DESCRIPTION OF SUPPLEMENTARY DATA

            The seven supplementary figures (A-G) show in greater detail how model predictions were derived. The various assumptions used in generating these predictions are described in the DISCUSSION and APPENDIX.

Coordinated models: Each of the flowcharts (Figures A-C) begins with one cleaved BAS3 molecule (labeled as an A end and a B end to indicate the rIIA and rIIB-containing ends of the cleaved BAS3 molecule, respectively) and one BAS1 molecule (labeled as rII ^-, which is defined throughout the supplementary material as rIIA^-B ^- molecules). The starting number of BAS1 molecules has no impact on the predicted recombinant ratios since the cleaved BAS3 molecule will by definition utilize only one of the available templates.

            Each of the flowcharts diagrams the possible recombinants formed based on HB80 and UV232 coconversion (all models), Holliday-junction resolution (Szostak et al. model only), and choice of repair template (coordinated ECR model only). The numbers next to each arrow on the flowcharts indicate the probability of that particular event occurring. The number in parentheses below each possible recombinant outcome indicates the cumulative probability of that particular outcome.

            The predicted recombinant ratios for each model were calculated as shown in Figure D. The different recombinant outcomes for each model are indicated in the first four columns, and the fifth column contains the probability of each of those outcomes occurring. Weighted recombinant outcomes were calculated by multiplying each of the values in columns 1-4 by the corresponding value in column 5. The weighted recombinant outcomes for rII ⁺, rIIA ^-, and rIIB were summed at the bottom of the spreadsheet and converted to ratios. These are the predicted recombinant ratios presented in Figure 4B for the coordinated repair models.

ECR model: In contrast to the coordinated model recombinant predictions, the ECR model predictions are sensitive to the number of starting BAS1 template molecules available. Thus, in order to generate predicted recombinant ratios for the mass lysate, more than one flowchart is required. We generated 18 flowcharts starting with one cleaved BAS3 molecule (again labeled as an A end and a B end) and from one to eighteen BAS1 (rII ^-) molecules. Figure E shows an example of one of these flowcharts (in this case with nine starting BAS1 molecules; the other 17 flowcharts are not shown). In flowcharts with different starting numbers of BAS1 molecules, the underlined probabilities are different, and the number of rII ^- molecules in each of the recombinant outcomes is different. For each of the 18 flowcharts, the weighted recombinant outcomes were determined as described above for the coordinated models. These weighted recombinant outcomes were then summed and converted to recombinant frequencies. Figure F shows how this was done for the Figure E flowchart (calculations for the other 17 flowcharts are not shown).

To generate the predicted recombinant ratios for the mass lysate (which will include a mixture of cells infected by different numbers of BAS1 particles), we utilized the spreadsheet shown in Figure G. The first column lists possible numbers of BAS1 particles per cell from one to eighteen. Cells receiving no BAS1 particles or more than eighteen BAS1 particles will be extremely infrequent and were therefore excluded from analysis. The second column indicates the probability of a cell being infected by that number of BAS1 particles. These probabilities were generated using the Poisson equation. The values in the third through sixth columns are the predicted recombinant frequencies for cells infected by different numbers of BAS1 molecules (calculated from the flowcharts as described above). The values in the seventh through tenth columns were generated by multiplying the values in the third through sixth columns by the values in the second column. Thus, the values in the seventh through tenth columns represent the weighted recombinant frequencies for the different infected cell types. The rII ⁺, rIIA ^-, and rIIB ^- weighted recombinant frequencies were summed at the bottom of the spreadsheet to give the predicted recombinant frequencies for the mass lysate, and these frequencies were then converted to recombinant ratios. These are the recombinant ratios presented in Figure 4B for the ECR model.

Supplementary Figures A - G