Fig. 2

(A) The line chart of PCCs (Pearson correlation coefficients) between dogs’ top nine motif-eigenvectors and those of the other four canids. The thresholds of conservation at each level are indicated by gray shading. The top nine motif-eigenvectors of dingoes and dholes are highly correlated with those of dogs, suggesting their top nine modules are highly conserved. In contrast, the PCCs between red foxes, wolves and dogs are significantly decreased to below 0.5 at the fourth and fifth levels, indicating a divergence in these two modules. This divergence in the fourth and fifth modules characterizes a saltation in Canidae. (B) Schematic representation of the saltation in the CREF modules. As mutations accumulate in the regulatory sequences, the relative distance between adjacent singular values approaches zero, and the sensitivity approaches infinity. Consequently, a 2-D eigen-direction polymorphism—represented by the shaded disk—emerges, as shown in the middle. (C) Rotations between the fourth and fifth motif-eigenvectors from dogs to the other four canids. The direction and degree of rotation are marked beside each angle. Except for wolves, the other three canids and dogs have almost identical 2-D eigenspaces. In the cases of dingoes, red foxes, and dholes, the rotation angle of the fourth motif-eigenvector is approximately equal to that of the fifth one. Large rotations in red foxes and wolves indicate a saltation in the evolution of cis-regulatory modules in Canidae.