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Open Access Highly Accessed Open Badges Research article

Evolution of variation in presence and absence of genes in bacterial pathways

Andrew R Francis1* and Mark M Tanaka2

Author affiliations

1 School of Computing, Engineering and Mathematics, University of Western Sydney, Penrith 2751, Locked Bag 1797, Australia

2 School of Biotechnology & Biomolecular Sciences, University Of New South Wales, Kensington 2052, Australia

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Citation and License

BMC Evolutionary Biology 2012, 12:55  doi:10.1186/1471-2148-12-55

Published: 20 April 2012



Bacterial genomes exhibit a remarkable degree of variation in the presence and absence of genes, which probably extends to the level of individual pathways. This variation may be a consequence of the significant evolutionary role played by horizontal gene transfer, but might also be explained by the loss of genes through mutation. A challenge is to understand why there would be variation in gene presence within pathways if they confer a benefit only when complete.


Here, we develop a mathematical model to study how variation in pathway content is produced by horizontal transfer, gene loss and partial exposure of a population to a novel environment.


We discuss the possibility that variation in gene presence acts as cryptic genetic variation on which selection acts when the appropriate environment occurs. We find that a high level of variation in gene presence can be readily explained by decay of the pathway through mutation when there is no longer exposure to the selective environment, or when selection becomes too weak to maintain the genes. In the context of pathway variation the role of horizontal gene transfer is probably the initial introduction of a complete novel pathway rather than in building up the variation in a genome without the pathway.

Bacteria; Evolution; Pathway; Cryptic genetic variation; de Finetti; Mathematical model; Horizontal gene transfer; Reductive evolution; Genome evolution