Fig. 6.

Evolutionary rate comparison for active versus developmentally regulated TADs. We divided our TAD presence/absence matrix into two submatrices: one containing developmentally regulated TADs (i.e., those enriched for BLUE or BLACK chromatin states) and another containing active TADs (i.e., those enriched for the YELLOW chromatin state). We used a maximum-likelihood approach to estimate the rate of TAD substitutions separately for these two categories using 100 bootstrap replicates. Developmentally regulated TADs have a significantly reduced rate of evolution compared with active TADs (the Wilcoxon rank sum test $P<3.878\times {10}^{-53}$). We also included the complete matrix of all TAD orthogroups for comparison. The substitution rates for this matrix are significantly higher than those from the BLUE/BLACK submatrix and significantly lower than those from the YELLOW submatrix (the Wilcoxon rank sum test $P<6.534\times {10}^{-48}$ and $P<2.126\times {10}^{-51}$, respectively).