Squamata

Squamata (from the Latin squamatus, "scaly") is the largest living order of non-avian reptiles (Sauropsida), comprising more than 11,500 described extant species of lizards (~7,300 spp.), snakes (Serpentes, ~4,000 spp.), and subterranean worm lizards (Amphisbaenia, ~200 spp.)—accounting for ~96% of all living non-avian reptiles and outnumbering all living mammalian or amphibian species. Together with its sole surviving sister order Rhynchocephalia (represented today only by the New Zealand tuatara, Sphenodon punctatus, from which squamates diverged during the Early–Middle Triassic, ~245 million years ago), Squamata forms the superorder Lepidosauria.

Crucially, modern molecular phylogenomics demonstrates that "lizards" (Lacertilia) are a paraphyletic grade: both snakes (Serpentes) and amphisbaenians are highly modified, secondarily limbless lizards nested deeply inside the squamate radiation—making a monitor lizard (Varanus) or glass lizard (Ophisaurus) far more closely related to a cobra or python than to a gecko or skink!

1. Streptostyly and Cranial Kinesis (Loss of the Lower Temporal Bar): Whereas the ancestral diapsid skull (retained in the tuatara Sphenodon and in crocodilians) possesses two intact bony temporal arches that lock the jaw-joint bone (quadrate) rigidly to the cheek (jugal and quadratojugal), squamates deleted the lower temporal bar (quadratojugal). Freed at its ventral end, the quadrate bone pivots forward and backward (streptostyly) against the squamosal bone of the braincase. In snakes (Macrostomia), this kinetic linkage was carried to an evolutionary extreme: the left and right lower jaw rami are unfused at the chin (connected only by an elastic ligament), the palatomaxillary arches move independently in a "pterygoid walk," and the elongated quadrate–supratemporal suspension swings outward, allowing a python or viper to swallow whole mammalian prey larger in diameter than its own head.
2. Paired Eversible Male Hemipenes: Uniquely among all amniotes (Whereas turtles, crocodilians, birds, and mammals possess a single median ventral phallus derived from the embryonic cloacal eminence), male squamates possess paired lateral intromittent organs—the hemipenes—housed inverted inside the base of the tail behind the cloacal vent (and homologous to paired hemiclitorides in females). As shown by Clifford J. Tabin, Patrick Tschopp, and colleagues (2014) using developmental cell-lineage tracing, the squamate genital tubercles arise from paired lateral limb-bud-related mesenchyme adjacent to the hindlimb buds rather than the ventral midline, and only one hemipenis is everted (via blood and lymph engorgement) during any single copulation, ornamented with species-specific calcified spines, calyces, and a spermatic groove (sulcus spermaticus).
3. Synchronous Epidermal Shedding (Ecdysis) and Caudal Autotomy: Unlike crocodilians and turtles (which shed individual microscopic flakes of dead skin continuously), squamates periodically shed their outer β-keratin (corneous beta-protein) and α-keratin epidermal generation in large patches (lizards) or as a single intact, inside-out sleeve including the transparent ocular spectacle / brille (in snakes and geckos). In addition, most lizards (and the tuatara) possess preformed intravertebral fracture planes running transversely across the middle of each caudal vertebra accompanied by arterial sphincters and cartilage-lined myosepta, enabling voluntary caudal autotomy (self-amputation of a thrashing decoy tail to escape predators, followed by regeneration of an unsegmented cartilaginous tube).
4. Forked Tongue and Vomeronasal (Jacobson's) Organ Chemoreception: In squamates (especially Scincomorpha, Lacertoidea, Anguimorpha, and Serpentes), the paired vomeronasal organs (Jacobson's organs) on the roof of the palate are completely separated from the nasal cavity and open into the roof of the mouth via narrow ducts. A forked tongue flicked into the air or onto the ground samples non-volatile chemical odorants on its two tines and delivers them to the left and right vomeronasal ducts, providing stereochemical tropotaxis (chemical directional tracking in stereo!).

Classical morphology divided Squamata into two suborders based on feeding mechanics: Iguania (fleshy-tongued ambush predators: iguanas, agamas, and chameleons, placed at the base of the tree) versus Scleroglossa (keratinized-tongued, vomeronasal-foraging geckos, skinks, lizards, and snakes). Nuclear phylogenomic datasets (Townsend et al., 2004; Vidal & Hedges, 2005; Wiens et al., 2012; Title et al., 2024) inverted this tree—showing that Gekkota and Dibamidae are the basal-most squamates, while Iguania, Anguimorpha, and Serpentes are sister clades united at the apex of the tree inside the venom clade Toxicofera:

How did snakes evolve an elongated, rib-packed trunk of 120 to >400 thoracic vertebrae while completely losing their limbs?

1. Heterochronic Axial Elongation via Oct4 and Gdf11: During vertebrate somitogenesis, the total number of trunk segments is set by a balance between FGF/Wnt/Oct4 (Pou5f1) signaling (which keeps presomitic mesoderm progenitors proliferating) and Gdf11 / Retinoic Acid signaling (which activates posterior Hox10–Hox13 genes to terminate trunk building and switch to the tail). As shown by Moises Mallo and colleagues (2016), snake embryos carry cis-regulatory reorganizations that keep the pluripotency factor Oct4 active far longer during trunk extension while expanding cervical/thoracic Hoxc6/Hoxc8 domains down the body, cranking the somite segmentation clock ~3–4 times faster relative to tissue growth to bud hundreds of rib-bearing vertebrae!
2. Progressive Decay of the ZRS Sonic Hedgehog Limb Enhancer: Basal snakes (pythons and boas) still bud transient embryonic hindlimb buds and retain vestigial internal pelvic bones and external keratinized pelvic spurs, whereas advanced caenophidian snakes (cobras, vipers, colubrids) never form hindlimb buds at all. In 2016, Evgeny Z. Kvon, Axel Visel, and colleagues and Francisca Leal & Martin J. Cohn discovered that snakes share a 17-base-pair deletion inside the limb-specific ZRS enhancer of Sonic hedgehog (Shh) that abolishes ETS1 transcription factor binding: when Kvon et al. used CRISPR–Cas9 to replace a mouse embryo's native ZRS enhancer with the python or cobra ZRS enhancer, the resulting "serpentized" mice grew up completely limbless—and restoring just those 17 deleted base pairs resurrected full limb-bud gene expression!

Why did Independent Limb Loss Evolve Over 25 Times in Lizards Alone?

Snakes are only one of at least 25 to 30 independent squamate lineages that evolved a serpentine, legless or near-legless body plan—including slow worms and glass lizards (Anguidae: Anguis, Ophisaurus), Australian flap-footed lizards (Pygopodidae), worm lizards (Amphisbaenia), blind skinks (Dibamidae), and over a dozen separate lineages of burrowing skinks (Scincidae: Acontias, Brachymeles, Lerista). You can easily distinguish a legless lizard (such as a glass lizard) from a true snake by four anatomical markers: most legless lizards retain movable eyelids, external ear openings, a notched (rather than deeply forked) tongue, and a very long, breakable tail that makes up more than half of their total body length (whereas a snake's body is almost entirely precloacal trunk with a short post-cloacal tail!).

How Did Venom Evolve in Snakes and Monitor/Helodermatid Lizards (The Toxicofera Hypothesis)?

As proposed by Bryan G. Fry and colleagues (2006), the ancestor of the clade Toxicofera (uniting Serpentes, Anguimorpha, and Iguania ~170 Ma) evolved specialized mandibular and maxillary dental glands secreting a baseline cocktail of physiologically active proteins (including cysteine-rich secretory proteins [CRISPs], kallikrein serine proteases, natriuretic peptides, and nerve growth factor). In Elapidae and Viperidae, tandem gene duplication and accelerated positive selection (d_N/d_S ≫ 1) weaponized housekeeping enzymes and disulfide-stabilized scaffolds into high-potency three-finger neurotoxins (3FTx), phospholipase A₂ myotoxins, and snake venom metalloproteinases (SVMPs) delivered via rear-grooved (opisthoglyphous), fixed front (proteroglyphous in elapids), or rotating hinged hypodermic (solenoglyphous in vipers) fangs.

1. Fry, B. G., Vidal, N., Norman, J. A., Vonk, F. J., Scheib, H., Ramjan, S. F. R., ... & Hedges, S. B. (2006). Early evolution of the venom system in lizards and snakes. Nature, 439(7076), 584–588. doi:10.1038/nature04328
2. Tschopp, P., Sherratt, E., Sanger, T. J., Gronostajski, R. M., Tabin, C. J., & Losos, J. B. (2014). A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature, 516(7531), 391–394. doi:10.1038/nature13819
3. Kvon, E. Z., Kamneva, O. K., Melo, U. S., Barozzi, I., Osterwalder, M., Mannion, B. J., ... & Visel, A. (2016). Progressive loss of function in a limb enhancer during snake evolution. Cell, 167(3), 633–642. doi:10.1016/j.cell.2016.09.028
4. Aires, R., Jurberg, A. D., Leal, F., Nóvoa, A., Cohn, M. J., & Mallo, M. (2016). Oct4 is a key regulator of vertebrate trunk length diversity. Developmental Cell, 38(3), 262–274. doi:10.1016/j.devcel.2016.06.021
5. Title, P. O., Singhal, S., Grundler, M. C., Costa, G. C., Pyron, R. A., Colli, G. R., ... & Rabosky, D. L. (2024). The macroevolutionary singularity of snakes. Science, 383(6685), 918–923. doi:10.1126/science.adh2449