Coalescence gene genealogy based on SCAR-MLST data.

<p>The historical coalescence gene genealogy of the global <i>Cryptococcus gattii</i> AFLP6/VGII population structure was reconstructed by using five nuclear SCAR-MLST loci from which homoplasious sites were removed resulting in a total number of 109 informative sites indicated on the branches as blue (‘Fragment 15′ locus), orange (‘Fragment 32′ locus), green (‘Fragment 34′ locus), red (‘Fragment 54′ locus) and purple (IGS1 locus) dots. Numbers next to these dots represents the position of the site within the sequence of informative sites (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s007" target="_blank">Table S1</a>). Haplotypes that represent lineages currently involved in outbreaks or case cluster are indicated along the lines of these haplotypes. Numbers behind the populations indicate the number of strains within the given population/haplotypes. Mouse virulence and IPR results are shown as red or green mice and macrophages, respectively, to represent virulent and non-virulent strains as indicated in Fig. 4 and 5, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s009" target="_blank">S3</a>. The ‘generation time to the most common recent ancestor’ (GTMRCA) in ‘generations before present’ is provided (bold), including the lower and upper boundaries.