Ochman on bacterial evolution

Yesterday I went to the annual Thomas S Whittam Memorial Lecture here at MSU. Howard Ochman talked about "Evolutionary Forces Affecting Bacterial Genomes", though he had changed the title to "Determinants of Genome Size and complexity.

Based on research in his lab had two conclusions about the evolution of bacterial genomes:

• Genome size is drifting
• GC-content is under selection

The very tight correlation between gene content and genome size (i.e., there is a linear relationship between number of genes and length of the genome) is driven by genetic drift, and not selection. People often say that small genomes are selected for, but clearly there are not. This is in part caused by a bias towards deletions (compared to insertions). I asked him why there is this bias, and he did not have an answer. (Well, he gave me an answer, but he also acknowledged that it didn't get to the point.) The common ancestor had a large genome, and many bacteria - particularly pathogens and endosymbionts - have subsequently lost DNA resulting in a reduced genome size (Kuo et al, 2009, but see Kuo and Ochman, 2010).

There are trends in the GC-content (amount of guanine and cytosize in the DNA) that differs among bacterial taxa. But closely related species have similar GC-content, and it turns out that genetic drift is not responsible for this, but that it is driven by selection. "Escherichia coli strains harboring G+C-rich versions of genes display higher growth rates" (Raghavan, 2012).

Genome size and abundance of pseudogenes correlates with the size of the effective population size: a larger N_e gives larger genomes, while smaller N_e results in smaller genomes. Pseudogene abundance is less straightforward, with the largest and smallest genomes and N_e both having few pseudogenes, but those intermediate in size having many.

References
Kuo CH, & Ochman H (2010). The extinction dynamics of bacterial pseudogenes. PLoS genetics, 6 (8) PMID: 20700439
Kuo CH, Moran NA, & Ochman H (2009). The consequences of genetic drift for bacterial genome complexity. Genome research, 19 (8), 1450-4 PMID: 19502381
Raghavan R, Kelkar YD, & Ochman H (2012). A selective force favoring increased G+C content in bacterial genes. Proceedings of the National Academy of Sciences of the United States of America, 109 (36), 14504-7 PMID: 22908296