Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment

Bentkowski, Piotr (2014) Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment. Doctoral thesis, University of East Anglia.

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Abstract

The size of the genomes of known free-living prokaryotes varies from � 1:3 Mbp to � 13
Mbp. This thesis proposes a possible explanation of this variation due to variability of
the physical conditions of the environment. In a stable environment, competition for the
resource becomes the main force of selection and smaller (thus cheaper) genomes are
favoured. In more variable conditions larger genomes will be preferred, as they have a
wider range of response to a less predictable environment. An agent-based model (ABM)
of genome evolution in an free-living prokaryotic population has been proposed. Using
the classic Hutchinson niche space model, a gene was defined as a Gaussian function over
a corresponding niche dimension. The cell can have more than one gene along a given
dimension, and the envelope of all the corresponding responses is considered a full description
of a cell’s phenotype over that dimension. Gene deletion, gene duplication, and
modifying mutations are permitted during reproduction, so the number of genes and their
phenotypic effect (height and position of the Gaussian envelope) are free to evolve. The
surface under the curve is fixed to prevent ‘supergenes’ from occurring. Change of the
environmental conditions is simulated as a bounded random walk with a varying length
of the step (a parameter representing variability of the environment). Using this approach,
the model is able to reproduce the phenomenon of genome streamlining in more stable
environments (analogical to e.g. oligotrophic gyre regions of the ocean) and genome
complexification in variable environments. Horizontal gene transfer (HGT) was also introduced,
but was found to act in a similar manner as gene duplication and shown no
important contribution to the speed of evolution and the adaptive potential of the population.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Environmental Sciences
Depositing User: Mia Reeves
Date Deposited: 17 Oct 2014 12:09
Last Modified: 17 Oct 2014 12:09
URI: https://ueaeprints.uea.ac.uk/id/eprint/50553
DOI:

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