Figure 8. Patterns of molecular evolution and loss of heterozygosity in diploids.

(A) Genomic positions of all mutations that experienced loss of heterozygosity (LOH) across all diploid populations (loss of heterozygosity defined by a mutation reaching >90% frequency). Orange marks represent mutations in the ADE pathway. Each horizontal line represents one population, and the histogram at right represents the total number of LOH fixations in each population, with populations arranged by environment. The top histogram represents the frequency of loss of heterozygosity across the genome, and the chromosomes underneath show the centromere location with a black circle. Genes with five or more LOH fixations are annotated. (B) The fraction of fixed nonsynonymous mutations that are in essential genes, plotted for mutations fixed in haploid populations, mutations fixed homozygously in diploid populations (LOH) and mutations fixed heterozygously in diploid populations, plotted separately for mutations annotated as high or moderate impact by SnpEff (high-impact mutations are likely to cause loss-of-function). The dashed line represents the fraction of the coding genome that is in essential genes. (C) The ratio of high-impact to moderate-impact fixations in the same three mutation groups as in (B), for mutations in non-essential genes only.

Figure 8—figure supplement 1. The ploidy state of two clones from each focal population, shown by FITC histograms of Sytox-stained cells.

The x-axis is in arbitrary fluorescence units, and the y-axis is normalized frequency. We have shaded the area where single-genome-copy cells (1N) usually fall to help identify haploids. Populations with abnormal FITC histograms are marked by asterisks. P1B03 is the only haploid population that became diploid. Based on sequencing data, this transition likely happened between generation 5000 and generation 7500 (Figure 3—figure supplement 3). P1H11 and P3F11 both had one diploid and one haploid clone, suggesting that diploids may be present in these populations, but have not fixed. P1B04 and P1B11 have strange FITC histograms, which we believe is due to clustering phenotypes in these populations (Figure 8—figure supplement 2). Based on continued fixations in sequencing data even at the final timepoint, it is unlikely that diploid haplotypes have played a significant role in any of these four populations up to this point in the evolution (Figure 3—figure supplements 3, 4 and 10).

Figure 8—figure supplement 2. Cell imaging from three populations with abnormal Sytox data.

Note the clustering phenotypes observed in later timepoints of P1B04 and P1B11. The microscope failed to capture an image for P1B04 generation 10190. All imaging data is available in Supplementary file 6.