The Euglenophyta (euglenoids), Apicomplexa, and Dinophyta (dinoflagellates) are a natural grouping in that they are the only algal groups to have one membrane of chloroplast endoplasmic reticulum. Chloroplast endoplasmic reticulum evolved when a chloroplast from a eukaryotic alga was taken into a food vesicle by a phagocytotic euglenoid, apicomplexan or dinoflagellate (Fig. IV.1) (Lee, 1977; Gibbs, 1978). Normally the cell would have digested the chloroplast as a source of food. However, in this case the chloroplast remained in the cytoplasm of the host as an endosymbiont. The host benefited from the association by receiving photosynthate from the endosymbiotic chloroplast. The endosymbiotic chloroplast benefited from the high concentration of carbon dioxide in the acidic environment of the host vesicle. Eventually the food vesicle membrane of the host became the single membrane of chloroplast endoplasmic reticulum surrounding the chloroplast. It is probable that the plastid of the euglenoids evolved by the capture of a green-algal chloroplast. The plastids of the dinoflagellates and apicomplexans probably are derived from an endosymbiotic red-algal chloroplast.

It appears that algae with chloroplast endoplasmic reticulum were selected for in evolution because of their ability to outcompete other algae in environments which are low in dissolved CO2. Before explaining the mechanism by which these algae are able to outcompete, it is necessary to understand the equilibria governing the distribution of carbon species in water.