Figure 7. Evolution of protein domain architectures.

(A) Protein domain combination gain and loss per lineage, including extant genomes and ancestral reconstructed nodes. Diameter and color of circles denote the number of different domain combinations (in different gene families) in that node of the tree. Bolder edges mark the line of descent between the LCAs of Opisthokonta and Bilateria, which was generally dominated by gains of protein domain combinations (see text). Red and green bars represent the inferred number of gains and losses, respectively. (B) Gain/loss ratio of protein domain diversity in selected ancestors, including animals (upper chart; from Metazoa to Unikonta/Amorphea) and unicellular holozoans (lower). Heatmap to the right represents the log-ratio value of the diversification rate for selected sub-sets of functionally-related protein domains relevant to multicellularity: green indicates higher-than-average diversification; pink less; white asterisks indicate two-fold or more increases or decreases (all comparisons relative to the whole set of protein domains). Source Data Figure 7—source data 1, 2, 3 and 4.

DOI: http://dx.doi.org/10.7554/eLife.26036.026

Figure 7—figure supplement 1. Gains and losses of individual protein domains across eukaryotes.

(A) Ancestral reconstruction of gains (green) and losses (red) of protein domains per lineage, based on Dollo parsimony. Note that, in contrast with the evolution of protein domain combinations here most nodes are dominated by losses. The most notable exceptions are the Metazoa and Opisthokonta LCAs (dominated by gains) and its unicellular ancestors from Holozoa to Choanoflagellata + Metazoa LCAs (in which gains and losses are in a relative stasis). Figure 7—source data 3. (B) Log-ratio of gains-to-losses for single protein domains (brown bars) and protein domain pairs (blue bars), based on the respective ancestral reconstructions. Positive values thus mean that gains are greater than losses. Loss of single protein domains dominates in most nodes, but gains in protein domain combinations can nevertheless outweigh losses in many ancestors (e.g., Holozoa or Metazoa LCAs).

DOI: http://dx.doi.org/10.7554/eLife.26036.031