## 2 Results  
To study the impact of budding division on the spatial organization of _S. cerevisiae_ colonies, we developed a 2D computational model to compare morphological characteristics and spatial arrangement of cells between budding and non-budding colonies in both nutrient-rich and nutrient-limited conditions (see Section 4 for a detailed discussion of our computational model and the metrics we use to evaluate our colonies). Note, by non-budding colonies we mean colonies where mother-bud pairs are not physically attached while the new daughter grows to a mature size. In the model, we represent each cell by an elastic sphere that moves, grows, buds and divides according to biophysical and cell-kinetic model parameters chosen to match experimentally derived values (Section 4.1, Table 1, Figures 12-14). Each simulation begins with a single newly born founder cell. We allow the colony to grow for \(\approx\)24 h until there are \(\approx\)15,000 cells. We compared our synthetic yeast colonies grown under different conditions (budding/non-budding, nutrient-rich/nutrient-limited) with metrics designed to capture the overall colony growth, shape, and spatial organization of cells (see Section 4.2). Results below are based on 50 simulations for each of these four conditions. Typical output from budding and non-budding colonies in nutrient-rich conditions is shown in Figure 2 (middle and bottom rows) and typical output from budding and non-budding colonies in nutrient-limited conditions is shown in Figure 11A-D.  
Figure 2: Simulated Yeast Colonies in Nutrient-Rich Conditions and Corresponding Lineage Relationships. We compared overall growth, shape and spatial organization between budding (Middle) and non-budding (Bottom) colonies. Colonies are depicted at three time points (**A**) 12 h (\(\sim\)100 cells); (**B**) 18 h (\(\sim\)1300 cells) and (**C**) 24 h (\(\sim\)15,000 cells). In addition to the physical layout of cells, we analyzed two different networks associated with our colonies, the lineage graph (\(G_{L}\), Top) and the spatial graph (\(G_{\mathrm{S}}\), see Section 4.2.2). (Top row) The lineage graph (\(G_{\mathrm{L}}\)) represents mother-daughter relationships and does not consider cell position in space. As such, the lineage graph is the same for the two different colonies depicted below (budding and non-budding). Cells in colonies and edges in the lineage graph are colored according to the unique subcolony each cell belongs to, where a **subcolony** is the subset of all cells whose common ancestor is the same immediate daughter of the founder cell: Founder (red), Subcolony 1 (maroon), Subcolony 2 (blue), Subcolony 3 (dark green), Subcolony 4 (light green), Subcolony 5 (laverder), Subcolony 6 (purple), Subcolony 7 (dark orange), Subcolony 8 (gold), Subcolony 9 (yellow), Subcolony 10 (rust), Subcolony 11 (magenta), Subcolony 12 (light pink) and Subcolony 13 (grey). Lineage graphs display the first five subcolonies only. (See Section 4.2.2 for details.)  
As we next discuss in greater detail, we find that metrics corresponding to the overall growth and shape of colonies are not impacted by budding division. However, we observe significant differences in metrics characterizing the local spatial organization and connectivity of budding versus non-budding colonies. Finally, we find that in addition to further impacting local spatial organization and colony connectivity, nutrient limitation changes the global organization of growing yeast colonies.  
Nutrient-Rich Growth: Budding Division Impacts Local Colony Organization in Simulated Yeast Colonies  
First, we consider colonies growing in \"nutrient-rich\" conditions. As described in Section 4.1.1, for budding colonies, we explicitly model the mechanical interactions that arise due to the formation of a new daughter cell from budding (Figure 12A). When simulating non-budding colonies, we treat mechanical interactions of mother-bud pairs and all other cell-cell pairs identically (Section 4.1.1 and Figure 12B).