% pubman genre = thesis
@phdthesis{item_3256970,
title = {{Genomic insights into pre- and post-contact human pathogens in the New World}},
author = {V{\aa}gene, {\AA}shild J.},
language = {eng},
doi = {https://publikationen.uni-tuebingen.de/xmlui/handle/10900/85350},
school = {Eberhard-Karls Universit{\"a}t},
address = {T{\"u}bingen},
year = {2018},
abstract = {{Ancient pathogen genomes recovered from archaeological human remains provide{\textless}br{\textgreater}primary evidence for infectious diseases that circulated amongst human populations in{\textless}br{\textgreater}the past, as well as valuable insights regarding past pathogen macroecology, hostadaptation,{\textless}br{\textgreater}spread and emergence. In this dissertation, I leverage recent molecular and{\textless}br{\textgreater}computational advances to detect and characterize the genomes of pathogenic bacteria{\textless}br{\textgreater}that affected indigenous human populations in the New World pre- and post- 16th{\textless}br{\textgreater}century European contact.{\textless}br{\textgreater}In the first paper I investigate strain members of the Mycobacterium tuberculosis{\textless}br{\textgreater}complex (MTBC), the causative agent of tuberculosis, in geographically dispersed{\textless}br{\textgreater}human populations from inland Colombia and coastal Peru. I reconstructed and{\textless}br{\textgreater}analyzed three pre-contact MTBC genomes belonging to the sub-clade Mycobacterium{\textless}br{\textgreater}pinnipedii, associated with infection in seals and sea lions today. M. pinnipedii strains{\textless}br{\textgreater}are hypothesized to have spread to coastal Peruvians via seal-to-human transmission{\textless}br{\textgreater}(Bos et al., 2014). However, this ecological model does not explain the spread of M.{\textless}br{\textgreater}pinnipedii to inland Colombian human populations. Different ecological models{\textless}br{\textgreater}accounting for its inland spread are discussed.{\textless}br{\textgreater}The second paper presents Salmonella enterica ssp. enterica Paratyphi C, a cause of{\textless}br{\textgreater}enteric fever, as a strong candidate pathogen for the post-contact 1545-1550 CE{\textless}br{\textgreater}{\textquotedblleft}cocoliztli{\textquotedblright} outbreak at Teposcolula-Yucundaa in Southern Mexico. The pathogenic{\textless}br{\textgreater}agent of this outbreak is unknown from archaeological and ethnohistorical evidence. In{\textless}br{\textgreater}this study I used a broad-scale computational screening approach, the MEGAN{\textless}br{\textgreater}ALignment Tool (MALT), and was able to detect S. enterica DNA against a complex{\textless}br{\textgreater}environmental DNA background in ten individuals buried in the epidemic cemetery.{\textless}br{\textgreater}This was done without prior knowledge of the target organism, thus demonstrating the{\textless}br{\textgreater}efficiency of such an approach in identifying ancient pathogens in archaeologically{\textless}br{\textgreater}preserved tissues. Genome-wide analyses of the ten S. Paratyphi C genomes are{\textless}br{\textgreater}presented.{\textless}br{\textgreater}In a third paper I applied MALT to screen for ancient pathogen DNA in the remains of{\textless}br{\textgreater}a sub-adult individual from a deviant burial, dated to the 16th or 17th century, in Moneen{\textless}br{\textgreater}Cave, Ireland. Negative results are reported for the presence of ancient pathogen DNA.{\textless}br{\textgreater}Instead this paper focuses on the reconstruction and analysis of this individual{\textquoteright}s{\textless}br{\textgreater}mitochondrial genome.}},
}