Esteban and Hutchinson BMC Genomics 2011, 12:261 http://www.biomedcentral.com/1471-2164/12/261 Page 6 of 12 Figure 2 dN/dS (ω) ratios of genes in the CPXV genome . The ratio for the gene is the average ω of all codons in the gene. Black: Genes with sites under diversifying selection (Genes for which the alternative model, allowing positively sites with ω>1, fits the data better than the model (p < 0.05)). White: Genes without sites under diversifying selection. A) Ratios determined using model M2a, with statistical significance determined by comparison with M1a. B) Ratios determined using model M8, with statistical significance determined by comparison with M7. possible site classes of purifying, neutral or diversifying selection. We identified 79 genes under diversifying selection, representing 45% of the analyzed genes in the genome. Of those, 25 (14% of genes analyzed) were identified with both models, indicating high confidence. Thus we identify diversifying selection as an important mechanism of evolution in poxviruses. Analysis of genes spanning the CPXV genome revealed that diversifying selection is a more important mechanism of molecular evolution in the genome’s terminal regions than in the central genes. This may be due to diversifying pressures applied by host interac- tions. Among different orthopoxvirus species and even strains, terminal regions are more diverse both in gene