Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Protozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eukaryotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the ancestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Retaria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Ciliophora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). The branching order of the five bikont groups is uncertain: Plantae may be sisters of or ancestral to chromalveolates (jointly designated corticates as they share cortical alveoli); Rhizaria and Excavata (jointly cabozoa) are probably sisters if the formerly green algal plastid of euglenoids and chlorarachneans (Cercozoa) was enslaved in a single event in their common ancestor. Apusozoa may be sisters of Excavata and centrohelid heliozoa may be sisters to Haptophyta.
