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  Beyond phylogenies: advancing analytical approaches for the field of ancient pathogenomics

Andrades Valtueña, A. (2021). Beyond phylogenies: advancing analytical approaches for the field of ancient pathogenomics. PhD Thesis, Friedrich-Schiller-Universität Jena, Fakultät für Biowissenschaften, Jena. doi:10.22032/dbt.49395.

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phd-thesis for free download (Any fulltext)
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 Creators:
Andrades Valtueña, Aida1, Author              
Krause, Johannes, Advisor
Warinner, Christina G.1, Advisor              
Garaizar Candina, Javier, Advisor
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1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: Alte DNA, Streptococcus mutans, Evolution, Phylogenie, Pathogenomik
 Abstract: Ancient pathogenomics is the field that studies past pathogens by recovering ancient DNA from archaeological remains. This discipline has been highly reliant on phylogenetic analyses, which provide information on: how past strains are related to their modern relatives; past diversity of the pathogen in question; and their geographical dispersal during past epidemics. However, in order to understand what genomic changes contributed to the dispersal, adaptation, and virulence evolution of pathogens, as well as to understand their past ecology, one needs to employ other analytical tools. In this thesis, I have employed and adapted the concepts of gene content, de novo assembly, and pangenomics to study the differences in virulence and functional potential of ancient bacterial strains. I have applied these approaches to Yersinia pestis, the bacterium responsible for plague, with a focus on its early genomic evolution in Eurasia between 5,000 to 3,000 years ago. I also demonstrate these concepts by applying these workflows to the first recovered ancient Streptococcus mutans genome from South Africa. This pathobiont is strongly associated with caries formation, one of the top ten health burdens affecting present day human populations. Overall, this thesis showcases the importance of expanding the ancient pathogenomics toolkit to include functional analytical approaches to study past pathogen genomes. Only in the light of archaeological contexts, will we gain insight into the emergence, ecology and long-term evolution of ancient pathogens.

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Language(s): eng - English
 Dates: 2021-07-082021-07-08
 Publication Status: Published in print
 Pages: 205
 Publishing info: Jena : Friedrich-Schiller-Universität Jena, Fakultät für Biowissenschaften
 Table of Contents: Introduction ... p. 4
Health and disease: connecting the past to the present ... p. 4
How can we learn from past disease? texts, mummies, bones and their tales ... p. 5
- Ancient dna ... p. 6
- Plague ... p. 9
-- Yersinia pestis ... p. 10
-- History of plague and contributions of ancient dna ... p. 12
- Caries ... p. 15
-- Evidence of caries in the archaeological record ... p. 16
-- Streptococcus mutans: a commensal with disease potential ... p. 17
- Comparative ancient pathogenomics ... p. 19
Aim ... p. 23
Manuscripts overview and author contribution ... p. 24
Manuscript a ... p. 30
Manuscript b ... p. 58
Manuscript c ... p. 89
Manuscript d ... p. 105
Manuscript e ... p. 122
Discussion ... p. 156
- Where to look for ancient pathogen dna? ... p. 156
- What have we learned from phylogenies? ... p. 160
- New insights from known genes and deletions ... p. 162
- Moving on from a single reference genome: de novo assembly and pangenomics ... p. 164
- What is knowledge without context: future outlooks for the field of ancient pathogenomics ... p. 167
Conclusion ... p. 171
 Rev. Type: -
 Identifiers: DOI: 10.22032/dbt.49395
Other: shh3157
 Degree: PhD

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