Fig. 1.

The Dicer protein family diversified independently in early animal and plant lineages, coincident with adaptive protein-coding changes in the Platform + PAZ + Connector (PPC) domain. We show a consensus phylogeny of Dicer and plant Dicer-like (DCL) proteins, inferred using a variety of alignment and tree-inference strategies (see Materials and Methods). Major taxonomic groups are indicated by branch color, and branches are scaled to the average number of substitutions/site across full-length sequence alignments. Support for key nodes (letters A–I) is indicated in supplementary fig. S1, Supplementary Material online. Protein-coding adaptation specific to the Platform + PAZ + Connector (PPC) domain was inferred using a branch-sites test (see Materials and Methods). Yellow circles indicate significant support for adaptive protein-coding changes on the indicated branch (P < 0.05 after correction for multiple tests). Protein-coding adaptation in other domains is shown in supplementary fig. S2, Supplementary Material online.