Genetic Stability and Evolution of the Allele, Used for Listeria Sensu Stricto Subtyping and Phylogenetic Inference

Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of , which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse isolates. In this study, evolutionary approaches were used to assess the validity of allelic typing for For a data set of 4,280 isolates, allelic typing showed a Simpson's index of diversity of 0.96. Analyses of 164 allelic types (ATs) found among the 6 species, representing these 4,280 isolates, indicate that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of , confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; displayed the lowest diversity and was the only species in which evolved in a clocklike manner, implying a unique natural history. Among the four lineages, evolution followed a molecular clock only in lineage IV. Moreover, displayed a significant negative Tajima value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. The absence of positive selection along with the violation of the molecular clock suggested a nearly neutral mechanism of evolution. While comparison with a whole-genome sequence-based phylogeny revealed that the phylogeny did not correctly reflect the ancestry of lineage IV, the availability of a large AT database allowed accurate species classification. allelic typing has been widely used for species delineation and subtyping of However, an informative evaluation of this method from an evolutionary perspective was missing. Our data indicate that the genetic stability of is affected by neither frequent homologous recombination nor positive selection, which supports that allelic typing provides reliable subtyping and classification of strains. However, multigene data are required for accurate phylogeny reconstruction of This study thus contributes to a better understanding of the evolution of and confirms the robustness of the subtyping system for .