Figure 3 - . The terms “convergence” and “parallelism” are used to describe the genetic basis of recurrent phenotypes at two different levels: (A) locus and (B) nucleotide or amino acid sites. (A) At the locus level, species 1 (sp1) and species 3 (sp3) share a recurrent phenotype. In the box at the left (‘Convergence’), the red ray indicates the molecular basis (gene1 and TF2, respectively) associated with the recurrent phenotype in sp1 and sp3, illustrating a case of molecular convergence in which genetic changes in the species reside at different signaling pathways. In the box at the right (‘Parallelism’), the example along the column ‘same metabolic pathway/same sequence’ illustrates a genetic basis of the recurrent phenotype in sp1 and sp3 settled at the enhancer (red ray), while that the column ‘same metabolic pathway/different sequence’ illustrates a case where genetic changes in sp1 and sp3 locate at different components of the same signaling pathway (red rays at the gene and the TF, respectively). (B) Site substitutions from different ancestral nucleotides or amino acids represent a convergence (left), while those resulting from the same trajectory are defined as a parallelism (right).