|Venomous snakes, such as the rattlesnake shown above, are the most well-known venomous squamates.|
Toxicofera (Greek for "those who bear toxins"), is a clade of squamates that includes the Serpentes (snakes), Anguimorpha (monitor lizards, gila monster, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). Toxicofera contains about 4600 species, (nearly 60%) of extant squamates  It encompasses all venomous reptile species, as well as numerous related non-venomous species. There is little morphological evidence to support this grouping, however it has been recovered by all recent molecular analyses.
- Suborder Serpentes (snakes)
- Suborder Iguania (iguanas, agamid lizards, chameleons, etc.)
- Infraorder Anguimorpha, consisting of:
Venom in squamates has historically been considered a rarity; while it has been known in Serpentes since ancient times, the actual percentage of snake species considered venomous was relatively small (around 25%).  Of the approximately 2,650 species of advanced snakes (Caenophidia), only the front-fanged species (~650) were considered venomous by the anthropocentric definition. Following the classification of Helodermatidae in the 19th century, their venom was thought to have developed independently. In snakes, the venom gland is in the upper jaw, but in helodermatids, it is found in the lower jaw. The origin of venom in squamates was thus considered relatively recent in evolutionary terms and the result of convergent evolution among the seemingly-polyphyletic venomous snake families.
In 2003 a study was published that described venom in snake subfamilies previously thought to lack it. Further study claimed nearly all "non-venomous" snakes produce venom to a certain extent, suggesting a single, and thus far more ancient origin for venom in Serpentes than had been considered until then. As a practical matter, Fry cautioned:
Some non-venomous snakes have been previously thought to have only mild 'toxic saliva'. But these results suggest that they actually possess true venoms. We even isolated from a rat snake [Coelognathus radiatus (formerly known as Elaphe radiata)], a snake common in pet stores, a typical cobra-style neurotoxin, one that is as potent as comparative toxins found in close relatives of the cobra. These snakes typically have smaller quantities of venom and lack fangs, but they can still deliver their venom via their numerous sharp teeth. But not all of these snakes are dangerous. It does mean, however, that we need to re-evaluate the relative danger of non-venomous snakes.
This prompted further research, which led to the discovery of venom (and venom genes) in species from groups which were not previously known to produce it, e.g. in Iguania (specifically Pogona barbata from the family Agamidae) and Varanidae (from Varanus varius). It is thought that this was the result of descent from a common venom-producing squamate ancestor; the hypothesis was described simply as the "venom clade" when first proposed to the scientific community. The venom clade included Anguidae for phylogenetic reasons and adopted a previously suggested clade name: Toxicofera.
It was estimated that the common ancestral species that first developed venom in the venom clade lived on the order of 200 million years ago. The venoms are thought to have evolved after genes normally active in various parts of the body duplicated and the copies found new use in the salivary glands.
Among snake families traditionally classified as venomous, the capacity seems to have evolved to extremes more than once by parallel evolution; 'non-venomous' snake lineages have either lost the ability to produce venom (but may still have lingering venom pseudogenes) or actually do produce venom in small quantities (e.g. 'toxic saliva'), likely sufficient to assist in small prey capture, but not normally cause harm to humans if bitten.
The newly discovered diversity of squamate species producing venoms is a treasure trove for those seeking to develop new pharmaceutical drugs; many of these venoms lower blood pressure, for example. Previously known venomous squamates have already provided the basis for medications such as Ancrod, Captopril, Eptifibatide, Exenatide and Tirofiban.
Other scientists such as University of Washington's biologist Kenneth V. Kardong and toxicologists Scott A. Weinstein and Tamara L. Smith, have stated that the allegation of venom glands found in many of these animals "has had the effect of underestimating the variety of complex roles played by oral secretions in the biology of reptiles, produced a very narrow view of oral secretions and resulted in misinterpretation of reptilian evolution". According to these scientists "reptilian oral secretions contribute to many biological roles other than to quickly dispatch prey". These researchers concluded that, "Calling all in this clade venomous implies an overall potential danger that does not exist, misleads in the assessment of medical risks, and confuses the biological assessment of squamate biochemical systems".
- Fry, B. et al. (February 2006). "Early evolution of the venom system in lizards and snakes" (PDF). Nature 439 (7076): 584–588. doi:10.1038/nature04328. PMID 16292255.
- Vidal, Nicolas, and S. Blair Hedges. "The molecular evolutionary tree of lizards, snakes, and amphisbaenians." Comptes rendus biologies 332, no. 2 (2009): 129-139.
- Pyron, Robert Alexander, Frank T. Burbrink, and John J. Wiens. "A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes." BMC evolutionary biology 13, no. 1 (2013): 93.
- Wiens, John J., Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, Jack W. Sites, and Tod W. Reeder. "Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species." Biology letters 8, no. 6 (2012): 1043-1046.
- Vidal, N. and Hedges, S. (February–March 2009). "The molecular evolutionary tree of lizards, snakes, and amphisbaenians". Comptes Rendus Biologies (PDF) 332 (2-3): 129–139. doi:10.1016/j.crvi.2008.07.010. PMID 19281946.
- Fry, B. et al. (March 2009). "Evolution and Diversification of the Toxicofera Reptile Venom System". Journal of Proteomics 72 (2): 127–136. doi:10.1016/j.jpot.2009.01.009. PMID 19457354.
- Fry, B. et al. (July 2003). "Molecular Evolution and Phylogeny of Elapid Snake Venom Three-Finger Toxins". Journal of Molecular Evolution (PDF) 57 (1): 110–129. doi:10.1007/s00239-003-2461-2. PMID 12962311.
- Fry, B. et al. (October 2003). "Isolation of a Neurotoxin (α-colubritoxin) from a Nonvenomous Colubrid: Evidence for Early Origin of Venom in Snakes". Journal of Molecular Evolution (PDF) 57 (4): 446–452. doi:10.1007/s00239-003-2497-3. PMID 14708577.
- Fry, B. and Wüster, W. (May 2004). "Assembling an Arsenal: Origin and Evolution of the Snake Venom Proteome Inferred from Phylogenetic Analysis of Toxin Sequences". Molecular Biology and Evolution (PDF) 21 (5): 870–883. doi:10.1093/molbev/msh091. PMID 15014162.
- Venom Hunt Finds 'Harmless' Snakes A Potential Danger December 16, 2003
- Vidal, N. and Hedges, S. (October–November 2005). "The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes". Comptes Rendus Biologies (PDF) 328 (10-11): 1000–1008. doi:10.1016/j.crvi.2005.10.001. PMID 16286089.
- Weinstein, Scott A.; Smith, Tamara L.; Kardong, Kenneth V. (14 July 2009). "Reptile Venom Glands Form, Function, and Future". In Stephen P. Mackessy. Handbook of Venoms and Toxins of Reptiles. Taylor & Francis. pp. 76–84. ISBN 978-1-4200-0866-1. Retrieved 18 July 2013.
- Lizards' poisonous secret is revealed November 16, 2005
- The Surprising Origin of Venom Revealed November 17, 2005
- Which Came First, the Snake or the Venom? November 21, 2005
- Genealogy of scaly reptiles rewritten by new research November 22, 2005
- Venomdoc Homepage, Downloads
- The Venom Cure: The Power of Poison
- Nature Podcast November 17, 2005 (segment on the venom clade begins approximately 22 minutes into the program)