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Nucleic acid and protein analyses have greatly modified and refined the modern phylogenetic animal tree. These data come from a variety of molecular sources, such as mitochondrial DNA, nuclear DNA, ribosomal RNA (rRNA), and certain cellular proteins. Many evolutionary relationships in the modern tree have only recently been determined from the molecular evidence. For example, a previously classified group of animals called lophophorates, which included brachiopods and bryozoans, were long-thought to be primitive deuterostomes. Extensive molecular analysis using rRNA data found these animals are actually protostomes, more closely related to annelids and mollusks. This discovery allowed for the distinction of the protostome clade Lophotrochozoa. Molecular data have also shed light on some differences within the lophotrochozoan group, and the placement of the Platyhelminthes is particularly problematic. Some scientists believe that the phyla Platyhelminthes and Rotifera should actually belong to their own clade of protostomes termed Platyzoa.

c. Parazoa : Sponge embroys have no germ layers, and therefore no true tissue differentiation. This feature categorizes sponges as separate from other animals whose embryos have two or three germ layers that generate true tissue differentiation.

All deuterostomes, bilatria and iophotrochozoans are true clades.