Fig 1.
The life cycle of budding yeast.
Fig 2.
(A) A schematic of the agent-based model, with the key biological and physical quantities. (B) Overview of the processes within a single cell cycle. Pd and Pb are the probabilities of cell death and normal budding (axial for haploid cells and bipolar for diploid cells), respectively. Ps and Pm are the frequencies of mating type switch and successful matings for haploid cells. The simulation stops when the maximal time or the maximal population is attained. (C) Normal budding patterns for haploid and diploid cells. Haploid cells bud in an axial manner: both mother and daughter cells have bud sites adjacent to the previous division site. Diploid cells bud in a bipolar budding pattern: mother cells have a new bud site adjacent to their daughters or on the opposite end of the cell, whereas daughter cells mostly choose a new bud site on the opposite end of the cell. (D) Mating type switch follows certain rules: (1) only experienced cells can switch mating type; (2) mating type switch occurs during the late G1 phase and the switched cells come in pairs; (3) mating type switch occurs at a high frequency. Inbreeding is defined as mating between mother and daughter cells or among siblings.
Table 1.
Parameters used in simulations and their references.
Fig 3.
Effect of the mating type switch frequency on diploid cell percentage and inbreeding percentage in (A) axial budding colonies (B) random budding colonies.
Each bar represents the average value (± standard deviation).
Table 2.
The time of first mating.
Fig 4.
Comparisons of colonies with axial and random haploid budding patterns.
(A) Percentage of diploid cells as time evolves. (B) Percentage of inbreeding calculated from the same simulations in (A).
Fig 5.
(A) Colony radius and sparseness for diploid colonies as population grows. In these simulations, we set the initial nutrient level U0 = 2. (B) Colony radius and sparseness in bipolar budding colonies as population grows. In these simulations, we set the initial nutrient level U0 = 1, 1.1, 1.25 or 2. (C) Colony radius and sparseness in random budding colonies as population grows. In these simulations, we set the initial nutrient level U0 = 1, 1.1, 1.25 or 2.
Fig 6.
Sample simulations of colonies with 150 cells under different nutrient levels.
(A) Bipolar budding under rich nutrient U0 = 2. (B) Bipolar budding under limited nutrient U0 = 1. (C) Random budding under rich nutrient U0 = 2. (D) Random budding under limited nutrient U0 = 1.
Fig 7.
(A-B) Comparisons of mating features between old and young colonies formed by axial/random budding cells with mating type switch frequency 70%. (A) Time evolution of total populations of the colonies; (B) Diploid cell percentages of the colonies. (C-D) Comparison of colony radius and sparseness between old and young colonies with different budding patterns under limited nutrient U0 = 1. (C) Bipolar budding colonies. (D) Random budding colonies.