Amphibians parted ways from other tetrapods about 320 mya. Some of these tetrapods gave rise to the amniotes. Living amniotes are represented by two classes: The class Mammalia and the class Reptilia which includes birds (Aves).

Amniotes get their names from the amniotic egg, a shared derived trait of the group. A shelled egg is the ancestral condition in amniotes but not all amniotes have stuck with it.  Many modern amniotes, including the vast majority of mammals, as well as many snakes and lizards  no longer lay eggs but give birth to live young. All archosaurs as well as all turtles have retained the ancestral shelled egg though. A shelled egg was a critical innovation for the colonization of land by reptiles. Although amphibians have been quite successful on land, most species must lay their eggs in water or in moist environments. A shelled egg protects the embryo against desiccation, and abrasion allowing amniotes to develop on land.

Ancestral amniotes had one or two pairs of holes (in addition to the orbits of the eye) on the side of their skull. These holes are called temporal fenestrae. The presence of one or two pairs of temporal fenestrae defines the two living lineages of amniotes. The synapids have one pair.  Mammals are the only living synapsids left on the planet. The diapsids have two temporal fenestrae. Reptiles (including birds) are the only diapsids left on the planet. Synapids and diapsids parted ways around 310 mya. 

Modern reptiles (including birds) form a monophyletic group (clade) which itself contains three smaller clades: Testudines (turtles), Archosauria (crocodilians and birds), and Lepidosauria (rhynchocephalians and squamates). Crocodilians and tuataras are the only diapsids to retain two temporal fenestrae to this day. All other modern reptiles including birds have lost one or both openings but they are nonetheless clearly descending from diapsid ancestors and are thus considered part of that lineage.

Squamates are by far the most diverse group of reptiles with nearly 11 000 species.  This clade includes lizards and snakes. Snakes form a clade (Serpentes) nested within the various other squamates we collectively call lizards. This means that some lizards are more closely related to snakes than they are to other lizards. All living snakes lack limbs even though snakes are tetrapods a group named after, and defined by the presence of four walking limbs. Snakes clearly evolved from an ancestor with four limbs which is why they rank among the tetrapods. Snakes are not the only limbless reptiles. At least 25 different lineages of squamates have lost their limbs, making the evolution of limblessness a striking example of convergent evolution.

Snakes are nonetheless the most specialized legless squamates. They share the following derived characteristics:

• Absence of sceral ossicle or ring
• Loss of many elements of the skull and hyoid including both temporal arches as well as numerous modifications to increase skull kinesis including a prokinetic joint (see section on feeding)
• 120 to 400 pre-cloacal vertebrae
• Absence of eyelids. Their cornea is covered by a clear extension of the skin spectacle (also found in some lizard like geckos)
• Absence of external ears
• Limited caudal autotomy

Snakes make up nearly half of all species of squamates! They have adapted to a wide range of habitats and lifestyles. Snakes live in trees, underground, in the open ocean. They have developed various types of locomotion including gliding and most species can use several types depending on the environment. Snakes are somewhat of a paradox. By getting rid of the traits that define tetrapods, they have become one of the most successful group of tetrapods! Something to ponder about. 

Turtles are in many respects the most puzzling group of amniotes. Turtles have undergone a major remodelling of the basic tetrapod body plan (think of a lizard or a salamander). The shell of turtles is part of the skeleton. It evolved through the remodelling of the axial and appendicular skeletons.

The dorsal part of the shell, called the carapace, is largely made out of oversized ribs that are fused with one another. During a turtle’s embryonic development, the ribs fan out and fuse with one another to form a bony dome. As the ribs fan out during development, they entrap the shoulder girdle. Turtles thus have a very peculiar body plan in which the shoulders and hips are inside the rib cage, not outside as in all other tetrapods! 

The ventral part of the shell, the plastron is derived in part from the clavicle and interclavicle bones as well as from dermal bones. Having a shell affects many aspects of  the anatomy and physiology of turtles particularly their respiration and locomotion as we will discuss later.

The position of turtles within amniotes is still unresolved.  Turtles used to be placed at the base of the reptile tree making them equally related to archosaurs and lepidosaurs. This hypothesis is based on early morphological analysis but it is now challenged by more recent analysis of fossils (morphology) and molecular sequences. Unfortunately, these more recent analyses tell different stories. Nearly all studies based molecules (e.g. DNA sequencing) place turtles as the sister taxon of archosaurs.  On the other hand, recent morphological studies place turtles as the sister taxon of lepidosaurs. 

Integument

Any kid curious about “herps” quickly learns that reptiles have scales and amphibians don’t. Indeed, amphibians have thin, wet glandular skin while reptiles have thick, dry, and scaly skin. Like in amphibians, the outer layer of the skin of reptiles is made up of dead, keratinized epidermal cells called the stratum corneum, but this layer is thicker and less permeable to water and gas than it is in amphibians.  These properties allow reptiles to live in drier environments than amphibians and many reptiles have water requirements that are only about 1 to 5% of amphibians owning to their relatively impermeable integument.

The reptilian scales are folded areas of the epidermis that form during embryonic development. Note that the scales of reptiles are not homologous to the scales of fish which are derived from the dermis.

The outermost surface of the epidermis is sculpted by microscopic ridges that affect the mechanical and optical properties of the skin.  This surface is called the  Oberhäutchen. The epidermis is formed by two types of keratin: alpha and beta-keratin. Alpha keratin is also found in amphibians and mammals. It is the molecule that makes the skin elastic. Beta keratin is only found in reptiles (including birds) and it adds rigidity and impermeability to the scales. Scales also contain lipids which increase their impermeability (lipids are water are hydrophobic).  The permeability of the reptilian skin is quite variable among species. Some aquatic species, like the musk turtles (Sternotherus sp.) have highly permeable skin and are capable of substantial cutaneous reparation, while desert species have extremely impermeable skin.

In addition to scales, Crocodilians and some lizards sport bony plates inside their dermis. These plates, called osteoderms, form a protective armor.  Lizards of the genus Heloderma, have many small osteoderms throughout their body giving them a beaded appearance.

The shell of turtles is not covered by scales but by thin non-overlapping plates of keratin called scutes. Scutes sit on the bones of the shell and they develop with the shell. The carapace (back part of the shell) is formed by enlarged ribs and vertebrae that interlock with one another. Thes cutes and the underlying bony plates are offset relative to one another. Turtles have scales on their legs and tail.

Reptiles (and amphibians) shed the outermost part of their epidermis. In turtles and in crocodylians, epidermal cells are shed continuously (as in humans).  In some turtles however, the outermost part of the scutes are shed periodically as large pieces. This is the case in map and painted turtles which can sometimes be seen basking with large pieces of scutes peeling off their carapace.

Snakes and lizards undergo shedding cycles during which the older, outer epidermis is shed at once and replaced by a newer epidermis. Between shedding cycles, the epidermis is composed of four layers of epidermal cells (the Oberhäutchen layer, β-layer, mesos layer and α-layer) resting on the basal layer or stratum germininativum.  The shedding cycle begins as cells from the stratum germinativum proliferate to produce a new skin generation. That new skin (inner generation) lays underneath the older skin (outer generation) that will be shed.  Fluids and enzymes build up between the new and the old skin generations and the older (outer) generation eventually peels off.  

Snakes that are about to shed often have cloudy eyes. This is due to the build-up of fluid under the ocular scale just before shedding. Snakes in that state have impaired vision and thus tend to remain hidden until they have shed. The frequency of shedding depends on growth rate and can vary from weeks to months.