Reptile
Reptiles are air-breathing, cold-blooded vertebrates that have skin covered in scales as opposed to hair or feathers. They are tetrapods (having or having descended from vertebrates with four limbs) and amniotes, whose embryos are surrounded by an amniotic membrane. Modern reptiles inhabit every continent with the exception of Antarctica, and are represented by four living orders:
- Crocodilia (crocodiles, gharials, caimans and alligators): 23 species
- Sphenodontia (tuatara from New Zealand): 2 species
- Squamata (lizards, snakes and amphisbaenids ("worm-lizards")): approximately 7,900 species
- Testudines (turtles and tortoises): approximately 300 species
The majority of reptile species are oviparous (egg-laying) although certain species of squamates are capable of giving live birth. This is achieved, either through  ovoviviparity (egg retention), or viviparity (offspring born without use of calcified eggs).  Many of the viviparous species feed their fetuses through various forms of placenta analogous to those of mammals with some providing initial care for their hatchlings. Extant reptiles range in size from the newly-discovered Jaragua Sphaero, at 1.6 cm (0.6 in), to the Saltwater Crocodile, at up to at least 7 m (23 feet).

# Classification

## History of classification
From the classical standpoint,  reptiles included all the amniotes except birds and mammals.  Thus reptiles were defined as the set of animals that includes crocodiles, alligators, tuatara, lizards, snakes, amphisbaenians and turtles, grouped together as the class Reptilia (Latin repere, "to creep").  This is still the usual definition of the term. However, in recent years, many taxonomists have begun to insist that taxa should be monophyletic, that is, groups should include all descendants of a particular form.  The reptiles as defined above would be paraphyletic, since they exclude both birds and mammals, although these also developed from the original reptile.  Colin Tudge writes:
The terms "Sauropsida" ("Lizard Faces") and "Theropsida" ("Beast Faces") were coined in 1916 by E.S. Goodrich to distinguish between lizards, birds, and their relatives on one hand (Sauropsida) and mammals and their extinct relatives (Theropsida) on the other. Goodrich supported this division by the nature of the hearts and blood vessels in each group, and other features such as the structure of the forebrain. According to Goodrich, both lineages evolved from an earlier stem group, the Protosauria ("First Lizards") which included some Paleozoic amphibians as well as early reptiles.
In 1956 D.M.S. Watson observed that the first two groups diverged very early in reptilian history, and so he divided Goodrich's Protosauria  among them.  He also reinterpreted the Sauropsida and Theropsida to exclude birds and mammals respectively. Thus his Sauropsida included Procolophonia, Eosuchia, Millerosauria, Chelonia (turtles), Squamata (lizards and snakes), Rhynchocephalia, Crocodilia, "thecodonts" (paraphyletic basal Archosauria), non-avian dinosaurs, pterosaurs, ichthyosaurs, and sauropyterygians.
This classification supplemented, but was never as popular as, the classification of the reptiles (according to Romer's classic Vertebrate Paleontology) into four subclasses according to the positioning of temporal fenestrae, openings in the sides of the skull behind the eyes. Those divisions were:
- Anapsida - no fenestrae
- Synapsida - one low fenestra (no longer considered true reptiles)
- Euryapsida - one high fenestra (now included within Diapsida)
- Diapsida - two fenestrae
All of the above but Synapsida fall under Sauropsida.

## Taxonomy
Classification to order level, after Benton, 2004.
- Series Amniota
Class Synapsida
Order Pelycosauria*
Order Therapsida
Class Mammalia
Class Sauropsida
Subclass Anapsida
Order Testudines (turtles)
Subclass Diapsida
Order Araeoscelidia
Order Younginiformes
Infraclass Ichthyosauria
Infraclass Lepidosauromorpha
Superorder Sauropterygia
Order Placodontia
Order Nothosauroidea
Order Plesiosauria
Superorder Lepidosauria
Order Sphenodontida (tuatara)
Order Squamata (lizards & snakes)
Infraclass Archosauromorpha
Order Prolacertiformes
Division Archosauria
Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Class Synapsida
Order Pelycosauria*
Order Therapsida
Class Mammalia
- Order Pelycosauria*
- Order Therapsida
Class Mammalia
- Class Mammalia
- Class Sauropsida
Subclass Anapsida
Order Testudines (turtles)
Subclass Diapsida
Order Araeoscelidia
Order Younginiformes
Infraclass Ichthyosauria
Infraclass Lepidosauromorpha
Superorder Sauropterygia
Order Placodontia
Order Nothosauroidea
Order Plesiosauria
Superorder Lepidosauria
Order Sphenodontida (tuatara)
Order Squamata (lizards & snakes)
Infraclass Archosauromorpha
Order Prolacertiformes
Division Archosauria
Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Subclass Anapsida
Order Testudines (turtles)
- Order Testudines (turtles)
- Subclass Diapsida
Order Araeoscelidia
Order Younginiformes
Infraclass Ichthyosauria
Infraclass Lepidosauromorpha
Superorder Sauropterygia
Order Placodontia
Order Nothosauroidea
Order Plesiosauria
Superorder Lepidosauria
Order Sphenodontida (tuatara)
Order Squamata (lizards & snakes)
Infraclass Archosauromorpha
Order Prolacertiformes
Division Archosauria
Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Order Araeoscelidia
- Order Younginiformes
- Infraclass Ichthyosauria
- Infraclass Lepidosauromorpha
Superorder Sauropterygia
Order Placodontia
Order Nothosauroidea
Order Plesiosauria
Superorder Lepidosauria
Order Sphenodontida (tuatara)
Order Squamata (lizards & snakes)
- Superorder Sauropterygia
Order Placodontia
Order Nothosauroidea
Order Plesiosauria
- Order Placodontia
- Order Nothosauroidea
- Order Plesiosauria
- Superorder Lepidosauria
Order Sphenodontida (tuatara)
Order Squamata (lizards & snakes)
- Order Sphenodontida (tuatara)
- Order Squamata (lizards & snakes)
- Infraclass Archosauromorpha
Order Prolacertiformes
Division Archosauria
Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Order Prolacertiformes
- Division Archosauria
Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Subdivision Crurotarsi
Superorder Crocodylomorpha
Order Crocodylia
- Superorder Crocodylomorpha
Order Crocodylia
- Order Crocodylia
- Subdivision Avemetatarsalia
Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Infradivision Ornithodira
Order Pterosauria
Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Order Pterosauria
- Superorder Dinosauria
Order Saurischia
Class Aves
Order Ornithischia
- Order Saurischia
Class Aves
- Class Aves
- Order Ornithischia

## Phylogeny
The cladogram presented here illustrates the "family tree" of reptiles, and follows a simplified version of the relationships found by Laurin and Gauthier (1996), presented as part of the Tree of Life Web Project.

# Evolution
Hylonomus is the oldest-known reptile, and was about 8 to 12 inches (20 to 30 cm) long. Westlothiana has been suggested as the oldest reptile, but is for the moment considered to be more related to amphibians than amniotes. Petrolacosaurus and Mesosaurus are other examples. The earliest reptiles were found in the swamp forests of the Carboniferous, but were largely overshadowed by bigger labyrinthodont amphibians such as Proterogynrius. It was only after the small ice age at the end of the Carboniferous that the reptiles grew to big sizes, producing species such as Edaphosaurus and Dimetrodon.
The first true "reptiles" (Sauropsids) are categorized as Anapsids, having a solid skull with holes only for nose, eyes, spinal cord, etc.  Turtles are believed by some to be surviving Anapsids, as they also share this skull structure; but this point has become contentious lately, with some arguing that turtles reverted to this primitive state in order to improve their armor.  Both sides have strong evidence, and the conflict has yet to be resolved.
Shortly after the first reptiles, two branches split off, one leading to the Anapsids, which did not develop holes in their skulls. The other group, Diapsida, possessed a pair of holes in their skulls behind the eyes, along with a second pair located higher on the skull. The Diapsida split yet again into two lineages, the lepidosaurs (which contain modern snakes, lizards and tuataras, as well as, debatably, the extinct sea reptiles of the Mesozoic) and the archosaurs (today represented by only crocodilians and birds under dinosaurs, but also containing pterosaurs and non-avian dinosaurs).
The earliest, solid-skulled amniotes also gave rise to a separate line, the Synapsida. Synapsids developed a pair of holes in their skulls behind the eyes (similar to the diapsids), which were used to both lighten the skull and increase the space for jaw muscles. The synapsids eventually evolved into mammals, and are often referred to as mammal-like reptiles, though they are not true members of Sauropsida. (A preferable term is "stem-mammals".)

# Systems

## Circulatory
Most reptiles have closed circulation via a three-chamber heart consisting of two atria and one, variably-partitioned ventricle. There is usually one pair of aortic arches. In spite of this, because of the fluid dynamics of blood flow through the heart, there is little mixing of oxygenated and deoxygenated blood in the three-chamber heart. Furthermore, the blood flow can be altered to shunt either deoxygenated blood to the body or oxygenated blood to the lungs, which gives the animal greater control over its blood flow, allowing more effective thermoregulation and longer diving times for aquatic species. There are some interesting exceptions among reptiles. For instance, crocodilians have an anatomically four-chambered heart that is capable of becoming a functionally three-chamber heart during dives (Mazzotti, 1989 pg 47). Also, it has been discovered that some snake and lizard species (e.g., monitor lizards and pythons) have three-chamber hearts that become functional four-chamber hearts during contraction. This is made possible by a muscular ridge that subdivides the ventricle during ventricular diastole and completely divides it during ventricular systole. Because of this ridge, some of these squamates are capable of producing ventricular pressure differentials that are equivalent to those seen in mammalian and avian hearts (Wang et al, 2003).

## Respiratory
All reptiles breathe using lungs. Aquatic turtles have developed more permeable skin, and some species have modified their cloaca to increase the area for gas exchange (Orenstein, 2001). Even with these adaptations, breathing is never fully accomplished without lungs. Lung ventilation is accomplished differently in each main reptile group. In squamates the lungs are ventilated almost exclusively by the axial musculature. This is also the same musculature that is used during locomotion. Because of this constraint, most squamates are forced to hold their breath during intense runs. Some, however, have found a way around it. Varanids, and a few other lizard species, employ buccal pumping as a complement to their normal "axial breathing." This allows the animals to completely fill their lungs during intense locomotion, and thus remain aerobically active for a long time. Tegu lizards are known to possess a proto-diaphragm, which separates the pulmonary cavity from the visceral cavity. While not actually capable of movement, it does allow for greater lung inflation, by taking the weight of the viscera off the lungs (Klein et al, 2003). Crocodilians actually have a muscular diaphragm that is analogous to the mammalian diaphragm. The difference is that the muscles for the crocodilian diaphragm pull the pubis (part of the pelvis, which is movable in crocodilians) back, which brings the liver down, thus freeing space for the lungs to expand. This type of diaphragmatic setup has been referred to as the "hepatic piston."
How turtles and tortoises breathe has been the subject of much study. To date, only a few species have been studied thoroughly enough to get an idea of how turtles do it. The results indicate that turtles & tortoises have found a variety of solutions to this problem. The problem is that most turtle shells are rigid and do not allow for the type of expansion and contraction that other amniotes use to ventilate their lungs. Some turtles such as the Indian flapshell (Lissemys punctata) have a sheet of muscle that envelopes the lungs. When it contracts, the turtle can exhale. When at rest, the turtle can retract the limbs into the body cavity and force air out of the lungs. When the turtle protracts its limbs, the pressure inside the lungs is reduced, and the turtle can suck air in. Turtle lungs are attached to the inside of the top of the shell (carapace), with the bottom of the lungs attached (via connective tissue) to the rest of the viscera. By using a series of special muscles (roughly equivalent to a diaphragm), turtles are capable of pushing their viscera up and down, resulting in effective respiration, since many of these muscles have attachment points in conjunction with their forelimbs (indeed, many of the muscles expand into the limb pockets during contraction).  Breathing during locomotion has been studied in three species, and they show different patterns. Adult female green sea turtles do not breathe as they crutch along their nesting beaches. They hold their breath during terrestrial locomotion and breathe in bouts as they rest. North American box turtles breathe continuously during locomotion, and the ventilation cycle is not coordinated with the limb movements (Landberg et al., 2003). They are probably using their abdominal muscles to breathe during locomotion. The last species to have been studied is red-eared sliders, which also breathe during locomotion, but they had smaller breaths during locomotion than during small pauses between locomotor bouts, indicating that there may be mechanical interference between the limb movements and the breathing apparatus. Box turtles have also been observed to breathe while completely sealed up inside their shells (ibid).
Most reptiles lack a secondary palate, meaning that they must hold their breath while swallowing. Crocodilians have evolved a bony secondary palate that allows them to continue breathing while remaining submerged (and protect their brains from getting kicked in by struggling prey). Skinks (family Scincidae) also have evolved a bony secondary palate, to varying degrees. Snakes took a different approach and extended their trachea instead. Their tracheal extension sticks out like a fleshy straw, and allows these animals to swallow large prey without suffering from asphyxiation.

## Excretory
Excretion is performed mainly by two small kidneys. In diapsids uric acid is the main nitrogenous waste product; turtles, like mammals, mainly excrete urea. Unlike the kidneys of mammals and birds, reptile kidneys are unable to produce liquid urine more concentrated than their body fluid. This is because they lack a specialized structure present in the nephrons of birds and mammals, called a Loop of Henle. Because of this, many reptiles use the colon to aid in the reabsorption of water. Some are also able to take up water stored in the bladder. Excess salts are also excreted by nasal and lingual salt-glands in some reptiles.

## Nervous
The reptilian nervous system contains the same basic part of the amphibian brain, but the reptile cerebrum and cerebellum are slightly larger. Most typical sense organs are well developed with certain exceptions most notably the snakes lack of external ears (middle and inner ears are present). All reptilians have advanced visual depth perception compared to other animals.
There are twelve pairs of cranial nerves.

## Reproductive
Most reptiles reproduce sexually, though some are capable of asexual reproduction. All reproductive activity occurs with the cloaca, the single exit/entrance at the base of the tail where waste is also eliminated.  Tuataras lack copulatory organs, so the male and female simply press their cloacas together as the male excretes sperm.  Most reptiles, however, have copulatory organs, which are usually retracted or inverted and stored inside the body.  In turtles and crocodilians, the male has a single median penis, while squamates including snakes and lizards possess a pair of hemipenes.
Most reptiles lay amniotic eggs covered with leathery or calcareous shells. An amnion, chorion and allantois are present during embryonic life. There are no larval stages of development.  Viviparity and ovoviviparity have only evolved in Squamates, and a substantial fraction of the species utilize this mode of reprduction, including all boas and most vipers.  The degree of viviparity varies: some species simply retain the eggs until just before hatching, others provide maternal nourishment to supplement the yolk, while still others lack any yolk and provide all nutrients via a placenta.
Asexual reproduction has been identified in squamates in six families of lizards and one snake. In some species of squamates, a population of females are able to produce a unisexual diploid clone of the mother. This asexual reproduction called parthenogenesis occurs in several species of gecko, and is particularly widespread in the teiids (especially Aspidocelis) and lacertids (Lacerta).  In captivity Komodo dragons (varanidae) have reproduced by parthenogenesis.
Parthenogenetic species are also suspected to occur among chameleons, agamids, xantusiids, and typhlopids  .