Title: Ancient Mycobacterium pinnipedii genomes recovered from non-coastal peoples from pre-contact era South America highlight the complexity of tuberculosis transmission in the past

Authors: Tanvi P. Honap^1,2, Åshild J. Vågene^3,4,5, Kelly M. Harkins⁶, Michael S. Rosenberg^2,7, Karen Giffin^3,8, Felipe Cárdenas-Arroyo⁹, Laura Paloma Leguizamón⁹, Judith Arnett^6,10, Jane E. Buikstra⁶, Alexander Herbig^3,4, Johannes Krause^3,4,8, Kirsten I. Bos^3,4,8, Anne C. Stone^6,11,12

Affiliations: ¹Department of Anthropology, University of Oklahoma, Norman, OK, USA; ²School of Life Sciences, Arizona State University, Tempe, AZ, USA; ³Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; ⁴Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany; ⁵Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; ⁶School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; ⁷Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA; ⁸Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; ⁹Colombian Institute of Anthropology and History (ICANH), Bogotá, Colombia; ¹⁰University of the Andes, School of Medicine, Bogotá, Colombia; ¹¹Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA; ¹²Institute of Human Origins, Arizona State University, Tempe, AZ, USA

Abstract: Mycobacterium pinnipedii is a member of the Mycobacterium tuberculosis complex, and today causes tuberculosis (TB) primarily in animals such as pinnipeds. Previous ancient DNA research has shown that peoples living in the coastal areas of Peru prior to European contact were infected by M. pinnipedii. This can be explained by a direct zoonotic transfer of TB to these ancient populations through hunting or handling of infected pinniped remains. However, bioarchaeological evidence shows the presence of TB in several pre-contact era South American populations with minimal access to marine mammals - a scenario incompatible with TB transmission directly from infected pinnipeds. Here, we investigated the causative agent of TB in ten pre-contact era, non-coastal individuals from South America. We reconstructed near-complete M. pinnipedii genomes from three contemporaneous individuals from inland Peru and Colombia. This demonstrates that M. pinnipedii caused TB in human populations living far beyond the coast, having spread either through human-to-human and/or animal-mediated routes. Overall, this study highlights that TB transmission in the pre-contact era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.