Abstract
The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history.
Highlights
The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome
The genetic changes occurring on a single bacterial cell can be classified into mutation and recombination events, and the events of interest differ whether the focus is on the core genome or the accessory genome
There are three biological mechanisms that can lead to homologous recombination, namely conjugation, transduction and transformation (Thomas and Nielsen 2005)
Summary
Bacterial microevolution is the study of the evolutionary forces that shape the genetic diversity of a natural population of bacteria. This evolutionary process takes place as a result of the genetic changes happening within each of the genomes of the bacterial cells constituting the population. Over time, these changes are amplified or weakened by the effects of both genetic drift and natural selection
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