I discuss eukaryote megaphylogeny and the timing of major innovations in the light of multigene trees and the rarity of marine/freshwater evolutionary transitions. The first eukaryotes were aerobic phagotrophs, probably substratum-associated heterotrophic amoeboflagellates. The primary eukaryote bifurcation generated unikonts (ancestrally probably unicentriolar, with a conical microtubular [MT] cytoskeleton) and bikonts (ciliary transformation from anterior cilium to ancestrally gliding posterior cilium; cytoskeleton of ventral MT bands). Unikonts diverged into Amoebozoa with anterior cilia, lost when lobosan broad pseudopods evolved for locomotion, and Choanozoa with posterior cilium and filose pseudopods that became unbranched tentacles/microvilli in holozoa and eventually the choanoflagellate/choanocyte collar. Of choanozoan ancestry, animals evolved epithelia, fibroblasts, eggs, and sperm. Fungi and Ichthyosporea evolved walls. Bikonts, ancestrally with ventral grooves, include three adaptively divergent megagroups: Rhizaria (Retaria and Cercozoa, ancestrally reticulofilose soft-surfaced gliding amoeboflagellates), and the originally planktonic Excavata, and the corticates (Plantae and chromalveolates) that suppressed pseudopodia. Excavata evolved cilia-generated feeding currents for grooval ingestion; corticates evolved cortical alveoli and ciliary hairs. Symbiogenetic origin and transfers of chloroplasts stimulated an explosive radiation of corticates--hard to resolve on multigene trees--and opisthokonts, and ensuing Cambrian explosions of animals and protists. Plantae lost phagotrophy and multiply evolved walls and macroalgae. Apusozoa, with dorsal pellicle and ventral pseudopods, are probably the most divergent bikonts or related to opisthokonts. Eukaryotes probably originated 800-850 My ago. Amoebozoa, Apusozoa, Loukozoa, and Metamonada may be the only extant eukaryote phyla pre-dating Neoproterozoic snowball earth. New subphyla are established for Choanozoa and Loukozoa; Amoebozoa are divided into three revised subphyla, with Variosea transferred into Conosa.