Monash University

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In Silico Discovery of Single Nucleotide Polymorphisms Under Positive Parallel Selection in Bacteria

posted on 2022-12-19, 00:00 authored by David James Edwards

Bacterial pathogen are continuously evolving; most changes are deleterious or neutral, but sometimes a mutation leads to functional change. Such mutations are so very rarely beneficial, that when they do arise in parallel in distantly related isolates (known as homoplasy) it implies that the change is likely positively selected because it confers an adaptive advantage to the bacteria. In this thesis a method is developed to identify and characterise potential homoplasies within a target bacterial population, using large-scale whole-genome data; the method is then applied the method to investigate patterns of positive selection in Mycobacterium tuberculosis. 


Principal supervisor

Anton Peleg

Additional supervisor 1

Kathryn Holt

Additional supervisor 2

Bernard Pope

Additional supervisor 3

Sebastian Duchene

Year of Award


Department, School or Centre

Central Clinical School

Additional Institution or Organisation

IITB Monash

Campus location



Doctor of Philosophy

Degree Type



Faculty of Medicine, Nursing and Health Sciences