a, Representative images showing examples of single-cell tdTomato+ clones produced at either the +3 (left; note LYZ1+ PCs in crypt base) or +4 (top middle) positions relative to the crypt base, or at the crypt–villus junction (bottom middle) one day after a single TAM injection. Position of LGR5+ CBCs is shown using non-TAM injected LGR5–GFP reporter mice (top left). Dotted lines indicate crypt boundaries (n = 3 mice). b, Images showing tdTomato+ clone size in the crypts of ClutdTomato mice analysed at the indicated time points (n ≥ 3 mice). c, Small intestinal crypts imaged for tdTomato+ clones (red) and Lgr5-GFP+ cells (green), are shown at different chase times, as indicated. White arrows indicate tdTomato+ cells that do not express GFP, whereas yellow arrows identify cells co-expressing tdTomato and GFP (n = 2 mice). d, Small intestines at the indicated chase times were stained and imaged for tdTomato and the indicated differentiated lineage marker: goblet cell, tuft cell, enteroendocrine cell (top; note white arrows that show lineage cells do not express tdTomato at 3 dpt and 45 dpt), or PC (bottom; note white arrows that indicate clonal tdTomato+ cells that do not express PC marker LYZ1 and yellow arrows identify cells co-expressing tdTomato and LYZ1) (n = 2 mice each, experiment repeated once revealing similar results). e, tdTomato+ ribbons (red) at 60 and 148 dpt were co-stained for markers (yellow) identifying the indicated differentiated cells. Yellow arrows indicate co-expressing cells and white arrows identify LYZ1+ PCs that do not express tdTomato (n = 2, mice). f, Schematic of the temporal hierarchy of lineage emergence within tdTomato+ clones. Scale bars, 35 μm (a–c); 30 μm (d, e).