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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.
