A New Perspective on Listeria monocytogenes Evolution
Figure 2
Homologous recombination is rare, but distorts phylogenetic reconstruction.
A) Proportions of ancestry in seven housekeeping genes of L. monocytogenes strains from three ancestral populations as inferred by the linkage model of structure. This plot shows one vertical line for each isolate in which the proportions of ancestry from the three sources are color-coded. For example, strain CLIP85 was inferred as having mixed ancestry, with approximately 75% of nucleotides originated from lineage III (blue), whereas 25% of them were inferred to have an origin in lineage II (green). A number of strains from lineage I have a small proportion of nucleotides with ancestry in lineage III, while strains of lineage II had some nucleotides from lineages I (red) or III (blue). The case of CLIP98 is particular, as it was inferred as deriving from lineage II by imports mainly from L. innocua (see text). B) Neighbor-joining phylogenetic analysis of concatenated housekeeping gene sequences, using the Tamura-Nei+G+I model. The three major L. monocytogenes lineages are recognized. Together, they included all strains except CLIP85 and CLIP98. Bootstrap support of lineages is given at corresponding branches. An asterisk (*) marks strains that were recognized by structure to contain a fraction of nucleotides imported from another ancestral population, with corresponding branches colored according to the source of the recombined nucleotides. Recombination events detected independently using with RDP3 are numbered from 1 to 7 (referring to Table S2), and the involved genes are indicated.