Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree

The biggest unsolved problems in chloroplast evolution are the origins of d inoflagellate and euglenoid chloroplasts, which have envelopes of three mem branes not two like plants and chromists, and of the sporozoan plastid, bou nded by four smooth membranes. I review evidence that all three of these pr otozoan plastid types originated by secondary symbiogenesis from eukaryotic endosymbionts. Instead of separate symbiogenetic events, I argue that dino flagellate and sporozoan plastids are directly related and that the common ancestor of dinoflagellates and Sporozoa was photosynthetic. I suggest that the last common ancestor of all Alveolata was photosynthetic and acquired its chlorophyll c-containing plastids in the same endosymbiogenetic event a s those of Chromista. Chromista and Alveolata are postulated to be a clade designated chromalveolates. I propose that euglenoids obtained their plasti ds from the same (possibly ulvophycean) green alga as chlorarachneans and t hat Discicristata (Euglenozoa plus Percolozoa) and Cercozoa (the group incl uding chlorarachneans) form a clade designated cabozoa (protozoa with chlor ophyll a + b). If both theories are correct, there were only two secondary symbiogenetic events (witnessed by the chlorarachnean and cryptomonad nucle omorphs) in the history of life, not seven as commonly assumed. This greatl y reduces the postulated number of independent origins of chloroplast prote in-targeting machinery and of gene transfers from endosymbiont to host nucl ei. I discuss the membrane and plastid losses and innovations in protein ta rgeting implied by these theories, the comparative evidence for them, and t heir implications for eukaryote megaphylogeny. The principle of evolutionar y conservatism leads to a novel theory for the function of periplastid vesi cles in membrane biogenesis of chlorarachneans and chromists and of the key steps in secondary symbiogenesis. Protozoan classification is also slightl y revised by abandoning the probably polyphyletic infrakingdom Actinopoda, grouping Foraminifera and Radiolaria as a new infrakingdom Retaria, placing Heliozoa within a revised infrakingdom Sarcomastigota, establishing a new flagellate phylum Loukozoa for Jakobea plus Anaeromonadea within an emended subkingdom Eozoa, and ranking Archezoa as an infrakingdom within Eozoa.