Article Figures & Data
Figures
- FIG 1
Phylogenetic trees inferred by the maximum likelihood method using sigB genes of 164 Listeria sensu stricto allelic types (a) and L. monocytogenes lineage I, II, and III isolates (b). Both trees were rooted by midpoint. For the phylogeny shown in panel a, the HKY substitution model with invariable sites and a gamma distribution (HKY+I+G substitution model) was used for constructing the tree with 1,000 bootstrap repetitions. Only bootstrap values of >70% are presented on the tree. L. monocytogenes is indicated in red, L. marthii is in brown, L. innocua is in green, L. welshimeri is in yellow, L. seeligeri is in blue, and L. ivanovii is in purple. For panel b, the GTR+G substitution model was used for constructing the tree with 1,000 bootstrap repetitions; only bootstrap values of >70% are presented in this tree. L. monocytogenes lineage I is indicated by triangles, lineage II is indicated by squares, and lineage III is indicated by circles.
- FIG 2
Phylogenetic tree inferred by the maximum likelihood method using the core genome SNPs of 21 Listeria sensu stricto isolates. kSNP2 with kmer size of 19 was used to identify core genome SNPs that were used for constructing the tree with the GTR+G substitution model and 1,000 bootstrap repetitions. The tree is rooted by the midpoint. Only bootstrap values of >70% are presented on the tree. L. monocytogenes is indicated in red, L. marthii is in brown, L. innocua is in green, L. welshimeri is in yellow, L. seeligeri is in blue, and L. ivanovii is in purple.
Tables
- TABLE 1
Descriptive analysis of nucleotide sequence data for the 660-bp sigB fragment
Taxon (no. of sequences) No. of: G+C content (%) πb kc Tajima's D valued No. of mutationse dN/dS ratiof Haplotypesa Polymorphic sites Mutations Syn Nonsyn Listeria sensu stricto (4,280) 160 181 255 38.0 0.075 48.953 1.944 NA NA 0.011 L. seeligeri (667) 23 49 51 38.3 0.017 11.239 1.524 49 2 0.013 L. welshimeri (565) 37 30 30 36.9 0.003 2.041 −1.374 24 6 0.027 L. innocua (1,226) 41 33 35 37.3 0.010 6.869 1.279 30 5 0.044 L. ivanovii (12) 4 25 25 39.6 0.015 9.879 0.861 23 2 0.017 L. marthii (14) 6 17 17 37.2 0.011 7.418 1.599 17 0 0.000 L. monocytogenes (1,796) 50 94 103 38.9 0.022 14.515 0.372 NA NA 0.017 Lineage I (1,032) 10 13 13 38.9 0.004 2.452 −0.885 13 0 0.000 Lineage II (692) 12 34 35 38.8 0.001 0.757 −2.206 31 4 0.033 Lineage III (59) 24 26 26 38.7 0.005 3.571 −1.160 23 3 0.020 Lineage IV (13) 4 3 3 38.7 0.001 0.462 −1.652 3 0 0.000 ↵a Sites with gaps are excluded in DnaSP, which was used to determine the number of haplotypes; as AT103, AT154, and AT165 have deletions in their sequences (2, 1, and 3 nucleotides, respectively), the number of Listeria sensu stricto haplotypes (n = 160) is less than the number of ATs (n = 164).
↵b Average pairwise nucleotide diversity per site.
↵c Average number of pairwise nucleotide differences per sequence.
↵d Tajima's D values significantly different from 0 are marked in boldface type.
↵e Syn indicates the number of synonymous mutations; Nonsyn indicates the number of nonsynonymous mutations. If the number of synonymous or nonsynonymous mutations could not be unambiguously inferred, e.g., in highly divergent populations where there are multiple mutations per site, the result is reported as NA (not available).
↵f The ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. The dN/dS ratio was calculated based on the average dN and dS values obtained by pairwise comparisons of sequences using approximate methods.
- TABLE 2
Putative recombination events inferred by RDP4 and PHI testa
Taxon Recombination determined by RDP4 P value for recombination determined by PHI testb Recombinant sequence Putative parental sequence (minor × major donor) Detection method(s) Listeria sensu stricto L. monocytogenes AT 98 L. marthii AT 143 × L. monocytogenes AT 83 Maxchi 0.930 L. monocytogenes AT 151 L. innocua AT 141 L. monocytogenes AT 75 × L. innocua AT 139 SiScan L. seeligeri L. seeligeri AT 9 L. seeligeri AT 68 × L. seeligeri AT 92 Maxchi 0.980 L. welshimeri 0.750 L. innocua L. innocua AT 124 L. innocua AT 139 × L. innocua AT 87 Bootscan, SiScan, 3Seq 0.002 L. innocua AT 33 L. ivanovii 1.000 L. marthii L. marthii AT 143 L. marthii AT 95 × L. marthii AT 18 Bootscan, Maxchi, LARD 0.440 L. monocytogenes 0.297 Lineage I 0.045 Lineage II 1.000 Lineage III 0.440 Lineage IV NA - TABLE 3
Results of positive selection analysis using PAML
Taxon Ln L M1aa Ln L M2ab Significance value for comparison of Ln L M1a and Ln L M2ac Ln L M7a Ln L M8b Significance value for comparison of Ln L M7 and Ln L M8c Listeria sensu stricto −3,692.729 −3,692.727 0.998 −3,685.556 −3,686.692 0.321 L. seeligeri −1,198.649 −1,198.649 1.000 −1,198.655 −1,198.655 1.000 L. welshimeri −1,138.146 −1,138.146 1.000 −1,138.166 −1,138.166 1.000 L. innocua −1,354.596 −1,353.314 0.277 −1,354.272 −1,352.991 0.278 L. ivanovii −956.510 −956.510 1.000 −956.511 −956.511 1.000 L. marthii −958.010 −958.009 0.999 −958.009 −958.010 0.999 L. monocytogenes −1,521.006 −1,521.006 0.999 −1,521.934 −1,521.047 0.412 Lineage I −947.277 −947.276 1.000 −947.276 −947.277 1.000 Lineage II −1,046.284 −1,046.283 1.000 −1,046.289 −1,045.390 0.407 Lineage III −1,057.886 −1,058.357 0.625 −1,057.889 −1,057.889 1.000 Lineage IV −872.673 −872.673 1.000 −872.673 −872.673 1.000 ↵a Ln L M1a and Ln L M7, log-normal likelihood scores for the null hypothesis that the data set evolved following a neutral model.
↵b Ln L M2a and Ln L M8, log-normal likelihood scores for the alternative hypothesis that the data set evolved under positive selection.
↵c The test statistic was calculated as 2[(−Ln L M1a) − (−Ln L M2a)] and 2[(−Ln L M7) − (−Ln L M8)].
- TABLE 4
Molecular evolution parameters for sigB
Taxon DNA substitution modela ti/tv ratiob Alphac P-invd Listeria sensu stricto HKY+I+G 3.37 0.90 0.61 L. seeligeri TrN+I 0.76 L. welshimeri HKY+I 4.24 0.90 L. innocua HKY+I+G 2.59 0.53 0.90 L. ivanovii HKY 7.91 L. marthii HKY+I 11.32 0.94 L. monocytogenes TrN+G 0.22 Lineage I HKY+I 2.35 0.93 Lineage II HKY 2.31 Lineage III TrN+I 0.81 Lineage IV HKY NA ↵a HKY, Hasegawa-Kishino-Yano model; I, invariable sites; G, gamma distribution; TrN, Tamura-Nei model.
↵b Ratio of transitions (ti) to transversions (tv). If the ratio could not be unambiguously inferred, the result is reported as NA (not available); this is reported only for the HKY model since the TrN model uses variable transition rates.
↵c The alpha parameter defines the shape of the gamma distribution; this is reported only if the DNA substitution model includes a gamma distribution.
↵d Proportion of invariable sites; this is reported only if the DNA substitution model includes an invariable-site parameter.
- TABLE 5
Test of the molecular clock
Taxon Ln L clocka Ln L no clockb Significancec Molecular clock conclusiond Detected by PAUP* Listeria sensu stricto −2,911.235 −2,750.182 0.000 Reject L. seeligeri −1,345.168 −1,302.799 0.000 Reject L. welshimeri −1,232.536 −1,215.159 0.480 Fail to reject L. innocua −1,524.065 −1,474.704 0.000 Reject L. ivanovii −1,055.664 −1,026.337 0.000 Reject L. marthii −1,034.063 −1,025.077 0.001 Reject L. monocytogenes −1,837.100 −1,713.537 0.000 Reject Lineage I −1,026.237 −1,015.145 0.008 Reject Lineage II −1,150.381 −1,108.575 0.000 Reject Lineage III −1,154.203 −1,136.741 0.039 Reject Lineage IV −915.453 −914.652 0.449 Fail to reject Detected by PAML Listeria sensu stricto −2,699.124 −2,544.663 0.000 Reject L. seeligeri −1,331.701 −1,289.192 0.000 Reject L. welshimeri −1,230.322 −1,213.313 0.515 Fail to reject L. innocua −1,450.986 −1,401.417 0.000 Reject L. ivanovii −1,042.710 −1,014.496 0.000 Reject L. marthii −1,031.025 −1,022.056 0.001 Reject L. monocytogenes −1,791.820 −1,666.501 0.000 Reject Lineage I −1,016.090 −1,005.958 0.016 Reject Lineage II −1,150.315 −1,108.882 0.000 Reject Lineage III −1,141.821 −1,123.196 0.022 Reject Lineage IV −914.253 −913.446 0.446 Fail to reject ↵a Ln L clock, log-normal likelihood score for the null hypotheses that the data set evolved following a molecular clock.
↵b Ln L clock, log-normal likelihood score for the alternative hypotheses that the data set did not evolve following a molecular clock.
↵c The test statistic for the molecular clock was calculated as 2[(−Ln L clock) − (−Ln L no clock)].
↵d Conclusion to reject or fail to reject the null hypothesis.
Supplemental material
- Supplemental file 1 -
Codon usage bias (Table S1), tree topology tests (Table S2), additional recombination analysis (Table S3), accession numbers of 21 whole-genome sequences (Table S4), rearranged tree topology (Fig. S1), and optimal tree topology (Fig. S2).
PDF, 162K
- Supplemental file 2 -
Metadata for 1,420 isolates and 164 sigB AT representative isolates used in this study (Data Set S1).
XLSX, 154K
- Supplemental file 1 -
