Ancient genomes reveal a deep history of Treponema pallidum in the Americas

Rodrigo Barquera, T. Lesley Sitter, Casey L. Kirkpatrick, Darío A. Ramirez, Arthur Kocher, Maria A. Spyrou, Lourdes R. Couoh, Jorge A. Talavera-González, Mario Castro, Tanya Hunnius, Evelyn K. Guevara, W. Derek Hamilton, Patrick Roberts, Erin Scott, Mariana Fabra, Gabriela V. Peña, Aryel Pacheco, Mónica Rodriguez, Eugenio Aspillaga, Anthi Tiliakou, Elizabeth A. Nelson, Karen L. Giffin, Raffaela A. Bianco, Adam B. Rohrlach, María los Ángeles García Martínez, Fabiola A. Ballesteros Solís, Antti Sajantila, Shelley R. Saunders, Rodrigo Nores, Alexander Herbig, Johannes Krause () and Kirsten I. Bos ()
Additional contact information
Rodrigo Barquera: Max Planck Institute for Evolutionary Anthropology
T. Lesley Sitter: Max Planck Institute for Evolutionary Anthropology
Casey L. Kirkpatrick: Max Planck Institute for Evolutionary Anthropology
Darío A. Ramirez: Museo de Antropologías
Arthur Kocher: Max Planck Institute for Evolutionary Anthropology
Maria A. Spyrou: Max Planck Institute for Evolutionary Anthropology
Lourdes R. Couoh: Instituto Nacional de Antropología e Historia
Jorge A. Talavera-González: Instituto Nacional de Antropología e Historia
Mario Castro: Museo Nacional de Historia Natural
Tanya Hunnius: Department of Anthropology
Evelyn K. Guevara: University of Helsinki
W. Derek Hamilton: Scottish Universities Environmental Research Centre
Patrick Roberts: Max Planck Institute for Geoanthropology
Erin Scott: Max Planck Institute of Geoanthropology
Mariana Fabra: Museo de Antropologías
Gabriela V. Peña: Museo de Ciencias Naturales y Antropológicas Juan C. Moyano
Aryel Pacheco: Durham University
Mónica Rodriguez: Independent researcher
Eugenio Aspillaga: University of Chile
Anthi Tiliakou: Max Planck Institute for Evolutionary Anthropology
Elizabeth A. Nelson: Max Planck Institute for Evolutionary Anthropology
Karen L. Giffin: Max Planck Institute for Evolutionary Anthropology
Raffaela A. Bianco: Max Planck Institute for Evolutionary Anthropology
Adam B. Rohrlach: Max Planck Institute for Evolutionary Anthropology
María los Ángeles García Martínez: Instituto Nacional de Antropología e Historia
Fabiola A. Ballesteros Solís: Instituto Nacional de Antropología e Historia
Antti Sajantila: University of Helsinki
Shelley R. Saunders: Department of Anthropology
Rodrigo Nores: Museo de Antropologías
Alexander Herbig: Max Planck Institute for Evolutionary Anthropology
Johannes Krause: Max Planck Institute for Evolutionary Anthropology
Kirsten I. Bos: Max Planck Institute for Evolutionary Anthropology

Nature, 2025, vol. 640, issue 8057, 186-193

Abstract: Abstract Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most notably, syphilis1. Debates on a common origin for these pathogens and the history of syphilis itself have weighed evidence for the ‘Columbian hypothesis’2, which argues for an American origin, against that for the ‘pre-Columbian hypothesis’3, which argues for the presence of the disease in Eurasia in the Medieval period and possibly earlier. Although molecular data has provided a genetic basis for distinction of the typed subspecies4, deep evolution of the complex has remained unresolved owing to limitations in the conclusions that can be drawn from the sparse palaeogenomic data that are currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the T. pallidum subsp. pallidum (syphilis), T. pallidum subsp. pertenue (yaws) and T. pallidum subsp. endemicum (bejel) lineages. Our data indicate unexplored diversity and an emergence of T. pallidum that post-dates human occupation in the Americas. Together, these results support an American origin for all T. pallidum characterized at the genomic level, both modern and ancient.

Date: 2025
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DOI: 10.1038/s41586-024-08515-5

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