Fig. 3: The hourglass model and chordate embryogenesis.
From: Amphioxus functional genomics and the origins of vertebrate gene regulation
a, Stages of minimal transcriptomic divergence (using the Jensen–Shannon distance metric) from four vertebrate species to each amphioxus stage. The grey box outlines the period of minimal divergence, with the corresponding vertebrate periods indicated (the range is given by the two less divergent stages). Dispersions correspond to the standard deviation computed on 100 bootstrap re-samplings of the orthologue sets (amphioxus–chicken: 5,720; amphioxus–zebrafish: 5,673; amphioxus–frog: 5,883; and amphioxus–medaka: 5,288). HH, Hamburger–Hamilton stage. b, Heat map of pairwise transcriptomic Jensen–Shannon distances between amphioxus (vertical) and zebrafish (horizontal) stages. A smaller distance (red) indicates higher similarity. dpf, days post-fertilization. c, Zebrafish and amphioxus pairwise Pearson correlation of relative enrichment z-scores for transcription-factor (TF) motifs in dynamic APREs, active at different developmental stages. Top, maximal correlation for each amphioxus stage against the zebrafish stages. Bottom, heat map with all pairwise correlations. 80 epi, 80% epiboly stage; 8 som, 8-somite stage. d, Sequence conservation levels within the cephalochordates of active APREs at each developmental stage, visualized as the distribution of average phastCons scores. The number of APREs at 8 hpf = 5,282; at 15 hpf = 17,387; at 36 hpf = 21,089; at 60 hpf = 22,674; and in hepatic diverticulum (hep) = 16,551. Dots correspond to the mean values and lines represent the interquartile range.
