Chromosome copy number variation was identified across the three <i>Bd</i>CH isolates (ACON and its progenitors CON2A and APEP) following 40 generations in culture with or without the addition of anti-microbial peptides (AMP), respectively.

<p>Read depth is normalised to total alignment depth. A tally of all loci (per kilobase) with between 25–75% reads agreeing with the reference nucleotide are shown below, and summarised by the most common allele (black line), the second most common allele (blue line), and bins between 32–34, 49–51 and 65–67% (red circles). ACON is putatively triploid across the largest six supercontigs, whereas CON2A has lost a copy of supercontig IV and gained a copy of supercontigs V. APEP has gained a copy of supercontigs V.</p

Samples used and details of alignments.

<p><i>Bd</i> isolates and locations that were resequenced. The first 4 columns provide information for the recommended naming scheme outlined by Berger <i>et al.</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003703#pgen.1003703-Berger1" target="_blank">[47]</a>. Passage numbers are best approximations from records prior to DNA extractions in January and May 2011. The sequenced depth and aligned depth were calculated from the number of nucleotides in all or aligned reads respectively and divided by 24 Mb (the length of the <i>Bd</i> JEL423 genome assembly). All isolates represent novel sequences, apart from JEL423 and TF5a1 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003703#pgen.1003703-Farrer1" target="_blank">[22]</a>. Amphibian hosts include <i>Afrixalus enseticola</i> (Ethiopian Banana frog), <i>Alytes muletensis</i> (Mallorcan Midwife Toad), <i>Alytes obstetricans</i> (Common Midwife Toad), <i>Amietia angolensis</i> (Angola River Frog), <i>Amietia fuscigula</i> (Cape River Frog), <i>Amietia vertebralis</i> (Ice Frog), <i>Discoglossus sardus</i> (Tyrrhenian Painted Frog), <i>Epidalea calamita</i> (Natterjack Toad), <i>Leptopelis sp.</i> (Big eyed Tree Frog), <i>Lithobates catesbeianus</i> (American Bullfrog), <i>Phyllomedusa lemur</i> (Lemur Leaf Frog). CM = Claude Miaud, DG = David Gower, JEL = Joyce Longcore, MF = Matthew Fisher, PH = Phineas Hamilton, PM = Peter Minting, RF = Rhys Farrer, TG = Trent Garner.</p

Boxplots for eight non-overlapping gene categories comprising every gene were compared for ratios of non-synonymous to synonymous mutations for each of the three lineages (dN/dS) and numbers of crossovers per phased positions (PP) within each gene (≥2PP) for all isolates (outliers omitted for both).

<p>Proteases and chitin-associated genes with predicted signal peptides had greater <i>dN</i>/<i>dS</i> ratios than those without for both <i>Bd</i>CAPE and <i>Bd</i>CH. CRN-like genes had the greatest upper quartile and upper tail showing these to be the most variable genes in the genome.</p

Read depth across 22 genomes was normalised by total alignment depth and plotted against location in the genome using a 10 Kb long non-overlapping sliding window.

<p>Base ploidy levels were determined using allele frequencies for supercontig 1 and shown at the start of each plot. Intra-chromosome read depth is largely consistent amongst the isolates, except over supercontig 14 due to a long stretch of rDNA. Shifts in read-depth between chromosomes demonstrate variation in chromosome copy number.</p

Haplotypes from isolates belonging to each of the separate lineages were tested for linkage disequilibrium using the index of association (I_A), rBarD and the 4-gamete test.

<p>To check differences between lineages were not resulting from different numbers of isolates, 2 subsets were made from <i>Bd</i>GPL. Subset 1 consisted of isolates VC1, AP15 and JEL423. Subset 2 consisted of subset 1, ETH4 and MODS27. For each isolate subset, the total length (in nucleotides) of all haplotypes and the total number of loci with ≥2 alleles is given. Over 30% of the <i>Bd</i>GPL haplotypes from any of the subsets were in significant disequilibrium, whilst only 11% of the haplotypes in <i>Bd</i>CH and 16% of the haplotypes in <i>Bd</i>CAPE were in disequilibrium, suggesting these populations are recombining more than the clonal <i>Bd</i>GPL. The numbers of variable sites per locus are also shown, demonstrating all lineages to be as likely to have arisen from out-crossing.</p

Summary of variant calling from Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus <i>Cryptococcus gattii</i>

Summary of variant calling from whole genome sequencing of 64 isolates of Cryptococcus gattii aligned to the nuclear genomes of VGIIa isolate R26

Summary of phenotypic analysis of Cryptococcus gattii strains. from Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus <i>Cryptococcus gattii</i>

Columns show the average intracellular proliferation rates (IPR) with standard error, percent of yeast with tubular mitochondria, average percent of C. gattii phagocytosis by macrophages, percent of cells that were expelled without being destroyed ('vomocytosis') and the percent of macrophage dept

Genetic differences from Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus <i>Cryptococcus gattii</i>

All genetic differences identified between VGIIc EJB52 and VGIIc EJB1

Presence/absence polymorphisms from Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus <i>Cryptococcus gattii</i>

Presence/absence polymorphism

Molecular characterisation of progeny from outgroup cross CBS10090 x NIH312.

<p><b>A</b>) Self-fertility of NIH312 x CBS10090 progeny. Green coloration indicates self-fertility and red coloration indicates no signs of self-fertility after four weeks. <b>B</b>) MLST analysis of NIH312 x CBS10090 progeny was conducted at eight unlinked loci, and scored as VGIII parental (blue), VGII parental (yellow), or both VGII and VGIII (green). The mitochondrial inheritance is also indicated (uniparental). The ploidy determination is listed based on FACS analysis. Progeny 9 is indicated as 1–2N due to an unclear FACS plot, although the molecular and self-fertility assays indicate it is diploid. ^†CBS10090 mitochondrial type by MLST, but subsequent sequencing indicated that it actually carries a recombinant genome (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003771#pgen-1003771-g010" target="_blank">Figure 10</a>).</p