Allelic richness ± standard deviation (SD) of LAM9C1 and C2 subpopulations according to country of isolation.

<p>Allelic richness is evaluated for 12-loci MIRU-VNTRs using a rarefaction procedure (when n>25 per lineage and per country); countries names are defined by ISO 3166–1 alpha-3 code.</p><p>Allelic richness ± standard deviation (SD) of LAM9C1 and C2 subpopulations according to country of isolation.</p

Geographic distribution of LAM sublineages in various countries of Americas (when n>36).

<p>Phylogenetic clade assignation using spoligotyping follows rules of SITVITWEB database. Country codes are shown as ISO 3166–1 alpha-3 code.</p

12-loci MIRU-VNTR based demographic and dating estimates of LAM9 sublineages inferred by a Bayesian approach on Msvar 1.3 algorithm.

<p>(A) 2D Kernel density plots producing a smooth estimate of the density of the marginal posterior distribution of N0 the current effective population size, and N1 the population size before expansion (in log scale) for LAM9C1 isolates. (B) Same figure for LAM9C2 isolates. t_a, time elapsed since last expansion began expressed in years (log scale); R = N0/N1 traduce median value of expansion ratio; μ, mutation rate per locus and per generation. All estimates correspond to median values, followed by 95% highest posterior densities indicated in parentheses.</p

Allele copy number of MIRU-VNTR markers in LAM9C1 and LAM9C2 <i>M</i>. <i>tuberculosis</i> isolates.

<p>ND: Not done</p><p>Allele copy number of MIRU-VNTR markers in LAM9C1 and LAM9C2 <i>M</i>. <i>tuberculosis</i> isolates.</p

Evolutionary relationships of the LAM9 sublineage isolates (n = 450).

<p>(A) Geographical distribution and LAM9C1 and C2 isolates defined by Bayesian cluster analysis using STRUCTURE software run on 12-loci MIRU-VNTRs. Each of the strains is represented by a thin vertical line, partitioned into black or white segments that represent the strains estimated proportion of membership in clusters LAM9C1 and LAM9C2 respectively. (B) MST analysis on combined spoligotyping and MIRU-VNTR data for strains prelabeled as LAM9C1 (n = 226) and C2 (n = 208) based on previous STRUCTURE analysis (strains in intermediate position between C1 and C2 are indicated as LAM9 Int, n = 16). The complexity of the lines denotes the number of allele/spacer changes between two patterns while the size of the circle is proportional to the total number of isolates sharing same pattern. Country codes are shown as ISO 3166–1 alpha-3 code.</p

Distribution of main <i>M</i>. <i>tuberculosis</i> lineages and sublineages in Americas according to SITVIT2 database (n = 21183 strains) based on spoligotyping.

<p>Distribution of main <i>M</i>. <i>tuberculosis</i> lineages and sublineages in Americas according to SITVIT2 database (n = 21183 strains) based on spoligotyping.</p

Sequence variation of tandem repeat units.

<p>Dashes indicate a base deletion, and dots indicate an identical base compared to the reference sequence. Letters on the left indicate allele sequence codes.</p

Primer sequence for each VNTR marker amplified by nested PCR.

<p>Primer sequence for each VNTR marker amplified by nested PCR.</p

Localization of <i>M</i>. <i>ulcerans</i> samples in French Guiana.

<p>In bold isolates belonging to genotype II.</p

Characteristics of <i>M</i>. <i>ulcerans</i> samples used in this study and sequence types based on sequence variations of tandem repeat units.

<p>VNTR, Variable Number Tandem Repeat; MIRU, Mycobacterial Interspersed Repetitive Unit; FG, French Guiana;</p><p>* DNA purified from culture; in bold results obtained after PCR and sequencing without needing nested PCR</p><p>Characteristics of <i>M</i>. <i>ulcerans</i> samples used in this study and sequence types based on sequence variations of tandem repeat units.</p