Fig 1. Parallelism profiling.

(A) In a hypothetical example, a phylogeny with descendant taxa D1 and D2 have convergent phenotypes (black). (B) Genetic regulatory networks to illustrate consequences of evolutionary changes in expression to gene A in D1 and separately to gene B in D2; both changes result in the black phenotype. (C) Changes in gene expression relative to taxa with the common ancestor’s phenotype. (D) Descendants D1 and D2 have a “core set” of differentially expressed genes in common.