Functional categories of genes lost in Metazoa. Gene loss specific to Metazoa is analyzed for distribution among functional categories. The fraction of lost genes belonging to each category (red bars) is compared with the fraction of genes among all studied gene families belonging to the same functional category (blue bars). Categories for which there is a statistically significant (P < 0.05) difference within a functional category are shown. The significance value (P-value) is shown above the bars.

(A) Evolutionary rates in the LCAs of Metazoa and fungi. The protein substitution rates in the LCAs are reflected by the length of branches preceding the split into individual clades. (B) Function of genes with rapid evolutionary rates in the LCA of Metazoa. The fraction of Metazoa-specific genes belonging to each category (red bars) is compared with the fraction of genes among all studied gene families belonging to the same functional category (blue bars). Functional categories are abbreviated as follows: F, Nucleotide transport and metabolism; S, Function unknown; T, Signal transduction mechanisms; N, Cell motility; K, Transcription; Y, Nuclear structure; E, Amino acid transport and metabolism; V, Defense mechanisms; Z, Cytoskeleton; Q, Secondary metabolites biosynthesis, transport and catabolism; M, Cell wall/membrane/envelope biogenesis; C, Energy production and conversion; L, Replication, recombination and repair; A, RNA processing and modification; O, Posttranslational modification, protein turnover, chaperones; J, Translation, ribosomal structure and biogenesis; W, Extracellular structures; P, Inorganic ion transport and metabolism; B, Chromatin structure and dynamics; H, Coenzyme transport and metabolism; D, Cell cycle control, cell division, chromosome partitioning; I, Lipid transport and metabolism; R, General function prediction only; G, Carbohydrate transport and metabolism; U, Intracellular trafficking, secretion and vesicular transport.

(A) Functional categories of Metazoa-specific genes. The fraction of Metazoa-specific genes belonging to each category (red bars) is compared with the fraction of genes among all studied gene families belonging to the same functional category (blue bars). Categories for which there is a statistically significant difference within a functional category are shown. The functional categories are abbreviated as follows, the significance value (P-value) is in parenthesis: T, Signal transduction mechanisms (1.64 × 10⁻²¹); N, Cell motility (0.0293); K,Transcription (0.0160); Y, Nuclear structure (0.0266); E, Amino acid transport and metabolism (0.0026); V, Defense mechanisms (0.0454); Z, Cytoskeleton (0.0097); C, Energy production and conversion (0.0009); L, Replication, recombination and repair (2.47 × 10⁻⁹); A, RNA processing and modification (8.27 × 10⁻⁷); O, Posttranslational modification, protein turnover, chaperones (8.02 × 10⁻⁷); J, Translation, ribosomal structure and biogenesis (2.08 × 10⁻¹¹); W, Extracellular structures (0.000002); P, Inorganic ion transport and metabolism (0.0420); B, Chromatin structure and dynamics (0.0020); H, Coenzyme transport and metabolism (0.00009); D, Cell cycle control, cell division, chromosome partitioning (0.0075); G, Carbohydrate transport and metabolism (0.0037); U, Intracellular trafficking, secretion and vesicular transport (0.0217). (B) The origin of Metazoa-specific proteins. Metazoa-specific proteins without direct orthologs in other taxa are analyzed for detectable homologues in the following groups: META, only in Metazoa; MET-BAC, in Metazoa and bacteria; META-BAC-ARCH, in Metazoa, bacteria and Archaea; EUK-ARCH, in different eukaryotes and Archaea; EUK, in different eukaryotes only; EUK-BAC, in different eukaryotes and bacteria; EUK-BAC-ARCH, in different eukaryotes, bacteria and Archaea; EUK-ARCH, in different eukaryotes and Archaea.

(A) Evolutionary rates in the separate lineages of Metazoa, fungi and plants. The protein substitution rates in the lineages are reflected by the length of branches after the split into individual clades. (B) Function of genes with rapid evolutionary rates in separate Metazoan phyla. Categories for which there is a statistically significant difference within a functional category are shown. The functional categories are abbreviated as follows, the significance value (P-value) is listed here in parenthesis: E, Amino acid transport and metabolism (0.033); Z, Cytoskeleton (0.023); L, Replication, recombination and repair (0.0037); O, Posttranslational modification, protein turnover, chaperones (0.0154); J, Translation, ribosomal structure and biogenesis (0.0000015); U, Intracellular trafficking, secretion and vesicular transport (0.0266).