According to the phylogenetic tree, from which domain did eukarya evolve? the first branch of the phylogenetic tree holds the species of the bacteria division. it contains thermotoga bacteria, green non-sulfur bacteria, cyanobacteria, gram-positive bacteria, and purple bacteria. the second branch of the phylogenetic tree holds species of the eukarya. it contains diplomonads, microsporidia, trichomonads, flagellates, entamoeba, slime molds, ciliates, plants, animals, and fungi. the last branch of the phylogenetic tree starts at the beginning of eukarya line and holds the species archa