A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia

Overview

A Treponema pallidum genome (TE1-3) dated to approximately 5,500 years before present was recovered from Middle Holocene hunter-gatherer contexts at the Tequendama I rock shelter in the Sabana de Bogotá, Colombia. The finding provides genomic evidence for the presence of T. pallidum in the Americas millennia prior to European contact and prior to the recognized diversification of extant T. pallidum subspecies associated with syphilis, yaws, and bejel.

Methods and approach

Material yielding the TE1-3 Treponema genome originated from Middle Holocene archaeological contexts at the Tequendama I rock shelter. The study reports ancient DNA analyses including authentication and phylogenetic inference applied to the recovered Treponema sequence data. Technical laboratory protocols and detailed bioinformatic workflows are not specified in the abstract and are therefore not recapitulated here.

Results

Phylogenetic analysis places TE1-3 as a sister lineage to all previously characterized T. pallidum subspecies, indicating that the recovered genome diverges prior to the differentiation of lineages currently associated with yaws, bejel, and syphilis. The genomic data extend the temporal range of treponemal pathogen genomes by several millennia and increase recognized diversity within the T. pallidum clade.

Implications

The TE1-3 genome supports a deep temporal presence of T. pallidum in the Americas and implies that major lineage diversification of T. pallidum postdates this Middle Holocene lineage. This outcome refines models of treponemal evolutionary history by demonstrating an earlier, previously undocumented branch of T. pallidum diversity in South America. Further genome recovery and contextualized analyses will be required to resolve timing and geographic patterns of subspecies emergence and to integrate these data with paleopathological and epidemiological records.