Extended Data Fig. 9: Simulations incorporating HCT-specific selection are necessary to recapitulate real HCT phylogenies.

a, Dot plot showing selected summary statistics for the samples from the posterior distribution (grey) compared to the data (red), when using a simulation framework that does not incorporate engraftment-specific selection. These summary statistics reflect the degree to which recipient phylogenies have increased pre-HCT coalescences (recipient:donor ratio of pre- HCT time point coalescences, y-axis), while maintaining overall diversity (number of singletons, x-axis). b, As in a, but now using a simulation framework that allows for engraftment-specific selection (Pruning selection). c, As in a, but with different summary statistics, now reflecting the degree to which peri-HCT coalescences are concentrated in a single clade (maximum number of peri-HCT coalescences in single clade, y-axis), while maintaining overall diversity (number of singletons, x-axis). d, Quantile-quantile (QQ) plots showing distributions of posterior p values for the three ABC models, calculated using Bayesian posterior p value checks with the rejection sampling method. In each panel, the posterior p values are ranked (x axis; quantile) and the posterior p value is shown (y axis), coloured by donor-recipient pair. The blue lines represent x = y and the grey lines represent y = 0.05. Left panel, model of age-related selection combined with a bottleneck for transplant into recipient; middle panel, model of age-related selection, bottleneck plus pruning selection; right panel, model of age-related selection, bottleneck plus growth selection.