Discrimination

index (D.I.) values of selected genes were calculated according to the method previously described [42] on the basis of allelic types [j], numbers of strains belonging to each type [nj], and the total numbers of strains analyzed [N] with the following equation (higher D.I. values indicate better discriminatory power): ClonalFrame v1.1 was employed to show the evolution of ρ/θ and r/m as chain run. These two complementary measures were used to assess the relative contribution of recombination and mutation in the creation of the sample population from a common ancestor. Specifically, Selleck Ferrostatin-1 ρ/θ is the ratio of rates at which recombination and mutation occur, representing a measure of how often recombination happen relative to mutation [43], while r/m is the ratio of probabilities that a given site is altered through recombination and mutation, representing a measure of how important the effect of recombination is in the diversification of the sample population relative to mutation [44]. To infer the population history in the L. innocua-L. monocytogenes clade, ClonalFrame GUI, which treated each

gene as an independent unit in the input file, was used to calculate the ratio of the sum of the Blasticidin S clinical trial external branches (the ones that connect a leaf of the tree) to the sum of the internal branches (the ones that connect two internal Cell Cycle inhibitor nodes of the tree) [45]. The distribution of these ratios was then compared to the distribution of the external/internal

branch length ratio as expected under the coalescent model [46]. If the external/internal branch length ratio is significantly smaller than expected, it means that the inferred genealogy is unexpectedly “”star-like”", which is consistent with an expansion of the population size. The chi-squared test was used to test significant associations between L. innocua subgroup and isolate source. Acknowledgements This study was supported by grants from National Natural Science Foundation (Contract No. 30870068). We thank Dr. Martin Wiedmann for kindly providing L. monocytogenes lineage III strains, and Drs. Dongyou triclocarban Liu and John Bowman for helpful discussion on the subtyping of Listeria strains. Electronic supplementary material Additional file 1: Table S1 and S2: Internalin Types (ITs) based on 14 L. monocytogenes-L. innocua -common and 4 L. innocua -specific (in grey shading) internalin genes. (DOC 334 KB) References 1. Schmid MW, Ng EYW, Lampidis R, Emmerth M, Walcher M, Kreft J, Goebel W, Wanger M, Schleifer K: Evolutionary history of the genus Listeria and its virulence genes. Syst Appl Microbiol 2005, 28:1–18.PubMedCrossRef 2.