Calculation of the Single Nucleotide Polymorphism mutation rate.

Each column is labelled to indicate the steps leading to the mutation rate numbers (see Methods for more details). We first calculate the number of SNPs per sub-clone detected in each clone tree generation. This represents the average number of de novo mutations in each clonal population (e.g. if the SNP/clone is 0.2, then approximately 1 in 5 clones will have a SNP). We divide this by the number of intraerythrocytic life cycles the parasites have undergone prior to the most recent cloning step, counting from the previous clonal dilution. The number of intraerythrocytic life cycles is reached by dividing the time in culture by the time per intraerythrocytic life cycle. This gives the SNPs/intraerythrocytic parasite life cycle for each clone tree generation. To derive the SNPs/life cycle/nucleotide, we divide by the haploid nuclear genome of P. falciparum (23,300,000 base pairs). The final mutation rate for each strain is an average from all the generations in the clone tree. We weight this average based on the number of subclones analysed in each generation, so that generations with more subclones have proportionally more representation in the average. Note that the first generation of subclones cannot be used to calculate the SNP mutation rate because the length of time in culture prior to our starting the experiment is not known. The W2 clone tree was too small to accurately determine the SNP mutation rate. The same process was used to calculate the exon 1 var recombination rates (S5 Table).Calculation of the Single Nucleotide Polymorphism mutation rate.