Fig. 4.

Rate of TAD evolution. We used a maximum-likelihood approach to estimate per-branch substitution rates across the 11-species phylogeny shown here for TAD domains (A) and TAD boundaries (B). There is rate variation among branches, especially within the D. melanogaster subgroup and branches are colored according to evolutionary rate. Across the entire tree, we estimate the rate of evolution for TADs (A) as 0.0257 substitutions per TAD per My (95% C.I. 0.0256–0.0258) with per-branch rates varying from $1.5\times {10}^{-06}$ to 0.15. The rate of evolution for TAD boundaries (B) is 0.0210 substitutions per TAD per My (95% C.I. 0.0208–0.0211) with per-branch rates varying from $1.4\times {10}^{-06}$ to 0.07.