Skip to Main content Skip to Navigation
Journal articles

A neutral theory of genome evolution and the frequency distribution of genes

Bart Haegeman 1, 2, * Joshua Weitz 3, 4, * 
* Corresponding author
1 MODEMIC - Modelling and Optimisation of the Dynamics of Ecosystems with MICro-organisme
CRISAM - Inria Sophia Antipolis - Méditerranée , MISTEA - Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie
Abstract : Background The gene composition of bacteria of the same species can differ significantly between isolates. Variability in gene composition can be summarized in terms of gene frequency distributions, in which individual genes are ranked according to the frequency of genomes in which they appear. Empirical gene frequency distributions possess a U-shape, such that there are many rare genes, some genes of intermediate occurrence, and many common genes. It would seem that U-shaped gene frequency distributions can be used to infer the essentiality and/or importance of a gene to a species. Here, we ask: can U-shaped gene frequency distributions, instead, arise generically via neutral processes of genome evolution? Results We introduce a neutral model of genome evolution which combines birth-death processes at the organismal level with gene uptake and loss at the genomic level. This model predicts that gene frequency distributions possess a characteristic U-shape even in the absence of selective forces driving genome and population structure. We compare the model predictions to empirical gene frequency distributions from 6 multiply sequenced species of bacterial pathogens. We fit the model with constant population size to data, matching U-shape distributions albeit without matching all quantitative features of the distribution. We find stronger model fits in the case where we consider exponentially growing populations. We also show that two alternative models which contain a "rigid" and "flexible" core component of genomes provide strong fits to gene frequency distributions. Conclusions The analysis of neutral models of genome evolution suggests that U-shaped gene frequency distributions provide less information than previously suggested regarding gene essentiality. We discuss the need for additional theory and genomic level information to disentangle the roles of evolutionary mechanisms operating within and amongst individuals in driving the dynamics of gene distributions.
Document type :
Journal articles
Complete list of metadata

Cited literature [5 references]  Display  Hide  Download

https://hal.inria.fr/hal-00784405
Contributor : Ed. BMC Connect in order to contact the contributor
Submitted on : Monday, February 4, 2013 - 1:01:02 PM
Last modification on : Wednesday, June 1, 2022 - 3:52:41 AM
Long-term archiving on: : Monday, June 17, 2013 - 6:37:23 PM

Identifiers

Citation

Bart Haegeman, Joshua Weitz. A neutral theory of genome evolution and the frequency distribution of genes. BMC Genomics, BioMed Central, 2012, pp.art 196. ⟨10.1186/1471-2164-13-196⟩. ⟨hal-00784405⟩

Share

Metrics

Record views

116

Files downloads

199