Number of populations using in the STRUCTURE analysis calculated according to [35].

<p>The results presenting in (A) show three populations in the Brazilian <i>Cryptococcus gattii</i> VGII and in (B) show four populations in the STs identified in different countries previously published and in Brazil.</p

Minimum spanning tree using the goeBURST algorithm.

<p><b>(A)</b> Minimum spanning tree using the goeBURST algorithm showing the high diversity identified among the 145 Brazilian <i>Cryptococcus gattii</i> VGII isolates and nine Brazilian sequence types (ST) according to the state where they were recovered. Dividing the country in two macro regions such as North (composing of the States of Amazonas, Roraima, Pará, Piauí, and Bahia) and South (States of Mato Grosso do Sul, São Paulo, and Rio de Janeiro) three main groups can be identified: 1) isolates mainly recovered from the South, representing all isolates derived from the ST301; 2) isolates mainly recovered from the North, representing those originated from the ST7 (VGIIb), and 3) the mixed group, which contains isolates derived from ST281. The main clonal complexes (CC) in each of these groups are: CC40, CC5, and CC20. The ancestors of the CC is highlighted by a black line. <b>(B)</b> Minimum spanning tree using the goeBURST algorithm of the isolates presented in (<b>A)</b>, and their comparison with 42 STs identified in different countries previously published. All country abbreviations are designated according to the alpha-2 code of ISO 3166–1. In both figures each circle represents a unique ST, and the circumference is proportional to the number of isolates within each ST. Solid, grey and dashed branches represent at least one, two to three, and more than four or five differences, respectively. All STs are different VGII lineages, only the three PNW outbreak genotypes are labelled specifically as VGIIa (ST20), VGIIb (ST7), and VGIIc (ST6).</p

Split decomposition analysis using the Neighbor-net algorithm of the each of seven MLST genes evidencing the diversity and branching ambiguities attributable to recombination events in the <i>CAP59</i> and <i>SOD1</i>.

<p>The phi test result implemented in the software SplitsTree is presented next to each allele.</p

Characteristics of the studied Brazilian regions.

<p>Characteristics of the studied Brazilian regions.</p

Population structure analysis inferred using multilocus sequence genotypes of <i>Cryptococcus gattii</i> isolates recovered from Brazil and using <i>K</i> = 3 (A), and comparison of these isolates with isolates recovered from different continents using <i>K</i> = 4 (B).

<p>Clusters of individuals based on prior-defined populations are referred according to the Brazilian States and/or Continent. Each vertical line represents one of the isolates included and each color (red, dark blue, dark green, and yellow) represents the most likely ancestry of each isolate from one of the three populations (A) or four populations (B). Individuals with multiple colours have admixed genotypes from the prior-defined populations. One clone per region was included, thus Figure A contains 100 isolates while Figure B contain 125 isolates. The taxa nomenclature includes AM: Amazonas, PA: Pará, PI: Piauí, RR: Roraima, BA: Bahia, ES: Espírito Santo, RJ: Rio de Janeiro, MS: Mato Grosso do Sul, AS: Asia, AU: Australia, AF: Africa, SA: South America, NA: North America, EU: Europe.</p

Linkage disequilibrium heat maps between polymorphic sites for all studied MLST loci (<i>CAP59</i>, <i>GPD1</i>, <i>PLB1</i>, <i>SOD1</i>, IGS1, <i>LAC1</i> and <i>URA5</i>).

<p>Pairwise D’ metricises are represented by heat colours (Colour Key). Recombination amongst Brazilian VGII strains has been shown, as evidenced amongst four sites (0.7%) in the locus <i>CAP59</i> and six sites (0.8%) in the locus <i>SOD1</i> (Fisher’s Exact Test P-value ≤ 0.05).</p