Fig. 3: Joint convergence of gene expression patterns and protein sequences.
a, Comparison of convergent branch pairs obtained by different methods in the vertebrate dataset. Branch pairs with OCN ≥ 3.0 and OCS ≥ 3.0 were analysed. The stochastic equality of the data was tested by a two-sided Brunner–Munzel test with W as the test statistic96. Box plot elements are defined as follows: centre line, median; box limits, upper and lower quartiles; whiskers, 1.5 × interquartile range. b, A schematic illustration of convergent expression evolution modelled with a multi-optima Ornstein–Uhlenbeck process. c, Venn diagrams showing the extent of overlap between protein and expression convergence. Circles represent the sets of branch pairs. d–g, Examples of the likely adaptive joint convergence. Aldo-keto reductase family 1 (AKR1, d), Nudix hydrolase 16 like 1 (NUDT16L1, e), Myeloid associated differentiation marker (MYADM, f) and dihydrodiol dehydrogenase (DHDH, g) are shown. The silhouettes represent the species (Supplementary Fig. 8a) that carries the gene, and the clades involved in the joint convergence are indicated with an enlarged size. The colours of branches and animal silhouettes indicate expression regimes. Branches involved in joint convergence are highlighted with thick lines, connected by the colour of the expression regime and annotated with convergence metrics. Localization of convergent and divergent substitutions on the protein structure is shown along with a close-up view of functionally important sites. Substrates and their analogues are shown as green sticks. Side chains forming the substrate-binding site are also shown as sticks. Note that these are the side chains in the protein from databases, so amino acid substitutions in the convergent lineages may result in distinct structures and arrangements. Site numbers correspond to those in the Protein Data Bank (PDB) entry or the AlphaFold structure (from d to g: 1Q13, 5W6X, AF-Q6DFR5-F1-model_v2 and 2O48). Icon credits for panels d–g: Rattus norvegicus, Rebecca Groom, under a Creative Commons license CC BY 3.0; Astyanax mexicanus, Milton Tan/PhyloPic under a Creative Commons license CC BY -NC-SA 3.0; all other images are from PhyloPic.com or were created by the author.
