Phylogenetic variation of the individualized S.
epidermidis isolates. A, two alternative scenarios of
within-individual evolution. Each circle represents a cluster of isolates
diverged from a single founder lineage colonizing a given host. In the first
scenario (left), all isolates from a given host diverged from a single founder
lineage; in the second scenario (right), isolates from each host diverged from
multiple distinct founder lineages. B, core-genome phylogeny (midpoint rooted)
based on 58498 core-genome SNP loci for the 1482 isolates sampled in this study
and 50 previously sequenced isolates from multiple diseased and healthy
individuals. Skin site of each isolate is indicated in green. C, individualized
S. epidermidis isolates evolved from multiple founder
lineages. Each founder lineage is represented by a circle and is defined as the
highest node from which at least 95% of the derived isolates (i.e. tip nodes)
were either found in the same subject or public strains. The size of the circle
represents the number of isolates derived from that lineage. D, pairwise
cophenetic distances of the 1482 isolates. Note that the distribution of
‘between-subject’ distances depends on the sample size per
subject, with p0, who had the most isolates cultivated, having the largest
contribution. The toeweb is highlighted to illustrate its unusual
between-subject similarity.