Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America
7 affiliations
- 1Department of Anthropology, University of California , Berkeley, CA 94720 ,
- 2Department of Anthropology, Emory University , Atlanta, GA 30322 ,
- 3Department of Anthropology, University of North Carolina at Charlotte , Charlotte, NC 28223 ,
- 4Department of Anthropology, University of Michigan , Ann Arbor, MI 48109 ,
- 5Department of Molecular and Cell Biology, University of California, Berkeley , Berkeley, CA 94720 ,
- 6Laboratorio y Centro de Análisis e Investigación Arqueológica, Üniversidad Interamericana De Puerto Rico - Recinto De Barranquitas , Barranquitas 00794 ,
- 7Instituto de Investigación, Universidad Tecnica de Manabí , Portoviejo 130105 ,
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.
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BibTeX
@article{lindo2026ancient,
title = {{Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America}},
author = {John Lindo and Daniel Rivas Alava and Sara Juengst and Yemko Pryor and Sophie K Joseph and Juan J Ortiz Aguilu and Richard Lunniss},
journal = {PNAS Nexus},
year = {2026},
month = oct,
doi = {10.1093/pnasnexus/pgag323},
url = {https://academic.oup.com/pnasnexus/article/doi/10.1093/pnasnexus/pgag323/9001935},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Ancient Ecuadorian genomes reveal millennia of genetic continuity on the Pacific Coast of South America
AU - John Lindo
AU - Daniel Rivas Alava
AU - Sara Juengst
AU - Yemko Pryor
AU - Sophie K Joseph
AU - Juan J Ortiz Aguilu
AU - Richard Lunniss
PY - 2026
DA - 2026/10/27
JO - PNAS Nexus
DO - 10.1093/pnasnexus/pgag323
UR - https://academic.oup.com/pnasnexus/article/doi/10.1093/pnasnexus/pgag323/9001935
AB - 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.
SN - 2752-6542
ER -