Figure 1.
Life cycle of D. discoideum showing the vegetative, social, and sexual.
During the vegetative cycle, single cells feed on bacteria and divide mitotically. Upon starvation, single cells aggregate and, depending on environmental conditions, enter the social cycle or the sexual stage. During the social stage, single cells aggregate and form a multicellular fruiting body that consists of a stalk made of dead cells holding aloft a sorus containing the fertile spores. During the sexual stage, two haploid cells fuse and ingest the other aggregating cells to form a macrocyst. This figure was published under CC Creative Commons Attribution - Share Alike 3.0, David Brown & Joan E. Strassmann and is available at http://www.dictybase.org/Multimedia/DdLifeCycles/index.html.
Figure 2.
Identification of unchanged sites and unique mutations.
Analysis pipeline and examples of rules used to identify mutations (red) unique to one mutation accumulation line, and unchanged nucleotides (green). Each line represents a hypothetical position in the genome and is characterized by the chromosome (Chr), position (Pos), and the reference base (Ref). Columns 4–6 list the majority consensus base for the three MA lines (MA31, MA47, MA55). Columns 7–9 show the number of reads covering this particular position in the three MA lines, columns 10–12 list the fraction of reads agreeing with the majority base. We used a minimum agreement of 90%. Column 13 gives the read coverage for this position for the self-mapping of the genome and indicates whether the position is uniquely mappable (if self-mapping coverage = 62). Columns 14–16 give the results from our filtering criteria, with unchanged sites indicated in green, mutations in red, and confirming bases in yellow. Positions that were not covered in all three lines were excluded from the analysis.
Figure 3.
The relationship of mutation rates and genome size or AT content.
Mutation rate (as X×10−9 per nucleotide) per generation and mutation rate per cell division are plotted as a function of genome size (in MB) (A and B) and as a function of AT content (C and D). We observed a significant relationship between mutation rate and genome size (Log10(mutation rate) = −1.0909+0.7505×log10(Genome size), with R2 = 0.58 and p = 0.0024.), but not for mutation rate per cell division or mutation rates and AT content. D. discoideum is represented by the red dot; the error bars indicate the Poisson confidence interval for our nuclear mutation rate. Mutation rates for Eubacteria and Archaea are given as averages of multiple estimates and are represented by open symbols. The average mutation rate of Eubacteria does not include Buchnera aphidicola due to its unusually high mutation rate, which is characteristic for endosymbionts. Circles represent mutation rate estimates obtained from high-throughput sequencing of MA lines; estimates obtained through other methods are represented by triangles. Mutation rates for yeast are calculated as the average from Lynch [8] and Nishant et al. [15]; all other estimates are from Lynch [8].