Figure: Sterile mutations experienced four general fates over 1000 generations of experimental evolution. The simplest case is a selective sweep: a spontaneous sterile mutation arises and increases in frequency until it fixes (upper left). More commonly, sterile alleles rose to some frequency, but were outcompeted by a more-fit lineage before they were able to fix (clonal interference, upper right). More complicated trajectories were also observed, wherein sterile strains rise, are subjected to clonal interference, and then increase in frequency again (lower left). This could reflect a second beneficial mutation occurring in a declining sterile population, or a second sterile mutation occurring in the background of the competing mutation (as shown). We were surprised to also observe a fourth type of trajectory where sterile strains rise to some frequency and remain there for hundreds of generations, suggesting the action of frequency-dependent selection (lower right).

We find that the fitness advantage of each mutant plays a surprisingly small role in determining its ultimate fate. Rather, underlying genetic variation is quickly generated and plays a dominant role in determining the fate of new beneficial mutations.

Figure: Targeted gene disruptions show that loss the yeast mating pathway G-beta subunit (Ste4), the MAP kinase kinase (Ste7), or the transcription factor (Ste12) increases growth rate; however, loss of the pheromone receptor (Ste2) or Far1 does not. Ste4, Ste7, and Ste12 are required for basal signaling in the mating pathway, Ste2 and Far1 only play a role in pheromone-induced signaling.

To determine the basis for this advantage, I measured the fitness of select gene deletions. Deletion of Ste4, Ste7, and Ste12 results in a fitness advantage; however deletion of the receptor (Ste2) or the protein responsible for cell cycle arrest (Far1) does not confer an increased fitness. This suggests that the fitness advantage comes from loss of basal signaling through the mating pathway.

Recent work suggests that translesion synthesis is used only as a last-ditch effort to fill in these gaps and cannot occur until the end of S-phase. Therefore, regions of the genome that are replicated early in S-phase have longer to undergo template switching to replicate past lesions, whereas regions replicated late are more likely to require translesion synthesis.

Figure: This figure shows the correlation between the replication profile and mutation rate across yeast Chromosome VI.

Combining our estimates of phenotypic mutation rates and effective target sizes we conclude that the per-base-pair mutation rate at URA3 and CAN1 is 3.80 x 10^-10 and 6.44 x 10^-10 per base pair per generation, respectively, suggesting that the mutation rate varies across the yeast genome.

Figure: When we were asked to submit potential cover art for the Lang and Murray Genetics paper, this is the best I could come up with.

The caption that went along with the cover art submission read as follows:

The Luria-Delbruck fluctuation assay is a common method for measuring mutation rates. In the fluctuation assay, many parallel cultures are inoculated with a small number of cells, grown under non-selective conditions, and plated to select for mutants. Although the number of mutations that arise during the growth of a culture will follow the Poisson distribution, the number of mutant cells will vary greatly since early mutations will lead to "jackpots," cultures that contain a large number mutant cells. Seventy-two parallel yeast cultures were grown and spot-plated onto eight agar plates containing the drug canavanine. The random nature of the mutational process can be seen in the variation in the number of canavanine resistant mutants in each culture, including a "jackpot" on the plate in the lower left corner.