Extended Data Fig. 7: Periods of maximal transcriptomic similarity across chordate development.

a, Stages of minimal transcriptomic distance obtained in the comparison between amphioxus and zebrafish for four alternative distance methods (Euclidean, Manhattan and Jensen–Shannon distances, and Spearman correlation). Values are normalized to minimal (0) and maximal (1) for each metric. b, Stages of minimal transcriptomic divergence shown as the smallest Jensen–Shannon distance between zebrafish stages and four chordate species. The shaded area surrounding the line that connects the stages is the standard deviation, derived from 100 bootstrap replicates of the orthologous gene set. The grey box outlines the ‘phylotypic’ period of minimal divergence; the corresponding periods are indicated for each species as the range provided by the two closest stages. c, d, Heat maps of pairwise transcriptomic distances (Jensen–Shannon distance metric) between pairs of chordate species, amphioxus and frog (c), and zebrafish and frog (d). In both heat maps, the smallest distance (red) indicates maximal similarity of the transcriptome. The periods of minimal divergence of the transcriptome are earlier for the amphioxus–frog comparison than for the zebrafish–frog comparison.