While there are substantial anatomical differences between the reptile orders, there is limited variation within the orders. This means that once the prosector has a fundamental understanding of the anatomy of the testudines, crocodilians, and squamates separately, they will be prepared for most reptile necropsies. Some of the differences between reptile groups are summarized in Table 16.1.

Two of the greatest sources of variation in reptile anatomy are body shape and skeletal anatomy. The axial skeleton is similar in crocodilians, squamates, and tuataras, and includes a bony skull, a vertebral column variably divided into often indistinct segments, and a tail of variable length. In reptiles, ball and socket articulations exist between vertebral bodies, not intervertebral discs as in mammals. The chelonian shell is the result of extensive ossification that forms a solid bony dorsal structure called the carapace that incorporates the vertebral column and ribs, and a ventral plastron formed by modified and fused clavicles, interclavicular bones, and floating ribs (gastralia; Hirasawa et al. 2014). The reptile appendicular skeleton however shows substantial variation, substantial, or complete reduction of both the pectoral and pelvic limbs in all snakes and certain lizards (legless lizards), while other species, such as some amphisbaenians, exhibit loss of the pelvic limbs with variable reduction to loss of the pectoral limbs. The skulls of reptiles exhibit substantial variation in bone thickness and dentition.

No reptiles possess a true diaphragm, and all organs are present in a single coelomic cavity. In crocodilians, a pseudodiaphragm is present caudal to the liver consisting of sheets of fibrous connective tissue and muscular attachments to the body wall.

The heart represents the main source of variation in the reptilian cardiovascular system and demonstrates the evolutionary pressure toward a four-chamber structure. In squamates and tuataras, there is variable and limited formation of an interventricular septum (IVS) that does not completely divide the ventricle into two sides; in chelonians, IVS formation is more prominent, but incomplete. In crocodilians, much like their avian relatives, there is separation of the ventricle into left and right compartments by a complete IVS. The ventricle of crocodilians is also attached to the pericardium at its apex by a band of fibrous connective tissue. The sinus venosus in noncrocodilian reptiles is quite prominent and considered by some to represent a fourth chamber (Kik and Mitchell 2005).

Reptile lungs are anatomically distinct from those of other vertebrates and are anatomically quite simple. Either the trachea (snakes) or paired bronchi (all other reptiles) open into a potential space surrounded by many blind sacs (faveolae) lined by simple vascularized septa. The lungs of chelonians are intimately associated with the overlying carapace (Figure 16.1). Reptile lungs are well developed bilaterally except in some snakes, including the colubrids, viperids, and elapids, where the left lung is reduced to completely absent. Snake lungs are also divided into three functional regions: a cranial respiratory portion, a middle transitional portion, and a caudal thin membranous portion that can extend up to 80% or more of the length of the body.

Reptiles lack lymph nodes. The hematolymphopoietic tissues include the bone marrow, spleen, thymus, and mucosal-associated lymphoid tissues that are present in all tissues with a mucosa. The thymus lies cranial to the heart, generally adjacent to the thyroid gland; partial regression occurs with age. In some snakes, the splenic and pancreatic parenchyma fuse (splenopancreas).

Urogenital variation among reptile groups can be considerable. All reptiles have bilateral kidneys. The kidneys of crocodilians, chelonians, and snakes are lobulated (snakes particularly so), but lizard and tuatara kidneys exhibit only partial lobulation. In all but snakes, the kidneys are in the coelomic cavity’s caudal recess (Figure 16.1). Urinary bladders are absent in snakes and crocodilians, variably present in lizards, and always present in the tuatara and chelonians (Holz 2020); all reptile urinary bladders open directly from the cloaca (urodeum). Fully developed ovaries and oviducts are present bilaterally in all reptiles (Figures 16.1 and 16.2). The bilateral, intracoelomic testicles are located craniomedial to the kidney (Figure 16.3). All male reptiles, other than tuatara, have phalli. In crocodilians and chelonians, a single phallus is present in the cloaca (proctodeum), while in squamates, paired phalli (hemipenes) are located in sheaths embedded within the body wall musculature caudal to the vent.

The reptile gastrointestinal tract exhibits limited variation among the clades. The reptile tongue, though, is quite variable. In crocodilians and some aquatic turtles, the tongue is lined by a thick keratinized epithelium, flattened, and has limited mobility. In tortoises and other turtles, the tongue has greater mobility, and the mucosa contains glands. Tuataras and lizards generally have large, mobile tongues with prominent mucus-producing glands. Snake tongues are elongated, housed in a sheath in the ventral oral cavity. The esophagus of crocodilians and chelonians is lined by a keratinized mucosa, while in squamates, it is thin, distensible, and lined by a nonkeratinized mucosa. All reptiles are monogastric with similar stomach anatomy. The small intestine in snakes appears linear but is often arranged in transverse loops with adhered serosa. The large intestine in carnivorous reptiles is short, but in herbivorous tortoises and lizards, it is enlarged and accompanied by a cecum to assist in hindgut fermentation. The colon ends in the coprodeum, the cranial-most portion of the cloaca, followed by the urodeum and proctodeum.

Reptile livers have two large, deep brown lobes (Figure 16.3; the right lobe is larger than the left). In snakes, the two lobes fuse centrally. The appearance of the parenchyma is variable based on nutritional status: lipid-laden hepatocytes impart a tan-gray appearance, while atrophied hepatocytes impart a dark brown to black appearance. All reptiles have gallbladders, but the location varies. In chelonians, the gallbladder is surrounded by the right liver lobe, in crocodilians and lizards, it is attached to the caudal margin of the right liver lobe (Figure 16.3

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