Cautions against oversimplifications from gene sampling and potential losses are valid and are growing (Archibald 2009; Bodyl et al. 2009; Howe et al. 2008; Inagaki et al. 2009; Stiller 2007; Stiller et al. 2009), though not always popular with the current multitude who continue to try to find the right place(s) for Cinderella’s slipper. Transitory and constant

associations There are multiple extant states of symbiotic associations between aquatic animals and photosynthetic organisms, both at the single cell level and multicellular levels. Many of them provide clues that might be useful in alternate considerations of how plastids differentiated and spread. An elaboration of many such examples is illustrated in the chapter by Johnson (2010) dealing with this website adaptive strategies in hosting cells and their organelles. These

adaptive strategies are mutualistic and are generally Stem Cell Compound Library driven by the sharing of basic metabolic resources. Dinoflagellate associations with coral tissue appear to be rather common, as are hydra and green algal associations (Trench 1979). To what extent there has been gene transfer between host and symbiont is generally not known. However, gene transfers between two very different Chl a/b algae to sea slug hosts have been demonstrated (Rumpho et al. 2008; Pierce et al. 2007). Another example from Stoecker’s laboratory (Johnson et al. 2007) highlights a ciliate that “fed” on flagellated cryptophytes and retained transcriptionally active cryptophyte nuclei. Such examples clearly suggest that transfer of genetic content is not uncommon among algal IKBKE groups and hosts. Yet, these associations, whether transitory or relatively stable, do not necessarily lead to evolutionary progressions as has been so commonly inferred for chloroplast lineage(s), especially among the collection of algae placed in the

chromalveolate group. Summary opinion The assumption of a one-time chloroplast origin and subsequent dispersals via specific hosts is clearly under threat from new data and multiple interpretations. With ever increasing examples of gene transfers (HGT, EGT) among prokaryotes and eukaryotes, of fungi to animals (Moran and Jarvick 2010), and between algae and animals, it is difficult to cling to some of the presently strongly held concepts of strictly linear progressions on which widely accepted models for the evolution of photosynthesis are based. It seems very unlikely that there was a straight linear progression to a PSI–PSII progenitor and one endosymbiotic cyanobacteria to chloroplast occurrence. Many phylogenomic applications have narrowed, rather than broadened, our views of evolutionary progressions.