Extended Data Fig. 3: Reconstruction of ancestral gene content.

a, Cladogram showing the phylogenetic relationships of 45 species representatives of all major eumetazoan taxa with species of gnathostomes and cyclostomes highlighted in blue and orange, respectively. Gene family gains and losses are indicated in selected nodes: green, novel homology groups (HG); blue, novel core HGs; red, lost HGs. b, Top 14 Protein Class GO hits for novel homology groups (HG) gained across different nodes of chordates, color coded by taxa (legend at the bottom right) and sorted by the Vertebrata node. The largest GO enriched terms are ‘transmembrante signal receptor’ and ‘intercellular signal molecule’ in vertebrates, and ‘defense/immunity protein’ in gnathostomes.