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  Genomic insights into pre- and post-contact human pathogens in the New World

Vågene, Å. J. (2018). Genomic insights into pre- and post-contact human pathogens in the New World. PhD Thesis, Eberhard-Karls Universität, Tübingen.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0002-D31B-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-9573-3
Genre: Thesis

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Vågene, Åshild J.1, Author              
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1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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 Abstract: Ancient pathogen genomes recovered from archaeological human remains provide primary evidence for infectious diseases that circulated amongst human populations in the past, as well as valuable insights regarding past pathogen macroecology, hostadaptation, spread and emergence. In this dissertation, I leverage recent molecular and computational advances to detect and characterize the genomes of pathogenic bacteria that affected indigenous human populations in the New World pre- and post- 16th century European contact. In the first paper I investigate strain members of the Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis, in geographically dispersed human populations from inland Colombia and coastal Peru. I reconstructed and analyzed three pre-contact MTBC genomes belonging to the sub-clade Mycobacterium pinnipedii, associated with infection in seals and sea lions today. M. pinnipedii strains are hypothesized to have spread to coastal Peruvians via seal-to-human transmission (Bos et al., 2014). However, this ecological model does not explain the spread of M. pinnipedii to inland Colombian human populations. Different ecological models accounting for its inland spread are discussed. The second paper presents Salmonella enterica ssp. enterica Paratyphi C, a cause of enteric fever, as a strong candidate pathogen for the post-contact 1545-1550 CE “cocoliztli” outbreak at Teposcolula-Yucundaa in Southern Mexico. The pathogenic agent of this outbreak is unknown from archaeological and ethnohistorical evidence. In this study I used a broad-scale computational screening approach, the MEGAN ALignment Tool (MALT), and was able to detect S. enterica DNA against a complex environmental DNA background in ten individuals buried in the epidemic cemetery. This was done without prior knowledge of the target organism, thus demonstrating the efficiency of such an approach in identifying ancient pathogens in archaeologically preserved tissues. Genome-wide analyses of the ten S. Paratyphi C genomes are presented. In a third paper I applied MALT to screen for ancient pathogen DNA in the remains of a sub-adult individual from a deviant burial, dated to the 16th or 17th century, in Moneen Cave, Ireland. Negative results are reported for the presence of ancient pathogen DNA. Instead this paper focuses on the reconstruction and analysis of this individual’s mitochondrial genome.

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Language(s): eng - English
 Dates: 2018-12-102018-12-13
 Publication Status: Published online
 Pages: 194
 Publishing info: Tübingen : Eberhard-Karls Universität
 Table of Contents: -
 Rev. Type: -
 Identifiers: Other: shh1154
 Degree: PhD

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