The advent of genome-wide association studies for bacteria

- The advent of the genome-wide association study (GWAS) approach provides a promising framework for dissecting the genetic basis of bacterial or archaeal phenotypes.
- Bacterial genomes tend to be shaped by stronger positive selection, stronger linkage disequilibrium and stronger population stratification than humans, with implications for GWAS power and resolution.
- An example GWAS in Mycobacterium tuberculosis genomes highlights the potentially confounding effects of linkage disequilibrium and population stratification.
- A comparison of the traditional GWAS approach versus a somewhat orthogonal method based upon evolutionary convergence (phyC) shows strengths and weaknesses of both approaches.