Our latest paper has just been published. It is on the evolution of Escherichia coli, which is a pathogenic bacterium. The work was led by Dr. Alan McNally, who has just moved from Nottingham Trent University to Birmingham University.
The work centres on the analysis of what we call the pangenome of this bacterium. There is a lot of variability in the genomic content of these strains of bacteria that we looked at. In fact although this is a tiny twig on the tree of life you found 12,000 different kinds of gene family. What is more, these genes appear to be frequently swapped around between the different kinds of bacterium. We found correlations between genetic genetic change in the genes and genetic change in the control region. The author summary is just below here and you can find a link to the actual paper at the bottom of this blog post. The analysis was quite enormous and a phenomenal number of computation of hours were used in order to try to disentangle the various evolutionary stories that we encountered.
We present an approach to evolutionary analysis of bacterial pathogens combining core genome, accessory genome, and gene regulatory region analyses. This enables unparalleled resolution of the evolution of a multi-drug resistant pandemic pathogen that would remain invisible to a core genome phylogenetic analysis alone. In particular, our combined analysis approach identifies population-level evidence for compensatory mutations offsetting the costs of resistance plasmid maintenance as a key event in the emergence of dominant MDR lineages of E. coli.
McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, et al. (2016) Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations. PLoS Genet 12(9): e1006280. doi: 10.1371/journal.pgen.1006280
You can pick up a copy here: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006280