Fig. 3: Loss of clonal diversity in recipients of HCT.

a, The number and size of clades with a clonal fraction ≥2% of haematopoiesis. Plots are divided by pair, and by recipient (R) or donor (D). Clones are defined as a lineage originating from 100 mutations of molecular time (corresponding to the first few years after birth). Bars are coloured by whether the clone has a known driver (orange) or not (green). b, The fold change in phylogenetic diversity in recipients compared with their donors as measured by the mean pairwise distance (left) or mean nearest taxon distance (right). The line colour illustrates whether the recipient diversity is decreased (cyan) or increased (red). c, The posterior estimates of the phylogenetic age of recipients (orange) and donors (green) as estimated by ABC, compared with the true donor age at the time of sampling. The solid lines indicate the relationship between phylogenetic age and true age, split by donors (green) and recipients (orange), as estimated by linear mixed-effects regression. d, The size of clonal expansions in each mature cell compartment, as found in targeted sequencing. Includes clones contributing ≥1% clonal fraction in at least one compartment. Bar colours are arbitrary, but are consistent within pairs to enable comparisons between cell types and donors/recipients. Pairs 1 and 2 have no clones of ≥1% and are therefore not shown. e, The change in Shannon diversity index (SDI) (recipient SDI minus donor SDI) in each mature cell compartment. f, The relationship between SDI and donor age, divided by donors (green) and recipients (orange), and split by mature cell type. The solid lines indicate the line derived from the maximum likelihood of the linear relationship split by donor (green) and recipient (orange). The grey shaded areas show the 95% confidence interval of this relationship. The points show the individual estimates of SDI for the n = 10 donors and n = 10 recipients. Gran, granulocytes; mono, monocytes.