eBURST diagrams of analyzed <i>Leishmania (Viannia)</i> strains.

<p>Six clonal complexes were found: CC1: <i>L. lainsoni</i>; CC2 <i>L. naiffi</i>; CC3 <i>L. shawi</i>; CC4 <i>L. braziliensis</i>; CC5 <i>L. braziliensis</i>; CC6 <i>L. guyanensis</i>. Predicted founders were identified for CC4 (DST12) and CC6 (DST37; IOC/L565). Only homozygous DSTs were used (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd.0001888.s001" target="_blank">Table S1</a>).</p

Haplotype analysis per marker for the 96 strains included in the present study.

<p>Percentages are relative to the number of different alleles.</p>*<p>HD - haplotype diversity.</p

Detail of target regions of each locus studied.

<p>Bp- base pairs; Fw - Foward; Rv – Reverse.</p>*<p>related to <i>L. braziliensis</i> genome.</p

Characteristics of each sequenced region for the 96 strains used in the present study.

<p>Percentages are relative to the total number of sites (% of length) or strains (% of total strains). PS – Polymorphic sites; PI - parsimony informative sites.</p

Kinetics of white blood cell counts in <i>Thrichomys laurentius</i> experimentally infected by <i>Leishmania braziliensis</i> (Lb) or <i>Leishmania infantum</i> (Li).

<p>Each point represents the mean values and standard errors. The * indicates the significant difference between values obtained from non-infected rodents (day 0) and and rodents infected by <i>L. braziliensis</i>.</p

Kinetics of red blood cell counts and hemoglobin levels in <i>Thrichomys laurentius</i> experimentally infected by <i>Leishmania braziliensis</i> (Lb) or <i>Leishmania infantum</i> (Li).

<p>Each point represents the mean value and standard errors. The continuous lines indicate the normal range defined by the medium values obtained for each group one-day before the inoculum and two-fold standard errors. The * indicates the significant difference between rodents infected either by <i>L. braziliensis</i> or <i>L. infantum</i>.</p

Maximum parsimony-based haplotype networks.

<p>A) G6PD; B) 6PGD; C) MPI; D) ICD. The 96 strains selected for the study (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd.0001888.s001" target="_blank">Table S1</a>) plus sequences of <i>Leishmania</i> (<i>Viannia</i>) strains retrieved from GenBank (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001888#pntd.0001888.s002" target="_blank">Table S2</a>) were included. Haplotype frequency is represented by the size of each node and the numbers of polymorphisms are indicated in the branches by dashes: one = 02 to 05 polymorphism; two = 06 to 10; three = more than 10 polymorphisms. Each species, considering the MLEE characterization, were assigned by different colors as coded by the legend.</p

NeighborNet graph based on concatenated sequences of four gene fragments of <i>Leishmania (Viannia)</i> subgenus.

<p>A bushy network structure is observed indicating homologous recombination. # = DSTs presenting ambiguous sites (possible heterozygous) in at least one locus; DSTs gathered in clonal complex are represented by different colored circles depending on the species: yellow - <i>L. braziliensis</i>; black – <i>L. guyanensis</i>; light blue – <i>L. shawi</i>; blue – <i>L. lainsoni</i>; red – <i>L. naiffi</i>. Singletons are represented by DST number only.</p

Kinetics of the humoral immune response (IFAT) in <i>Thrichomys laurentius</i> experimentally infected by <i>Leishmania braziliensis</i> (Lb) or <i>Leishmania infantum</i> (Li).

<p>Each point represents the mean value and standard errors of the IgG titers of infected rodents.</p

Characteristics of each sequenced region for all available <i>L. (Viannia)</i> (retrieved from GenBank plus the 96 strains included) and for <i>L. braziliensis</i> complex samples.

<p>Percentages are relative to the total number of sites (% of length).</p>*<p>PI - parsimony informative sites.</p