That Eukaryote "Tree of Life" page makes a lot of references to endosymbiosis with protists. Prokaryotes aren't even considered as a seperate branch anymore. Instead, Archae are now seen as a seperate branch with Eubacteria being the third. They really show an excellent photo of symbiotic bacteria attached to a flagellate. And then they come right out and state: "the formation of the eukaryotic cell was a consequence of genome fusions between a host cell and endosymbionts representing distinct evolutionary lineages...The origins of mitochondria from cyanobacteria.... Chloroplasts are also rooted in endosymbiosis when a cyanobacterium took up residence in an ancient eukaryote. These primary endosymbionts were destined to become the chloroplasts which are found in eukaryotic algae." You might want to browse through some of the links on the righthand side of the page and also the reference links at the bottom. Dinoflagellates, genus Symbiodinium, commonlly called zooxanthellae, are endosymbionts that form coral reefs by providing their hosts with energy for the carbonate deposition. I'm focussing in on endosymbiosis in flagella development with flagellates, dinoflagellates, bacteria and algae.