Additional file 3 of Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks

Additional file 3: Fig. S3 A. Ectodermal dGRNs of Sp and Lv redrawn to reflect timing of first expression. Earliest time points are at the top and normalized hours post-fertilization are indicated on the right side of the dGRN models. Maternal genes are in the gray area at the top of each dGRN. The light yellow area shows the generalized early expression of all ectoderm. The purple and light green regions show the subregions that are further specified following Nodal signaling that initiates those regional separations [51]. B. Endodermal dGRNs of Sp and Lv redrawn to reflect timing of first expression. Earliest time points are at the top and normalized hours post-fertilization is indicated on the right side of the GRN models. Maternal genes are in the gray areas. At sixth cleavage an equatorial division separates the veg1 endoderm (light orange) from the veg2 endoderm cells (light yellow). These two regions are then specified somewhat differently. Time of development for both species is in red to the right of each GRN model. C. Skeletogenic mesenchyme dGRNs of Sp and Lv redrawn to reflect timing of first expression. Earliest time points are at the top and normalized hours post-fertilization is indicated on the right side of the GRN models. Maternally expressed genes are in the gray area. The dGRN models are simplified to show inputs into multiple differentiation genes. The Lv skeletogenic mesenchyme model includes snail and twist which were identified and through perturbation studies included in that GRN model [64, 65]. Connections in the Sp GRN model are identical to the Lv model except snail and twist were not tested in Sp