Luhmann, Nina: Phylogenetic assembly of paleogenomes integrating ancient DNA data. 2017
Inhalt
- 1 Introduction
- 1.1 Background
- 1.1.1 Reconstructing ancestral genomes
- 1.1.2 Sequencing of ancient DNA
- 1.1.3 Ancient genome scaffolding and ancestral reconstruction
- 1.2 Thesis overview
- 2 The SCJ Small Parsimony Problem integrating an aDNA assembly
- 2.1 Consistent reconstructions using the Fitch algorithm
- 2.2 Generalization to the Sankoff-Rousseau algorithm
- 2.2.1 Edge-weighted SCJ Labeling Problem
- 2.2.2 Overview of the Sankoff-Rousseau algorithm
- 2.2.3 Sankoff-Rousseau on adjacencies with edge lengths
- 2.2.4 Reconstructing consistent genomes
- 2.3 Integrating aDNA sequencing information
- 2.4 Evaluation
- 2.5 Discussion
- 3 The SCJ Small Parsimony Problem for weighted adjacencies
- 3.1 Generalization by weighting adjacencies
- 3.2 Methods
- 3.2.1 Decomposition into independent subproblems
- 3.2.2 Application to the Weighted SCJ Labeling Problem
- 3.2.3 Complexity analysis
- 3.2.4 An Integer Linear Program for complex components
- 3.2.5 Sampling co-optimal labelings
- 3.2.6 Weighting ancestral adjacencies
- 3.2.7 An extinct leaf
- 3.2.8 Implementation
- 3.3 Results
- 3.4 Discussion
- 4 Mind the gap: completing ancestral marker orders
- 4.1 Gap Filling as a shortest path problem
- 4.2 Local ancestral reconstruction based on Gap Filling
- 4.3 Discussion
- 5 Reconstruction and analysis of two ancient Yersinia pestis strains
- 5.1 Sequencing data and reference genomes
- 5.2 Local reconstruction of both ancient strains
- 5.2.1 Reconstructing the London outbreak strain
- 5.2.2 Reconstructing the Marseille outbreak strain
- 5.2.3 Comparison of both reconstructed ancient genomes
- 5.2.4 Discussion of local reconstruction
- 5.3 Global reconstruction of London ancestor with EWRA
- 5.4 Global reconstruction of London ancestor with PhySca
- 5.4.1 Ancestral reconstruction with Boltzmann weights
- 5.4.2 Ancestral reconstruction with aDNA weights
- 5.5 Global reconstruction of London and Marseille strains
- 6 Conclusion and Perspectives
- Bibliography