Formalist features determining the tempo and mode of evolution in Pseudomonas fluorescens SBW25 : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Evolutionary Genetics at Massey University, Auckland, New Zealand
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Date
2015
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Massey University
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Abstract
In order to explain the adaptive process, it is necessary to understand the generation of
heritable phenotypic variation. For much of the history of evolutionary biology, the
production of phenotypic variation was believed to be unbiased, and adaptation the
primary outcome of selection acting on randomly generated variation (mutation). While
true, ‘internal’ features of organisms may also play a role by increasing the rate of
mutation at specific loci, or rendering certain genes better able to translate mutation
into phenotypic variation. This thesis, using a bacterial model system, demonstrates
how these internal features – localised mutation rates and genetic architectures – can
influence the production of phenotypic variation.
Previous work involving the bacterium Pseudomonas fluorescens SBW25 has shown
that mutations at three loci, wsp, aws and mws, can cause the adaptive wrinkly
spreader (WS) phenotype. For each locus, the causal mutations are primarily in
negative regulators of di-guanylate cyclase (DGC) activity, which readily convert
mutation into the WS phenotype. Mutations causing WS at other loci were predicted to
arise, but to do so with less frequent types of mutation. The data presented in this
thesis confirms this prediction. My work began with the identification and
characterisation of a single rare WS-causing mutation: an in-frame deletion that
generates a translational fusion of genes fadA and fwsR. The fusion couples a DGC
(encoded by fwsR) to a membrane-spanning domain (encoded by fadA) causing
relocalisation of the DGC to the cell membrane and the WS phenotype. This is one of
the few examples of adaptation caused by gene fusion and protein relocation in a realtime
evolution experiment. I next took an experimental evolution approach to isolate
further rare WS types and characterized these, revealing a range of rarely taken
mutational pathways to WS. Lastly, I describe an example of extreme molecular
parallelism, in which a cell chaining phenotype is caused – without exception – by a
single nucleotide substitution within the gene nlpD, despite multiple mutational
pathways to this phenotype. Characterisation of different nlpD mutants suggests this
molecular parallelism is caused by a high local mutation rate, possibly related to the
initiation of transcription within this gene.
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Pseudomonas fluorescens, Evolution, Genetics, Evolutionary genetics, Research Subject Categories::NATURAL SCIENCES::Biology::Cell and molecular biology::Genetics