Figure 2. Gain and loss of protein domains within the Opisthokonta.

(a) The number of Pfam protein domains that were gained or lost at each evolutionary period was inferred by Dollo parsimony, which does not consider multiple independent evolution of a domain. Total number of protein domains, and the inferred numbers of domain gain (+) and loss (−) events are depicted at the tree edges. The full list of domains is in Supplementary Table S4. (b,c) GO terms that were enriched by the evolution of protein domains (b) or depleted by the loss of protein domains (c) were sought via the topology-weighted algorithm. The significant GO terms (P<1.0e−3) are shown at the tree edges together with the number of included Pfam domains. Terms including fewer than seven gained or lost domains are not shown. The list of domains included in each GO is in Supplementary Tables S5 and S6.