Fig. 3: Lineage information enables the recovery of parameters controlling resistance evolution.

A Simulated population size (Left) and cell lineage (Middle) changes across 4 experimental drug-treatment replicates (DT1-4) and their lineage diversity statistics (Right). Total cell population size trajectories (dashed lines) and the top 20 lineage population sizes (coloured lines)/relative frequencies (shaded areas) across four experimental drug-treatment replicates (DT1-4, rows). Lineage colours are consistent between replicates. Four total cell size observations per replicate (two intermediate population size timepoints (O1 & O2) and two passage size timepoints (P1 & P2)) are highlighted. B A subset of the simulated lineage diversity statistics for each sub-population’s two timepoints (P1-2, rows) used for the parameter inference step, highlighted by one of the model parameters (Top: sensitive to resistant phenotype transition probability per cell division - μ) and the fitness penalty of resistance (Bottom: controlled by δ) compared to the true diversity statistics for the given simulation (red points). Adjacent panels show the normalised lineage diversity distance as a function of the two parameters, with the true parameter value highlighted (red dashed line). C Posterior distributions (n = 50, 4 experimental replicates) of the inferred parameter values using the combined cell population size and cell lineage statistics (true parameter values - red dashed lines). Boxplots show the median, the first and third quartiles, and whiskers 1.5x the interquartile range. Source data including the full list of parameters used for the simulation are provided as a Source Data file.