Generators of phenotypic diversity illustrated as a game of chance.

<p>Evolution is a multifactorial process that depends on numerous complex factors, including routes to diversity that can be deleterious, neutral, or advantageous depending on the environment. Here we depict these evolutionary trajectories using the analogy of a roulette wheel in which one possible path yields a winner that develops a new trait that allows the microorganism to survive in novel conditions, such as a host treated with antimicrobial agents. However, as in roulette, the odds are against the gambler and the other routes and outcomes are deleterious.</p

Summary of basidia dissected from opposite sex mating between strains 431α and XL280a.

1<p>: The strain names correspond to those in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s009" target="_blank">S4 Table</a>.</p>2<p>: Mixture of basidiospores from two basidia.</p>3<p>: No spore germinated.</p><p>Summary of basidia dissected from opposite sex mating between strains 431α and XL280a.</p

Recombination frequencies during α-α unisexual and a-α bisexual reproduction.

1<p>: Numbers within square brackets are genetic distances in the same intervals during <b>a</b>-α bisexual reproduction.</p>2<p>: The minimum recombination frequency (kb/cM) within the interval was calculated using 0.1 cM as the estimated maximum genetic distance.</p>3<p>: Marker intervals that showed significantly higher recombination frequencies compared to chromosomal intervals within the same LG as well as the chromosomal average.</p>4<p>: Could not be inferred due to discrepancies between marker orders within linkage groups and their relative physical location on chromosome 4.</p><p>Recombination frequencies during α-α unisexual and a-α bisexual reproduction.</p

Biased allele inheritance among progeny from α-α unisexual reproduction.

<p>The X-axis shows the positions of the markers, and the Y-axis indicates the percentage (%) of unisexual progeny that inherited allele “b” from parental strain XL280αSS at each marker. The dashed line indicates 60%. The green circle highlights a cluster of four markers that showed particularly high allele “b” frequencies, while the red circle highlights a cluster of three markers that showed relatively lower allele “b” frequencies. The red and green columns indicate the locations of the centromere and <i>MAT</i> locus, respectively.</p

Crossovers are distributed along chromosome 4 during α-α unisexual and a-α bisexual reproduction.

<p>Blue bars represent the number of progeny from α-α unisexual reproduction between strains 431α and XL280αSS, while the red bars represent the number of genotypes from <b>a</b>-α bisexual reproduction between strains 431α and XL280<b>a</b>. The 12 progeny from α-α unisexual reproduction, as well as the 2 genotypes from <b>a</b>-α bisexual reproduction that were disomic for chromosome 4 were excluded.</p

Phenotypic analyses of progeny from α-α unisexual and a-α bisexual reproduction.

<p>A) Top: Different phenotypic categories that were observed among the meiotic progeny from α-α unisexual and <b>a</b>-α bisexual reproduction. Bottom: Summary of percentage (%) of progeny that belonged to different phenotypic categories in α-α unisexual and <b>a</b>-α bisexual reproduction. Blue triangles highlight the phenotypes of parental strain 431α; red triangles highlight the phenotypes of the parental strains XL280αSS and XL280<b>a</b>. B) Phenotypic segregation of hyphal growth among the meiotic progeny from α-α unisexual and <b>a</b>-α bisexual reproduction. The numbers represent the percentage of progeny that belong to different phenotypic categories. Blue triangles highlight the phenotypes of parental strain 431α; red triangles highlight the phenotypes of the parental strains XL280αSS and XL280<b>a</b>. C) The small and large colonies of the meiotic progeny SSB309 when grown on YPD solid medium at 30°C.</p

Biased allele inheritance among progeny from a-α bisexual reproduction.

<p>Numbers in the top row indicate the loci/genetic markers used for genotyping progeny from <b>a</b>-α bisexual reproduction, with the markers flanking the centromere are highlighted in red and the markers within the <i>MAT</i> locus are highlighted in green (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen-1004849-t002" target="_blank">Table 2</a> for detailed information). For simplicity, only the unique genotypes are shown for each of the eight basidia that showed biased allele inheritance. The markers that exhibited biased allele inheritance are highlighted by rectangles, with red color indicating a bias toward the “a” allele and green color indicating a bias toward the “b” allele.</p

Meiotic progeny disomic for chromosome 4 are produced by α-α unisexual and a-α bisexual reproduction.

<p>Top panel: Meiotic progeny from α-α unisexual reproduction between strains 431α and XL280αSS that are disomic for chromosome 4 are shown. Bottom panel: Meiotic progeny from the <b>a</b>-α bisexual reproduction between strains 431α and XL280<b>a</b> that are disomic for chromosome 4 are depicted. The marker numbers in each panel correspond to those listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen-1004849-t002" target="_blank">Table 2</a>. For simplicity, not all of the markers for α-α unisexual reproduction are shown (please see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s007" target="_blank">S3 Table</a> for complete genotyping profiles). The markers located within the <i>MAT</i> locus are highlighted in green, while the markers flanking the centromere are highlighted in red. The values for ploidy were estimated based on FACS analyses and whole genome sequencing (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s001" target="_blank">S1</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s002" target="_blank">S2 Figure</a>), where 1N represents haploid and 2N represents diploid. Additionally, the “+” and “−” following 1N or 2N indicate the presence and absence of specific chromosomes, respectively. For example: 2N+2^2,3 (SSB359-small) represents diploid (2N) with additional two chromosomes (ch. 2 and 3). The small colony from progeny SSB552 appears to be a mixture of individuals with varying ploidy levels (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s002" target="_blank">S2 Figure</a>), and is thus designated as “undetermined” here.</p

Recombination within the <i>MAT</i> locus during α-α unisexual reproduction.

<p>A) Of the 42 genetic markers (only No. 21 to No. 42 are shown here for simplicity) that were analyzed for progeny from α-α unisexual reproduction, progeny SSB369 inherited “a” alleles from parental strain 431α for all but 6 markers (No. 31–No. 36; see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen-1004849-t002" target="_blank">Table 2</a> for detailed marker information), which were continuous and located either within or at the edge of the <i>MAT</i> locus. The run of allele “b” stopped between markers No. 36 and No. 37 within the <i>MAT</i> locus at the 5′ end, and between markers No. 30 and No. 31 that flank the <i>MAT</i> locus at the 3′ end. The red dashed-lined rectangle indicates the <i>MAT</i> locus. B) Fine mapping conducted by sequencing the region between markers No. 36 and No. 37 showed that in progeny SSB369 the breakpoint within the <i>MAT</i> locus for the run of “b” alleles is located inside the <i>GEF1</i> gene, within a region of 150 bp in size.</p

Transient aneuploid and persistent diploid progeny are generated from α-α unisexual reproduction.

<p>A) The three panels show the read depths of all chromosomes in the three parental strains: 431α, XL280αSS, and XL280<b>a</b>. For each panel, the x-axis indicates the 14 chromosomes and the y-axis indicates the read depth from the Illumina sequencing. These strains had only one copy of chromosome 4, as no heterozygosity was detected for any marker from chromosome 4 that was analyzed, and thus, all are haploid. This was also consistent with results from the FACS analyses (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s001" target="_blank">S1 Figure</a>). B) The six panels show the read depths of all chromosomes in strains derived from three meiotic progeny from α-α unisexual reproduction between strains 431α and XL280αSS. For each panel, the x-axis indicates the 14 chromosomes and the y-axis indicates the read depth from the Illumina sequencing. All of these strains showed heterozygosity at multiple markers along chromosome 4 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen-1004849-g006" target="_blank">Fig. 6</a>), indicating they had at least two copies of chromosome 4. FACS analyses indicated that these strains were likely diploid (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004849#pgen.1004849.s001" target="_blank">S1 Figure</a>), which was consistent with the sequencing results shown here suggesting all of the meiotic progeny had two copies for the majority of the chromosomes (including chromosome 4). The two panels within each of the three dashed-lined rectangles are sequencing results of small and large colonies, respectively, that were derived from the same meiotic progeny. C) The distribution of SNPs along chromosome 14 in the small and large colonies of the progeny SSB309, as well as the two parental strains 431α and XL280αSS. The genome sequence of each isolate was mapped against the published genome sequence of strain JEC21. The light blue bars indicate SNPs compared to JEC21, dark blue bars indicate heterozygous sites, while grey areas indicate regions that are identical to JEC21. The centromeric region of chromosome 14 is highlighted by the green rectangle.</p