Weitz Group @ Georgia Tech Theoretical Ecology and Quantitative Biology



Weitz group proposes a neutral theory of genome evolution (BMC Genomics, 2012, 13:196)

Posted by jsweitz

Bart Haegeman and Joshua S Weitz co-authored a new article in BMC Genomics in which they propose a neutral theory of genome evolution and the frequency distribution of genes.

The study was motivated by the observation that the gene content of genomes of closely related bacteria can differ significantly. For example, pair-wise comparisons of genome sequences from isolates of the same species often do not share a substantial fraction of their gene content. Variability in gene composition can be summarized in terms of gene frequency distributions, in which 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 (i.e., accessory genes), some genes of intermediate occurrence (i.e, character genes), and many genes that appear in all or nearly all genomes (i.e., core genes). Here we ask: is it possible, instead, to recapitulate findings of U shaped gene frequency distributions with a strictly neutral model of genome evolution?

In this paper, we answer this question in the affirmative by proposing a simple and analytically tractable neutral model of genome evolution that self-consistently accounts for the birth and death of genomes and changes in the gene composition of individual genomes. In this model, genomes undergo birth-death processes in a neutral sense and also acquire and lose genes via exchange with the environment. We fit our model to gene frequency distributions from 6 pathogen species. We discuss ways in which different levels of information can be included in interpreting variation in gene composition in the genomes of similar microbes.