Fish anatomy

Moray eels have two sets of jaws: the oral jaws that capture prey and the pharyngeal jaws that advance into the mouth and move prey from the oral jaws to the esophagus for swallowing.

The vertebrate jaw probably originally evolved in the Silurian period and appeared in the Placoderm fish which further diversified in the Devonian. Jaws are thought to derive from the pharyngeal arches that support the gills in fish. The two most anterior of these arches are thought to have become the jaw itself (see hyomandibula) and the hyoid arch, which braces the jaw against the braincase and increases mechanical efficiency. While there is no fossil evidence directly to support this theory, it makes sense in light of the numbers of pharyngeal arches that are visible in extant jawed animals (the gnathostomes), which have seven arches, and primitive jawless vertebrates (the Agnatha), which have nine.

Jaws of a great white shark

External video
Video of a slingjaw wrasse catching prey by protruding its jaw
Video of a red bay snook catching prey by suction feeding

It is thought that the original selective advantage garnered by the jaw was not related to feeding, but to increase respiration efficiency. The jaws were used in the buccal pump (observable in modern fish and amphibians) that pumps water across the gills of fish or air into the lungs of amphibians. Over evolutionary time, the more familiar use of jaws in feeding was selected for and became a very important function in vertebrates.

Linkage systems are widely distributed in animals. The most thorough overview of the different types of linkages in animals has been provided by M. Muller,[15] who also designed a new classification system which is especially well suited for biological systems. Linkage mechanisms are especially frequent and various in the head of bony fishes, such as wrasses, which have evolved many specialized aquatic feeding mechanisms. Especially advanced are the linkage mechanisms of jaw protrusion. For suction feeding a system of connected four-bar linkages is responsible for the coordinated opening of the mouth and 3-D expansion of the buccal cavity. Other linkages are responsible for protrusion of the premaxilla.

Zenion hololepis is a small deep water fish with large eyes.

The deep sea half-naked hatchetfish has eyes which look overhead where it can see the silhouettes of prey.

Fish eyes are similar to terrestrial vertebrates like birds and mammals, but have a more spherical lens. Their retinas generally have both rod cells and cone cells (for scotopic and photopic vision), and most species have colour vision. Some fish can see ultraviolet and some can see polarized light. Amongst jawless fish, the lamprey has well-developed eyes, while the hagfish has only primitive eyespots.[16] The ancestors of modern hagfish, thought to be protovertebrate,[17] were evidently pushed to very deep, dark waters, where they were less vulnerable to sighted predators and where it is advantageous to have a convex eyespot, which gathers more light than a flat or concave one. Unlike humans, fish normally adjust focus by moving the lens closer to or further from the retina.[18]

Gill of a rainbow trout

The gills, located under the operculum, are a respiratory organ for the extraction of oxygen from water and for the excretion of carbon dioxide. They are not usually visible, but can be seen in some species, such as the frilled shark. The labyrinth organ of Anabantoidei and Clariidae is used to allow the fish to extract oxygen from the air. Gill rakers are finger-like projections off the gill arch which function in filter feeders to retain filtered prey. They may be bony or cartilaginous.

The epidermis of fish consists entirely of live cells, with only minimal quantities of keratin in the cells of the superficial layer. It is generally permeable. The dermis of bony fish typically contains relatively little of the connective tissue found in tetrapods. Instead, in most species, it is largely replaced by solid, protective bony scales. Apart from some particularly large dermal bones that form parts of the skull, these scales are lost in tetrapods, although many reptiles do have scales of a different kind, as do pangolins. Cartilaginous fish have numerous tooth-like denticles embedded in their skin in place of true scales.

Sweat glands and sebaceous glands are both unique to mammals, but other types of skin glands are found in fish. Fish typically have numerous individual mucus-secreting skin cells that aid in insulation and protection, but may also have venom glands, photophores, or cells that produce a more watery serous fluid.[19] Melanin colours the skin of many species, but in fish the epidermis is often relatively colourless. Instead, the colour of the skin is largely due to chromatophores in the dermis, which, in addition to melanin, may contain guanine or carotenoid pigments. Many species, such as flounders, change the colour of their skin by adjusting the relative size of their chromatophores.[19]

Cycloid scales covering rohu

The outer body of many fish is covered with scales, which are part of the fish's integumentary system. The scales originate from the mesoderm (skin), and may be similar in structure to teeth. Some species are covered instead by scutes. Others have no outer covering on the skin. Most fish are covered in a protective layer of slime (mucus).

There are four principal types of fish scales.

• Placoid scales, also called dermal denticles, are similar to teeth in that they are made of dentin covered by enamel. They are typical of sharks and rays.
• Ganoid scales are flat, basal-looking scales that cover a fish's body with little overlapping. They are typical of gar and bichirs.
• Cycloid scales are small, oval-shaped scales with growth rings like the rings of a tree. Bowfin and remora have cycloid scales.
• Ctenoid scales are similar to cycloid scales, also having growth rings. They are distinguished by spines that cover one edge. Halibut have this type of scale.

Another less common type of scale is the scute, which may be an external, shield-like bony plate; a modified, thickened scale that is often keeled or spiny; or a projecting, modified (rough and strongly ridged) scale. Scutes are usually associated with the lateral line, but may be found on the caudal peduncle (where they form caudal keels) or along the ventral profile. Some fish, such as pineconefish, are completely or partially covered in scutes.

The lateral line is clearly visible as a line of receptors running along the side of this Atlantic cod.

The lateral line is a sense organ used to detect movement and vibration in the surrounding water. For example, fish can use their lateral line system to follow the vortices produced by fleeing prey. In most species, it consists of a line of receptors running along each side of the fish.

Photophores are light-emitting organs which appear as luminous spots on some fishes. The light can be produced from compounds during the digestion of prey, from specialized mitochondrial cells in the organism called photocytes, or from symbiotic bacteria. Photophores are used for attracting food or confusing predators.

The haddock, a type of cod, is ray-finned. It has three dorsal and two anal fins.

Types of caudal fin:
heterocercal (A), protocercal (B), homocercal (C), and diphycercal (D).

Sharks possess a heterocercal caudal fin. The dorsal portion is usually larger than the ventral portion.

The high performance bigeye tuna is equipped with a homocercal caudal fin, finlets and keels.

Fins are the most distinctive features of fish. They are either composed of bony spines or rays protruding from the body with skin covering them and joining them together, either in a webbed fashion as seen in most bony fish, or similar to a flipper as seen in sharks. Apart from the tail or caudal fin, fins have no direct connection with the spine and are supported by muscles only. Their principal function is to help the fish swim. Fins can also be used for gliding or crawling, as seen in the flying fish and frogfish. Fins located in different places on the fish serve different purposes, such as moving forward, turning, and keeping an upright position. For every fin, there are a number of fish species in which this particular fin has been lost during evolution.

In bony fish, most fins may have spines or rays. A fin may contain only spiny rays, only soft rays, or a combination of both. If both are present, the spiny rays are always anterior. Spines are generally stiff, sharp and unsegmented. Rays are generally soft, flexible, segmented, and may be branched. This segmentation of rays is the main difference that distinguishes them from spines; spines may be flexible in certain species, but never segmented.

Spines have a variety of uses. In catfish, they are used as a form of defense; many catfish have the ability to lock their spines outwards. Triggerfish also use spines to lock themselves in crevices to prevent them being pulled out.

Lepidotrichia are bony, bilaterally-paired, segmented fin rays found in bony fishes. They develop around actinotrichia as part of the dermal exoskeleton. Lepidotrichia may have some cartilage or bone in them as well. They are actually segmented and appear as a series of disks stacked one on top of another. The genetic basis for the formation of the fin rays is thought to be genes coding for the proteins actinodin 1 and actinodin 2.[20]

• Dorsal fins: Located on the back of the fish, dorsal fins serve to prevent the fish from rolling and assist in sudden turns and stops. Most fishes have one dorsal fin, but some fishes have two or three. In anglerfish, the anterior of the dorsal fin is modified into an illicium and esca, a biological equivalent to a fishing rod and lure. The two to three bones that support the dorsal fin are called the proximal, middle, and distal pterygiophores. In spinous fins, the distal pterygiophore is often fused to the middle or not present at all.
• Caudal/Tail fins: Also called the tail fins, caudal fins are attached to the end of the caudal peduncle and used for propulsion. The caudal peduncle is the narrow part of the fish's body. The hypural joint is the joint between the caudal fin and the last of the vertebrae. The hypural is often fan-shaped. The tail may be heterocercal, reversed heterocercal, protocercal, diphycercal, or homocercal.
  • Heterocercal: vertebrae extend into the upper lobe of the tail, making it longer (as in sharks)
  • Reversed heterocercal: vertebrae extend into the lower lobe of the tail, making it longer (as in the Anaspida)
  • Protocercal: vertebrae extend to the tip of the tail; the tail is symmetrical but not expanded (as in lancelets)
  • Diphycercal: vertebrae extend to the tip of the tail; the tail is symmetrical and expanded (as in the bichir, lungfish, lamprey and coelacanth). Most Palaeozoic fishes had a diphycercal heterocercal tail.[21]
  • Homocercal: vertebrae extend a very short distance into the upper lobe of the tail; tail still appears superficially symmetric. Most fish have a homocercal tail, but it can be expressed in a variety of shapes. The tail fin can be rounded at the end, truncated (almost vertical edge, as in salmon), forked (ending in two prongs), emarginate (with a slight inward curve), or continuous (dorsal, caudal, and anal fins attached, as in eels).
• Anal fins: Located on the ventral surface behind the anus, this fin is used to stabilize the fish while swimming.
• Pectoral fins: Found in pairs on each side, usually just behind the operculum. Pectoral fins are homologous to the forelimbs of tetrapods, and aid walking in several fish species such as some anglerfish and the mudskipper. A peculiar function of pectoral fins, highly developed in some fish, is the creation of the dynamic lifting force that assists some fish such as sharks in maintaining depth and also enables the "flight" for flying fish. Certain rays of the pectoral fins may be adapted into finger-like projections, such as in sea robins and flying gurnards.
  • "Cephalic fins": The "horns" of manta rays and their relatives, sometimes called cephalic fins, are actually a modification of the anterior portion of the pectoral fin.
• Pelvic/Ventral fins: Found in pairs on each side ventrally below the pectoral fins, pelvic fins are homologous to the hindlimbs of tetrapods. They assist the fish in going up or down through the water, turning sharply, and stopping quickly. In gobies, the pelvic fins are often fused into a single sucker disk that can be used to attach to objects.
• Adipose fin: A soft, fleshy fin found on the back behind the dorsal fin and just in front of the caudal fin. It is absent in many fish families, but is found in Salmonidae, characins and catfishes. Its function has remained a mystery, and is frequently clipped off to mark hatchery-raised fish, though data from 2005 showed that trout with their adipose fin removed have an 8% higher tailbeat frequency.[22] Additional research published in 2011 has suggested that the fin may be vital for the detection of and response to stimuli such as touch, sound and changes in pressure. Canadian researchers identified a neural network in the fin, indicating that it likely has a sensory function, but are still not sure exactly what the consequences of removing it are.[23]
• Caudal keel: A lateral ridge, usually composed of scutes, on the caudal peduncle just in front of the tail fin. Found on some types of fast-swimming fish, it provides stability and support to the caudal fin, much like the keel of a ship. There may be a single paired keel, one on each side, or two pairs above and below.
• Finlets: Small fins generally between the dorsal and the caudal fins, but may also be between the anal fin and the caudal fin. In bichirs, there are only finlets on the dorsal surface and no dorsal fin. In some fish such as tuna or sauries, they are rayless, non-retractable, and found between the last dorsal or anal fin and the caudal fin.

As with other vertebrates, the intestines of fish consist of two segments, the small intestine and the large intestine. In most higher vertebrates, the small intestine is further divided into the duodenum and other parts. In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.[24] In bony fish, the intestine is relatively short, typically around one and a half times the length of the fish's body. It commonly has a number of pyloric caeca, small pouch-like structures along its length that help to increase the overall surface area of the organ for digesting food. There is no ileocaecal valve in teleosts, with the boundary between the small intestine and the rectum being marked only by the end of the digestive epithelium.[19] There is no small intestine as such in non-teleost fish, such as sharks, sturgeons, and lungfish. Instead, the digestive part of the gut forms a spiral intestine, connecting the stomach to the rectum. In this type of gut, the intestine itself is relatively straight, but has a long fold running along the inner surface in a spiral fashion, sometimes for dozens of turns. This fold creates a valve-like structure that greatly increases both the surface area and the effective length of the intestine. The lining of the spiral intestine is similar to that of the small intestine in teleosts and non-mammalian tetrapods.[19] In lampreys, the spiral valve is extremely small, possibly because their diet requires little digestion. Hagfish have no spiral valve at all, with digestion occurring for almost the entire length of the intestine, which is not subdivided into different regions.[19]

The pyloric caecum is a pouch, usually peritoneal, at the beginning of the large intestine. It receives faecal material from the ileum, and connects to the ascending colon of the large intestine. It is present in most amniotes, and also in lungfish.[25] Many fish in addition have a number of small outpocketings, also called pyloric caeca, along their intestine; despite the name they are not homologous to the caecum of amniotes. Their purpose is to increase the overall surface area of the digestive epithelium, therefore optimizing the absorption of sugars, amino acids, and dipeptides, among other nutrients.[25][26]

The black swallower is a species of deep sea fish with an extensible stomach which allows it to swallow fish larger than itself.

Internal organs of a female Atlantic cod:
1=Liver, 2=Gas bladder, 3=Ovary, 4=Pyloric caeca, 5=Stomach, 6=Intestine

As with other vertebrates, the relative positions of the esophageal and duodenal openings to the stomach remain relatively constant. As a result, the stomach always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the esophagus opening directly into the intestine. These fish consume diets that either require little storage of food, no pre-digestion with gastric juices, or both.[27]

The kidneys of fish are typically narrow, elongated organs, occupying a significant portion of the trunk. They are similar to the mesonephros of higher vertebrates (reptiles, birds and mammals). The kidneys contain clusters of nephrons, serviced by collecting ducts which usually drain into a mesonephric duct. However, the situation is not always so simple. In cartilaginous fish there is also a shorter duct which drains the posterior (metanephric) parts of the kidney, and joins with the mesonephric duct at the bladder or cloaca. Indeed, in many cartilaginous fish, the anterior portion of the kidney may degenerate or cease to function altogether in the adult.[28] Hagfish and lamprey kidneys are unusually simple. They consist of a row of nephrons, each emptying directly into the mesonephric duct.[28]

The spleen is found in nearly all vertebrates. It is a non-vital organ, similar in structure to a large lymph node. It acts primarily as a blood filter, and plays important roles in regards to red blood cells and the immune system.[29] In cartilaginous and bony fish it consists primarily of red pulp and is normally a somewhat elongated organ as it actually lies inside the serosal lining of the intestine.[30] The only vertebrates lacking a spleen are the lampreys and hagfishes. Even in these animals, there is a diffuse layer of haematopoietic tissue within the gut wall, which has a similar structure to red pulp, and is presumed to be homologous to the spleen of higher vertebrates.[30]

The liver is a large vital organ present in all fish. It has a wide range of functions, including detoxification, protein synthesis, and production of biochemicals necessary for digestion. It is very susceptible to contamination by organic and inorganic compounds because they can accumulate over time and cause potentially life-threatening conditions. Because of the liver's capacity for detoxification and storage of harmful components, it is often used as an environmental biomarker.[31]

Blood flow through the heart: sinus venosus, atrium, ventricle, and outflow tract

Cardiovascular cycle in a fish

Fish have what is often described as a two-chambered heart,[32] consisting of one atrium to receive blood and one ventricle to pump it,[33] in contrast to three chambers (two atria, one ventricle) of amphibian and most reptile hearts and four chambers (two atria, two ventricles) of mammal and bird hearts.[32] However, the fish heart has entry and exit compartments that may be called chambers, so it is also sometimes described as three-chambered,[33] or four-chambered,[34] depending on what is counted as a chamber. The atrium and ventricle are sometimes considered "true chambers", while the others are considered "accessory chambers".[35]

The four compartments are arranged sequentially:

1. Sinus venosus: A thin-walled sac or reservoir with some cardiac muscle that collects deoxygenated blood through the incoming hepatic and cardinal veins.[33]
2. Atrium: A thicker-walled, muscular chamber that sends blood to the ventricle.[33]
3. Ventricle: A thick-walled, muscular chamber that pumps the blood to the fourth part, the outflow tract.[33] The shape of the ventricle varies considerably, usually tubular in fish with elongated bodies, pyramidal with a triangular base in others, or sometimes sac-like in some marine fish.[34]
4. Outflow tract (OFT): Goes to the ventral aorta and consists of the tubular conus arteriosus, bulbus arteriosus, or both.[34] The conus arteriosus, typically found in more primitive species of fish, contracts to assist blood flow to the aorta, while the bulbus anteriosus does not.[35][36]

Ostial valves, consisting of flap-like connective tissues, prevent blood from flowing backward through the compartments.[34] The ostial valve between the sinus venosus and atrium is called the sino-atrial valve, which closes during ventricular contraction.[34] Between the atrium and ventricle is an ostial valve called the atrioventricular valve, and between the bulbus arteriosus and ventricle is an ostial valve called the bulbo-ventricular valve.[34] The conus arteriosus has a variable number of semilunar valves.[35]

The ventral aorta delivers blood to the gills where it is oxygenated and flows, through the dorsal aorta, into the rest of the body. (In tetrapods, the ventral aorta is divided in two; one half forms the ascending aorta, while the other forms the pulmonary artery).[30]

The circulatory systems of all vertebrates are closed. Fish have the simplest circulatory system, consisting of only one circuit, with the blood being pumped through the capillaries of the gills and on to the capillaries of the body tissues. This is known as single cycle circulation.[37]

In the adult fish, the four compartments are not arranged in a straight row, instead forming an S-shape with the latter two compartments lying above the former two. This relatively simpler pattern is found in cartilaginous fish and in the ray-finned fish. In teleosts, the conus arteriosus is very small and can more accurately be described as part of the aorta rather than of the heart proper. The conus arteriosus is not present in any amniotes, presumably having been absorbed into the ventricles over the course of evolution. Similarly, while the sinus venosus is present as a vestigial structure in some reptiles and birds, it is otherwise absorbed into the right atrium and is no longer distinguishable.[30]

The swim bladder of a rudd

The swim bladder or gas bladder is an internal organ that contributes to the ability of a fish to control its buoyancy, and thus to stay at the current water depth, ascend, or descend without having to waste energy in swimming. The bladder is found only in the bony fishes. In the more primitive groups like some Leuciscinae, bichirs and lungfish, the bladder is open to the esophagus and doubles as a lung. It is often absent in fast swimming fishes such as the tuna and mackerel families. Fish with bladders open to the esophagus are called physostomes, while fish with the bladder closed are called physoclists. In the latter, the gas content of the bladder is controlled through a rete mirabilis, a network of blood vessels affecting gas exchange between the bladder and the blood.[38]

Fishes of the superorder Ostariophysi possess a structure called the Weberian apparatus, a modification which allows them to hear better. This ability may explain the marked success of ostariophysian fishes.[39] The apparatus is made up of a set of bones known as Weberian ossicles, a chain of small bones that connect the auditory system to the swim bladder of fishes.[40] The ossicles connect the gas bladder wall with Y-shaped lymph sinus that is next to the lymph-filled transverse canal joining the saccules of the right and left ears. This allows the transmission of vibrations to the inner ear. A fully functioning Weberian apparatus consists of the swim bladder, the Weberian ossicles, a portion of the anterior vertebral column, and some muscles and ligaments.[40]

Most male fish have two testes of similar size. In the case of sharks, the testis on the right side is usually larger. The primitive jawless fish have only a single testis located in the midline of the body, although even this forms from the fusion of paired structures in the embryo.[30]

Under a tough membranous shell, the tunica albuginea, the testis of some teleost fish, contains very fine coiled tubes called seminiferous tubules. The tubules are lined with a layer of cells (germ cells) that from puberty into old age, develop into sperm cells (also known as spermatozoa or male gametes). The developing sperm travel through the seminiferous tubules to the rete testis located in the mediastinum testis, to the efferent ducts, and then to the epididymis where newly created sperm cells mature (see spermatogenesis). The sperm move into the vas deferens, and are eventually expelled through the urethra and out of the urethral orifice through muscular contractions.

However, most fish do not possess seminiferous tubules. Instead, the sperm are produced in spherical structures called sperm ampullae. These are seasonal structures, releasing their contents during the breeding season and then being reabsorbed by the body. Before the next breeding season, new sperm ampullae begin to form and ripen. The ampullae are otherwise essentially identical to the seminiferous tubules in higher vertebrates, including the same range of cell types.[42]

In terms of spermatogonia distribution, the structure of teleost testes have two types: in the most common, spermatogonia occur all along the seminiferous tubules, while in Atherinomorpha, they are confined to the distal portion of these structures. Fish can present cystic or semi-cystic spermatogenesis in relation to the release phase of germ cells in cysts to the lumen of the seminiferous tubules.[41]

Many of the features found in ovaries are common to all vertebrates, including the presence of follicular cells and tunica albuginea There may be hundreds or even millions of fertile eggs present in the ovary of a fish at any given time. Fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary.[42] The ovary of teleosts is often contains a hollow, lymph-filled space which opens into the oviduct, and into which the eggs are shed.[42] Most normal female fish have two ovaries. In some elasmobranchs, only the right ovary develops fully. In the primitive jawless fish and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo.[42]

Fish ovaries may be of three types: gymnovarian, secondary gymnovarian or cystovarian. In the first type, the oocytes are released directly into the coelomic cavity and then enter the ostium, then through the oviduct and are eliminated. Secondary gymnovarian ovaries shed ova into the coelom from which they go directly into the oviduct. In the third type, the oocytes are conveyed to the exterior through the oviduct.[43] Gymnovaries are the primitive condition found in lungfish, sturgeon, and bowfin. Cystovaries characterize most teleosts, where the ovary lumen has continuity with the oviduct.[41] Secondary gymnovaries are found in salmonids and a few other teleosts.

Fish typically have quite small brains relative to body size compared with other vertebrates, typically one-fifteenth the brain mass of a similarly sized bird or mammal.[44] However, some fish have relatively large brains, most notably mormyrids and sharks, which have brains about as massive relative to body weight as birds and marsupials.[45]

Fish brains are divided into several regions. At the front are the olfactory lobes, a pair of structures that receive and process signals from the nostrils via the two olfactory nerves.[44] Similar to the way humans smell chemicals in the air, fish smell chemicals in the water by tasting them. The olfactory lobes are very large in fish that hunt primarily by smell, such as hagfish, sharks, and catfish. Behind the olfactory lobes is the two-lobed telencephalon, the structural equivalent to the cerebrum in higher vertebrates. In fish the telencephalon is concerned mostly with olfaction.[44] Together these structures form the forebrain.

The forebrain is connected to the midbrain via the diencephalon (in the diagram, this structure is below the optic lobes and consequently not visible). The diencephalon performs functions associated with hormones and homeostasis.[44] The pineal body lies just above the diencephalon. This structure detects light, maintains circadian rhythms, and controls color changes.[44] The midbrain or mesencephalon contains the two optic lobes. These are very large in species that hunt by sight, such as rainbow trout and cichlids.[44]

The hindbrain or metencephalon is particularly involved in swimming and balance.[44] The cerebellum is a single-lobed structure that is typically the biggest part of the brain.[44] Hagfish and lampreys have relatively small cerebellae, while the mormyrid cerebellum is massive and apparently involved in their electrical sense.[44]

The brain stem or myelencephalon is the brain's posterior.[44] As well as controlling some muscles and body organs, in bony fish at least, the brain stem governs respiration and osmoregulation.[44]

Vertebrates are the only chordate group to exhibit a proper brain. A slight swelling of the anterior end of the dorsal nerve cord is found in the lancelet, though it lacks the eyes and other complex sense organs comparable to those of vertebrates. Other chordates do not show any trends towards cephalisation.[8] The central nervous system is based on a hollow nerve tube running along the length of the animal, from which the peripheral nervous system branches out to innervate the various systems. The front end of the nerve tube is expanded by a thickening of the walls and expansion of the central canal of spinal cord into three primary brain vesicles; the prosencephalon (forebrain), mesencephalon (midbrain) and rhombencephalon (hindbrain) then further differentiated in the various vertebrate groups.[46] Two laterally placed eyes form around outgrows from the midbrain, except in hagfish, though this may be a secondary loss.[47][48] The forebrain is well developed and subdivided in most tetrapods, while the midbrain dominates in many fish and some salamanders. Vesicles of the forebrain are usually paired, giving rise to hemispheres like the cerebral hemispheres in mammals.[46] The resulting anatomy of the central nervous system, with a single, hollow ventral nerve cord topped by a series of (often paired) vesicles is unique to vertebrates.[8]

Cross-section of the brain of a porbeagle shark with the cerebellum highlighted

The circuits in the cerebellum are similar across all classes of vertebrates, including fish, reptiles, birds, and mammals.[49] There is also an analogous brain structure in cephalopods with well-developed brains, such as octopuses.[50] This has been taken as evidence that the cerebellum performs functions important to all animal species with a brain.

There is considerable variation in the size and shape of the cerebellum in different vertebrate species. In amphibians, lampreys, and hagfish, the cerebellum is little developed; in the latter two groups, it is barely distinguishable from the brain-stem. Although the spinocerebellum is present in these groups, the primary structures are small paired nuclei corresponding to the vestibulocerebellum.[42]

The cerebellum of cartilaginous and bony fishes is extraordinarily large and complex. In at least one important respect, it differs in internal structure from the mammalian cerebellum: The fish cerebellum does not contain discrete deep cerebellar nuclei. Instead, the primary targets of Purkinje cells are a distinct type of cell distributed across the cerebellar cortex, a type not seen in mammals. In mormyrids (a family of weakly electrosensitive freshwater fish), the cerebellum is considerably larger than the rest of the brain put together. The largest part of it is a special structure called the valvula, which has an unusually regular architecture and receives much of its input from the electrosensory system.[51]

Most species of fish and amphibians possess a lateral line system that senses pressure waves in water. One of the brain areas that receives primary input from the lateral line organ, the medial octavolateral nucleus, has a cerebellum-like structure, with granule cells and parallel fibers. In electrosensitive fish, the input from the electrosensory system goes to the dorsal octavolateral nucleus, which also has a cerebellum-like structure. In ray-finned fishes (by far the largest group), the optic tectum has a layer—the marginal layer—that is cerebellum-like.[49]

A neuron is "identified" if it has properties that distinguish it from every other neuron in the same animal—properties such as location, neurotransmitter, gene expression pattern, and connectivity—and if every individual organism belonging to the same species has one and only one neuron with the same set of properties.[52] In vertebrate nervous systems, very few neurons are "identified" in this sense (in humans, there are believed to be none). In simpler nervous systems, some or all neurons may be thus unique.[53]

In vertebrates, the best known identified neurons are the gigantic Mauthner cells of fish.[54] Every fish has two Mauthner cells, located in the bottom part of the brainstem, one on the left side and one on the right. Each Mauthner cell has an axon that crosses over, innervating neurons at the same brain level and then travelling down through the spinal cord, making numerous connections as it goes. The synapses generated by a Mauthner cell are so powerful that a single action potential gives rise to a major behavioral response: within milliseconds the fish curves its body into a C-shape, then straightens, thereby propelling itself rapidly forward. Functionally, this is a fast escape response, triggered most easily by a strong sound wave or pressure wave impinging on the lateral line organ of the fish. Mauthner cells are not the only identified neurons in fish—there are about 20 more types, including pairs of "Mauthner cell analogs" in each spinal segmental nucleus. Although a Mauthner cell is capable of bringing about an escape response all by itself, in the context of ordinary behavior, other types of cells usually contribute to shaping the amplitude and direction of the response.

Mauthner cells have been described as command neurons. A command neuron is a special type of identified neuron, defined as a neuron that is capable of driving a specific behavior all by itself.[55] Such neurons appear most commonly in the fast escape systems of various species—the squid giant axon and squid giant synapse, used for pioneering experiments in neurophysiology because of their enormous size, both participate in the fast escape circuit of the squid. The concept of a command neuron has, however, become controversial, because of studies showing that some neurons that initially appeared to fit the description were really only capable of evoking a response in a limited set of circumstances.[56]