By synthesizing data from individual gene phylogenies, large concatenated gene trees, and other kinds of molecular, morphological, and biochemical markers, we begin to see the broad outlines of a global phylogenetic tree of eukaryotes. This tree is apparently composed of five large assemblages, or "supergroups." Plants and algae, or more generally eukaryotes with plastids (the photosynthetic organelle of plants and algae and their nonphotosynthetic derivatives) are scattered among four of the five supergroups. This is because plastids have had a complex evolutionary history involving several endosymbiotic events that have led to their transmission from one group to another. Here, the history of the plastid and of its various hosts is reviewed with particular attention to the number and nature of the endosymbiotic events that led to the current distribution of plastids. There is accumulating evidence to support a single primary origin of plastids from a cyanobacterium (with one intriguing possible exception in the little-studied amoeba Paulinella), followed by the diversification of glaucophytes, red and green algae, with plants evolving from green algae. Following this, some of these algae were themselves involved in secondary endosymbiotic events. The best current evidence indicates that two independent secondary endosymbioses involving green algae gave rise to euglenids and chlorarachniophytes, whereas a single endosymbiosis with a red algae gave rise to the chromalveolates, a diverse group including cryptomonads, haptophytes, heterokonts, and alveolates. Dinoflagellates (alveolates) have since taken up other algae in serial secondary and tertiary endosymbioses, raising a number of controversies over the origin of their plastids, and by extension, the recently discovered cryptic plastid of the closely related apicomplexan parasites.
