demographic and biological history of the Pacific coast of South America.