The bilaterian lineage divided early on into two clades: protostomes and deuterostomes. The name "deuterostome" means "mouth second" and refers to an important developmental feature unique to this group. In the earliest stages of embryo development, a small ball of cells (the gastrula) invaginates on one side and grows into a pocket that forms an additional layer of cells. In protostomes, the opening of this pocket eventually develops into a mouth. In deuterostomes, the opening develops into the anus, and the mouth is formed later. The Deuterostomia include two large and diverse groups of animals: (i) the echinoderms and hemichordates (spiny-skinned ocean-dwelling creatures, including starfish and sea urchins) and (ii) the chordates (which include fish and other vertebrates). Although there are molecular phylogenetic data to support this broad separation, scientists continue to debate the evolutionary relationships among the deuterostomes and the ancestry of chordates.

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