Fig. 6. Reconstruction of the cellular trajectories of zebrafish and frog embryogenesis.

a, Comparative developmental timelines for mouse, zebrafish and frog, spread over two time scales, and approximate (as temperature dependent, particularly for frog). Gastrulation and somitogenesis refer to the timing of onset of these processes⁹⁹. Pharyngula refers to the timing of onset of PA formation¹⁰⁰. Black dots refer to time points sampled across seven studies. Gray rounded rectangles indicate developmental windows covered by cellular trajectory reconstructions. b, Directed acyclic graph showing inferred relationships between cell states across early zebrafish development. Each row corresponds to one of 63 cell-type annotations and columns to developmental stages spanning hours postfertilization 3.3 (hpf3.3) to hpf24. Nodes denote cell states, and node colors denote germ layers. All edge weights greater than 0.2 are shown in grayscale. c, Directed acyclic graph showing inferred relationships between cell states across early frog development. Each row corresponds to one of 60 cell-type annotations, columns to developmental stages spanning S8 (hpf5, 23 °C) to S22 (hpf24, 23 °C), nodes to cell states and node colors to germ layers. All edge weights greater than 0.2 are shown in grayscale. DEL, deep cell layer; EVL, enveloping layer.