Fig. 2.

New phylogenetic approach to identify evolutionary changes in gene expression, called SBF. Step 1, we label each of the nodes in the species tree, and identify equivalent speciation nodes across every gene tree (an exemplar is shown here). Step 2, we map expression values (TPM10K) to the tips (expression values are mapped and reconstructed for each homologous zooid separately). Step 3, we reconstruct ancestral trait expression values at all internal nodes where expression data are available. Step 4, we calculate scaled change in gene expression (child node expression−parent node expression/branch length). Branch length is calibrated to the species tree branch lengths. Step 5, we identify branches in gene trees that correspond to equivalent branches in the species tree. There may be more than one branch in a gene tree that corresponds to the same branch in the species tree.