9%), and IT2 and IT4 (13/34, 38.2%) respectively. In addition, one IT3 strain 0063 and one IT5 strain L43 present in two individual branches formed subgroups

C and D respectively (Table 2). Phylogeny and population history of L. innocua As aforementioned, L. innocua was genetically monophyletic (π = 1.06%) as compared CHIR-99021 order to L. monocytogenes (π = 4.38%). When sequence data were analyzed after stratification by subgroups, the number of polymorphisms and genetic diversity within each subpopulations were reduced (Table 3), suggesting a barrier for genetic exchange OSI-027 clinical trial between these L. innocua subgroups. Such barrier was also observed between L. monocytogenes lineages (Table 3), consistent with one previous report [21]. Tajima’s D test revealed that L. innocua and L. monocytogenes did not evolve under neutrality. A marginal positive value of Tajima’s D observed for ribC in L. monocytogenes (1.9963, 0.05 < p < 0.10) became smaller or negative when analyses were performed for separate lineages, suggesting a divided population structure. Similarly, significant or marginal positive Tajima's D values were observed for gyrB (2.0401, p < 0.05) in L. monocytogenes lineage II, and for sigB (2.0426, p < 0.05) and gap (1.7746, 0.05 check details < p < 0.10) in lineage III, supporting that lineages II and III represented diverse populations as compared to lineage I (Table 4). On the other hand, gyrB (-2.2650, p < 0.01), betL (-2.5954,

p < 0.001) and gap (-2.4190, p < 0.01) showed significant negative Tajima's D values in L. innocua, indicative Digestive enzyme of a bottleneck or selective sweep [22, 23]. Also, Tajima’s D were marginal negative for betL in L. innocua subgroup A (-1.7315, 0.05 < p < 0.10) and gap in subgroup B (-1.6523, 0.05 < p < 0.10) (Table 4). Table 4 Tajima's D test for the L. innocua-L. monocytogenes clade Gene L. innocua L. monocytogenes   A B all I II III all gyrB

-0.3479 0.3871 -2.2650** -1.6671# 2.0401* 0.0136 0.7361 dapE 0.7970 1.1138 -1.0723 -0.0394 -0.4958 0.9003 -0.3265 hisJ 1.2046 0.1750 0.2478 -0.1104 -0.6528 0.0336 1.4256 sigB -0.1097 0.5901 0.2092 0.5444 -1.1117 2.0426* 1.2456 ribC 0.0511 0.2773 0.2987 1.5368 -1.5344 0.4909 1.9963# purM 0.5044 0.2217 -1.4464 0.0235 -0.2856 0.9867 0.4698 betL -1.7315# -1.5047 -2.5954*** -0.2912 -0.1839 0.5179 0.0554 gap -1.1648 -1.6523# -2.4190** -0.6910 -0.8223 1.7746# 0.2481 tuf N/Aa 0.9505 -0.0101 N/A 0.8198 0.5380 0.4709 Concatenated 0.1719 0.1492 0.3847 0.3655 -0.7070 0. 7379 0.7452 #, 0.05 < p < 0.10; *, p < 0.05; **, p < 0.01; ***, p < 0.001. a. No polymorphisms in the data, resulting in inability to compute Tajima’s test. The exterior/interior branch length ratio test demonstrated that L. innocua and its subgroup A as well as L. monocytogenes and its lineage I showed a significantly smaller exterior/interior branch length ratio (p < 0.05) than expected under the coalescent model (Figure 2).