Extended data Fig. 7: Examples and consistency of clonal deceleration from simulations and real data.

a, Simulated BNPR trajectories from Wright-Fisher simulations with a fixed population size across 800 generations for a range of fitness effects (0.005, 0.010, 0.015, 0.020, 0.025, 0.030). b, Comparison between Wright-Fisher simulations (grey) and BNPR estimates from phylogenies obtained from these simulations (pink). The horizontal golden line in each plot represents the HSC population carrying capacity (200,000). c, Representation of effective population size (Neff) trajectories using three distinct methods (BNPR, mcmc.popsize and skyline; details in the Supplementary Methods) for their estimation across a range of clade sizes and fitness effects. d, Quantification of the association between true and inferred fitness values for three distinct methods of Neff estimation. e, Schematic representation of all trajectories from Mitchell et al.³⁶ and how extrapolating from the initial growth rate leads to the overestimation of the observed clone size (here the observed clone size is obtained by scaling the proportion of tips in a clade by a total Neff of either 200,000 or 1,000,000 HSC x yr). f, Quantification of the deceleration effect from real data and simulations (n = 177/n = 37/n = 633 clones detected in simulated phylogenies (top)/haematopoietic phylogenies (middle)/with targeted sequencing (bottom) respectively). The boxes represent the 25th, 50th (median) and 75th percentiles of the data; the whiskers represent the lowest (or highest) datum within 1 interquartile range from the 25th (or 75th) percentile.