Fig. 1. Pooling-based phylogenetic methods for inferring accelerated evolution in TFBSs.

In the first method, we fit the group-level LRT to the concatenated alignment of TFBSs bound by the same transcription factor, which allows us to examine whether the group of TFBSs as a whole evolved at an elevated substitution rate in the foreground lineage compared to the background lineage. In the second method, we fit the element-level LRT to the alignment of each individual TFBS, which provides an element-level p-value. Then, we fit a beta-uniform mixture model to the distribution of p-values in each TFBS group to estimate the proportion of accelerated TFBSs. Colored rectangles and hexagons represent TFBSs and transcription factors, respectively. r₁ and r₂ represent relative substitution rates in the foreground and background lineages, respectively.