Supplementary Text
Population structure and recombination
Phylogenetic trees of clonal organisms reflect ancestry, but both the topology and branch lengths can
be distorted when recombination occurs. We therefore investigated the population structure within the
sequences by the linkage model of STRUCTURE (Falush et al., 2003), a population genetic approach
which identifies SNPs associated with distinct ancestral populations and estimates the quantitative
degree of recombination between those ancestral populations in modern isolates (admixture) as well
as their proportions of ancestry from the different ancestral sources. Thus, the linkage model detects
admixture between populations whereas CLONALFRAME detects admixture with bacteria from
external lineages. Initial comparative analyses showed that the four Lineages and L. monocytogenes
were derived from only four ancestral populations (see experimental procedures for details). Only
very little admixture was detected in Lineages I, II, III and L. innocua, indicating largely clonal
descent from one of the four ancestral populations (Fig. S4). In contrast, ~80% of the ancestry of
Lineage IV is derived from the ancestor of lineage III, and the remainder derives from the ancestral
populations of L. innocua (~15%) and Lineage I (~5%). A phylogenetic tree based on the proportion
of ancestry from each of the four ancestral populations is consistent with these conclusions (Fig. S4
top). Three of the primary branches within that tree delineate STs assigned to Lineages I, II and L.
innocua by CLONALFRAME. The fourth major branch separates into Lineages III and IV, as
previously, but ST512 and ST351 of Lineage III now cluster within Lineage IV. In addition to the
admixture between Lineages III and IV, we also detected minor traces of admixture in 24% (37/154)
of STs in Lineage I , 18% (30/164) in Lineage II and 80% (21/26) of L. innocua (Fig. S4).
We also performed quantitative estimates of the frequency of homologous recombination with
external lineages using CLONALFRAME. r/m, the ratio of the probabilities that a given nucleotide was
altered due to recombination versus mutation, was low in Lineage I (r/m=0.2) and >3fold higher
within Lineage II (r/m=0.7) and the entire dataset (r/m=0.77). These estimates are similar to
CLONALFRAME estimates based on only 34 STs (Vos and Didelot, 2009), which placed the frequency
of recombination in L. monocytogenes near the lower end of the range found in multiple species, and
also similar to LDHAT estimates of intra-population admixture (Ragon et al., 2008). Thus,
recombination seems to happen within L. monocytgenes but at frequencies lower than that of
mutation, and the population structure of L. monocytogenes and L. innocua is therefore largely clonal,
with occasional minor exceptions. Our calculations are also compatible with the findings by
STRUCTURE that admixture was most frequent in Lineages III, IV and L. innocua (Fig. S4).
These conclusions confirm that microevolution of L. monocytogenes is largely clonal, i.e. that
diversification is driven predominantly by mutation rather than recombination. The lower frequency
of recombination in Lineage I (r/m=0.2) than in the overall population (r/m=0.8) may help to explain
why the population structure of Lineage I is more homogeneous than the other Lineages. Higher r/m
ratios (Lineage I: 0.66; Lineage II: 4.42) were calculated from results with an alternative MLST
scheme based on four housekeeping genes plus three virulence associated genes (den Bakker et al.,
2008). However, some of these genes are under positive selection (Nightingale et al., 2005), which
can also result in homoplasies and clustered mutations that influence estimates of recombination.
Furthermore, those analyses investigated ~200 isolates from various sources isolated within a four
year time period in New York State (den Bakker et al., 2008), and might not be representative of the
global population structure of Lineages I and II.
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