Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Kirsten I. Bos, Kelly M. Harkins, Alexander Herbig, Mireia Coscolla, Nico Weber, Iñaki Comas, Stephen A. Forrest, Josephine M. Bryant, Simon R. Harris, Verena J. Schuenemann, Tessa J. Campbell, Kerttu Majander, Alicia K. Wilbur, Ricardo A. Guichon, Dawnie L. Wolfe Steadman, Della Collins Cook, Stefan Niemann, Marcel A. Behr, Martin Zumarraga, Ricardo Bastida, Daniel Huson, Kay Nieselt, Douglas Young, Julian Parkhill, Jane E. Buikstra et al.

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Nature 514, 494–497 (23 October 2014) doi:10.1038/nature13591

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Figure 1: Archaeological description of the skeletal samples.a, Map of Peru showing locations of archaeological sites; CGIAR SRTM 90m Digital Elevation Database version 4.1 ( b, c, Skeletal lesions of active tuberculosis from two individuals positive for M. tuberculosi…

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of theM. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.

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Figure 3: Phylogenetic analysis. a, Bayesian maximum clade credibility tree of 261 MTBC genomes (excluding Hungarian mummy), with estimated divergence dates shown in years before present using a model of population expansion. b, Maximum parsimony tree for lineage 6 an…