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Title: Comparative genomics and epidemiology of the amphibian-killing fungus Batrachochytrium dendrobatidis
Author: Farrer, Rhys
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2013
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The primary aim of this thesis was to study the population structure and epidemiology of the fungal pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). I have addressed these questions by collecting and isolating Bd from multiple infected host species. I have then extracted and sequenced whole nuclear and mitochondrial genomes for 50 isolates of Bd using the ABI SOLiD 3 and Illumina HiSeq 2000 platforms. The first aspect of the analysis was to tailor a new method for identifying variant sites amongst the isolates, as well as verifying the accuracy of the alignment and SNP-calling methods. Next, using a number of phylogenetic methods, I identified a population split into at least three deeply divergent lineages. Two of these lineages were found in multiple continents and are associated with known introductions by anthropogenic means. Isolates belonging to one clade, which we named the Global Panzootic Lineage (BdGPL), have emerged across at least five continents and are associated with the onset of epizootics in all five continents we tested. Dating the divergence between BdGPL isolates suggested a recent common ancestor in the 20th Century, and that the widespread trade of amphibians is an important mechanism of transmission. In contrast, BdGPL diverged from the other two lineages approximately 1000 years ago, clearly refuting a single emergence hypothesis. The two newly identified divergent lineages were the Cape lineage (BdCAPE) that appeared to have originated from the Cape Province in South Africa and a Swiss lineage (BdCH) comprised of a single isolate from a pond in Gamlikon, Switzerland. The secondary aim of this thesis was to identify and compare virulence determinants and other genomic features responsible for known differences in phenotypes. Using a variety of statistical and computational methods, I identified compelling evidence for genetic recombination targeting virulence factors, selection of those and other virulence factors, and rapid changes in ploidy and aneuploidy amongst the isolates of all three lineages. These genomic features shed light on the emergence, patterns of global spread, and modes of evolution in the pathogen(s) responsible for contemporary disease-driven losses in amphibian biodiversity. Finally, I discuss how these findings update our understanding of Bd and the importance for tracking and understanding the dynamics of other current emerging pathogens in an increasingly globalised habitat.
Supervisor: Fisher, Matthew ; Garner, Trenton ; Francois, Balloux Sponsor: Natural Environment Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available