Estimating the evolutionary history of plasmids and viruses

Overview

In the case of cellular life - bacteria, archaea and eukaryotes - determining the 'tree of life' is a comparatively well-studied problem.

This vertical evolutionary history can be estimated using concatenated gene phylogenies, where single copy marker genes are concatenated into a single multiple sequence alignment which is then used in a phylogenetic tree reconstruction algorithm.

Viral genomes and plasmid sequences, meanwhile, are more challenging to fit into a phylogenetic framework.

Research activities

Concatenated gene phylogenies have been used to infer phylogeny in a subset of viruses, but neither viruses nor plasmids have sufficient numbers of genes common to all entities to apply concatenated gene-based phylogenetics.

Working with collaborators in local and international universities, the proposed project will develop new phylogenetic methods to estimate the evolutionary history of non-cellular genomic elements.

This estimated history will then be related the evolution of these entities to that of cellular life to form a unified view, reshaping our understanding of evolution globally.

Keywords

• phylogenetics
• virus
• phage
• plasmid
• evolution
• tree of life
• bioinformatics

Contact

Contact the supervisor for more information.