An external meatus is formed in higher Vertebrata by the growth of the parts around the tympanic membrane, but a concha of the ear is well developed only in Mammalia.
The alimentary tract consists of a stomodaeum, mesenteron (= archen-teron), and a proctodaeum, but in some Amphibia (Frog, Newt) the blastopore persists as the anus. The stomodaeum forms the major part of the oral cavity. This cavity becomes divided in Chelonia, Crocodilia, some Aves and all Mammalia into an upper nasal portion, and a lower buccal portion by the formation of a hard or, in Mammals, of a hard and soft palate. Teeth and glands are developed in the mouth. The teeth are composed typically of two substances, enamel and dentine. The former is derived from the inner surface of a cellular structure, the enamel organ, which is formed by a downgrowth of the epiblastic rete mucosum, covering an upgrowth of the mesoblast, the dental papilla. The cells on the outer surface of the latter or the odontoblasts give origin to the dentine, whilst the central part of the papilla persists as a vascular pulp supplied also with nerves. The teeth formed in this manner are phylogenetically identical, with the exoskeletal spines of certain Fishes (Elasmobranchii). A third substance, cement (crusta petrosa), formed by the connective tissue surrounding the base of the tooth, agrees histologically with bone, but is found only on the roots of some teeth when implanted in sockets.
The teeth are attached to the underlying jaws either by a fibrous membrane (some Fish) or by bone, i.e. by anchylosis (some Fish, Amphibia and Reptilia), or are implanted in grooves or sockets (a few Fish, Reptilia and all Mammalia). Their shape, situation, number, etc, vary immensely. They are found in the pharynx of many Fish, and here the enamel organ is derived from hypoblast and not epiblast as in the stomodaeal region. New teeth in succession to old teeth are either formed without limit of numbers, as in most Pisces; Amphibia, Reptilia, or are restricted to a second set in some Mammalia. In other Mammalia there are no successional teeth at all. The enamel organ of these successional teeth is typically derived from the pedicle of a pre-existing enamel organ, but in Teleostei independently from the rete mucosum. A partial absorption of the old tooth generally occurs when it is replaced. In some Mammalia the teeth grow from persistent pulps as fast as their exposed surfaces are worn away, e. g. the incisors of Rodentia. Specialised oral glands are found from Amphibia onwards. Their structure, number and position vary much, but Mammalia are characterised by three well-developed pairs - parotid, sub-maxillary and sublingual, in addition to minor glands.
A muscular growth from the floor of the mouth above the basihyal region constitutes the tongue. It is well developed in Amphibia and higher forms.
The mesenteron (archenteron) is divisible into two or three regions. The first, fore-gut, extends from the stomodaeum to the point of origin of the liver, and comprises a pharynx, oesophagus, and stomach. The second constitutes the mid-gut or small intestine; the third the hind-gut, large intestine, or colon. The two latter are sometimes difficult to distinguish. Their limits are either indicated by the presence of one or two lateral caeca, by a difference of calibre or of the mucous membrane. A post-anal section of the mesenteron has also been distinguished in the embryo, but some doubt attaches to its significance. The anterior limit of the oral part of the mesenteron is lost except in Cyclostomi, where it is indicated by the velum. The pharynx of Vertebrata represents a portion and a portion only of the primitive respiratory or branchial section of the fore-gut. Its walls are perforated by a series of branchial or visceral clefts. The greatest number of these known in an adult form is eight, of which the first is the spiracle lying between Meckel's arch and the hyoid (cf. note, p. 338), the position in which the Eustachian tube develops in higher Vertebrata. The remainder are branchial clefts, or in Mammalia and Sauropsida where branchiae do not exist even in the embryo, visceral clefts, limited to four in number.
The clefts are formed by hypoblastic outgrowths from the throat reaching to the epiblast which eventually thins away over them, thus leaving an aperture. The septum or wall between each pair of clefts is supported by a branchial arch, and contains an aortic, i.e. a vascular arch. The anterior and posterior walls of the pouches bear vascular processes, branchiae or internal gills in Pisces. External gills, such as are found in Amphibia, permanently or temporarily, are outgrowths covered with epidermis near the dorsal ends of the branchial arches. There is reason to believe that the branchial clefts were very numerous in the ancestral Vertebrata, and that the true digestive portion of the alimentary canal commenced, as in Amphioxus, with the region to which the liver is attached. The oesophagus and stomach are separated by a cardiac constriction little marked in most Ichthyopsida. The stomach and mid-gut are marked off by a similar constriction known as the pylorus or pyloric valve, due to great development of the circular muscular coat of the alimentary canal. The rest of the tract varies much in calibre, length, and consequently in the degree to which it is coiled. In Mammalia the terminal section of the colon is straight, and is hence termed rectum.
The intestine terminates in the embryo in a cloaca, common to it and the urogenital ducts, a condition which persists in some Pisces, all Amphibia, and Sauropsida and the Proto-theria among Mammals. But the primitive condition is lost in other cases, and the rectum opens separately from the urogenital ducts, as in Holocephali, Teleostei among Pisces, Eu- and Meta-theria among Mammalia; and occasionally the urinary ducts apart from the genital (Holocephali and some Teleostei, the female Rat and a few other Mammalia). The walls of the alimentary canal consist typically from without inwards of a serous coat; of a longitudinal and a circular coat of non-striated muscle-cells; of a submucous connective tissue; and a mucous coat, the two latter often thrown into variously disposed folds in the mid-gut. The sub-mucous coat contains blood-vessels, lymphatic tissue and vessels. The mucous coat is a single layer of epithelial (hypoblast) cells, which form tubular glands in the stomach of all Vertebrata, in the intestine of Amphibia and higher classes. Two glands, a liver and a pancreas, are connected with the commencement of the mesenteron. The former is a ventral outgrowth of hypoblast into the mesoblast, either double or single at first, but always becoming double at last.