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The Chondrpiscia are jawed fish-like animals with paired fins, paired nostrils, scales, two-chambered hearts, and skeletons made of cartilage rather than bone. The skeleton of Chondrpiscia is made from a rubbery cartilage like a tissue, lighter and more flexible than bone. The jaw is not attached to the cranium.The jaw, vertebrae, and gill arches, "skeletal" element which extra support due to heavier physical stresses and need for extra strength, have a layer tiny crystalline hexagonal plates of silica arranged in a mosaic, giving these structures much of the same strength found in real and much heavier bony tissue. The fin "skeleton" structures are elongated and supported with soft, unsegmented filaments of elastic protein resembling the horny keratin in hair and feathers.

Chondrpiscians extract oxygen from seawater as it passes over their gills, like other fish. While moving, water passes through the mouth and over the gills - this process is known as "ram ventilation". While at rest, most chondrpiscians pump water over their gills to ensure a constant supply of oxygenated water. A small subset of species that spend their life constantly swimming, have lost the ability to pump water through their gills. These species are obligate ram ventilators and would presumably asphyxiate if unable to stay in motion.

The respiration and circulation process begins when deoxygenated blood travels to the two-chambered heart. Here the blood is pumped to the gills via the ventral aorta artery where it branches off into afferent brachial arteries. Reoxygenation takes place in the gills and the reoxygenated blood flows into the efferent brachial arteries, which come together to form the dorsal aorta. The blood flows from the dorsal aorta throughout the body. The deoxygenated blood from the body then flows through the posterior cardinal veins and enters the posterior cardinal sinuses. From there blood enters the ventricle of the heart and the cycle repeats.

Chondrpiscians do not have gas-filled swim bladders, but instead rely on a large liver filled with oil that contains squalene. The liver may constitute up to 30% of their body mass for buoyancy. Its effectiveness is limited, so they employ dynamic lift to maintain depth and sink when they stop swimming. Some species, if inverted or stroked on the nose, enter a natural state of tonic immobility. Some species are able to ingest air from the surface and store it in their stomachs, using the stomach as a swim bladder.

The blood and other tissue of chondrpiscians is isotonic to their marine environments, allowing them to be in osmotic balance with the seawater. This adaptation prevents most chondrpiscians from surviving in fresh water, and they are therefore confined to a marine environment. A few exceptions to this rule exist, and have developed a way to adopt kidney function to excrete large amounts of urea.

Chondrpiscian teeth are not attached to the jaw, but embedded in the flesh, and in many species are constantly replaced throughout the animal's life. All chondrpiscians have multiple rows of teeth along the edges of their upper and lower jaws. New teeth grow continuously in a groove just inside the mouth and move forward from inside the mouth on a "conveyor belt" formed by the skin in which they are anchored.

Chondrpiscian caudal fins vary considerably between species and are adapted to the lifestyle. The tail provides thrust and so speed and acceleration are dependent on tail shape. Different tail shapes have evolved in adaptation to different environments. Most possess a heterocercal caudal fin in which the dorsal portion is usually noticeably larger than the ventral portion. This is due to the fact that the vertebral column extends into that dorsal portion, allowing for a greater surface area for muscle attachment which would then be used for more efficient locomotion among the negatively buoyancy.

Chondrpiscians skin is covered with dermal teeth, arranged in a complex dermal corset made of flexible collagenous fibres and silica scales, arranged as a helical network surrounding their body. This works as an outer skeleton, providing attachment for their swimming muscles and thus saving energy. Their dermal teeth give them hydrodynamic advantages as they reduce turbulence when swimming.

Most species are mildly homeothermic - able to maintain their body temperature above the surrounding water temperature. This is possible because of the presence of the suprahepatic rete, a counter current exchange mechanism that reduces the loss of body heat. Muscular contraction also generates a mild amount of body heat. However, this differs significantly from true homeothermy, as found in mammals and birds, in which heat is generated, maintained, and regulated by metabolic activity.

Chondrpiscian sex is easily determined. Males have modified pelvic fins which have become a pair of claspers. The name is somewhat misleading as they are not used to hold on to the female, but fulfill the role of the mammalian penis. Most chondrpiscians lay eggs. In most of these species, the developing embryo is protected by an egg case with the consistency of leather. Sometimes these cases are corkscrewed into crevices for protection.

Chondrpiscians have a brain weight relative to body size that comes close to that of terrestrial mammals.