Template:Phylogeny/Squamata/doc

This template contains a phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species in the combined phylogenomic and supermatrix analysis by Zheng & Wiens (2016))^[1].

This is a documentation subpage for Template:Phylogeny/Squamata. It may contain usage information, categories and other content that is not part of the original template page.

The template optionally uses {{clade transclude}} as a wrapper that allows partial transclusion of parts of the phylogenetic tree selected by |label= or |subtree=.

Full phylogenetic tree

{{Phylogeny/Squamata}}

Squamata

Dibamia Dibamidae (dibamids)   Bifurcata Gekkota ⊞ (gekkos) ⊟ Pygopodomorpha Diplodactylidae Underwood 1954 Pygopodidae Boulenger 1884 Carphodactylidae Gekkomorpha Eublepharidae Gekkonoidea Sphaerodactylidae Underwood 1954 Phyllodactylidae Gekkonidae   Unidentata Scinciformata ⊞ (skinks and relatives) Scincomorpha Scincidae Cordylomorpha Xantusiidae Gerrhosauridae Cordylidae ⊟   Episquamata Laterata ⊞ (true lizards and amphisbaenians) Teiformata Gymnophthalmidae Merrem 1820 Teiidae Gray 1827 Lacertibaenia Lacertiformata Lacertidae Amphisbaenia ⊞ (amphisbaenians) Rhineuridae Vanzolini 1951 Bipedidae Taylor 1951 Blanidae Kearney & Stuart 2004 Cadeidae Vidal & Hedges 2008 Trogonophiidae Gray 1865 Amphisbaenidae Gray 1865 ⊟ ⊟ (=Lacertoidea)   Toxicofera Anguimorpha ⊞ (anguids) Palaeoanguimorpha Shinisauria Shinisauridae Ahl 1930 sensu Conrad 2006 Varanoidea Lanthanotidae Varanidae Neoanguimorpha Helodermatoidea Helodermatidae Gray 1837 Xenosauroidea Xenosauridae Anguioidea Diploglossidae Anniellidae Anguidae Gray 1825 ⊟   Iguania ⊞ (iguanias) Acrodonta Chamaeleonidae Agamidae Gray 1827 Pleurodonta Leiocephalidae Iguanidae Hoplocercidae Frost & Etheridge 1989 Crotaphytidae Corytophanidae Tropiduridae Phrynosomatidae Dactyloidae Polychrotidae Liolaemidae Leiosauridae Opluridae ⊟   Serpentes ⊞ (snakes) Scolecophidia Leptotyphlopidae Stejneger 1892 Gerrhopilidae Vidal et al. 2010 Xenotyphlopidae Vidal et al. 2010 Typhlopidae Merrem 1820 Anomalepididae Alethinophidia Amerophidia Aniliidae Tropidophiidae Brongersma 1951 Afrophidia Booidea Uropeltidae Anomochilidae Cylindrophiidae Xenopeltidae Bonaparte 1845 Loxocemidae Pythonidae Fitzinger 1826 Calabariidae Boidae Xenophidiidae Bolyeriidae Hoffstetter 1946 Caenophidia Acrochordidae Bonaparte 1831 Xenodermidae Colubroidea Pareidae Viperidae Proteroglypha Homalopsidae Colubridae Lamprophiidae Elapidae ⊟

Partial transclusion of groups

A simple example:

{{Phylogeny/Squamata|label=Toxicofera|wrap=}}

Toxicofera

Anguimorpha ⊞ (anguids) Palaeoanguimorpha Shinisauria Shinisauridae Ahl 1930 sensu Conrad 2006 Varanoidea Lanthanotidae Varanidae Neoanguimorpha Helodermatoidea Helodermatidae Gray 1837 Xenosauroidea Xenosauridae Anguioidea Diploglossidae Anniellidae Anguidae Gray 1825 ⊟   Iguania ⊞ (iguanias) Acrodonta Chamaeleonidae Agamidae Gray 1827 Pleurodonta Leiocephalidae Iguanidae Hoplocercidae Frost & Etheridge 1989 Crotaphytidae Corytophanidae Tropiduridae Phrynosomatidae Dactyloidae Polychrotidae Liolaemidae Leiosauridae Opluridae ⊟   Serpentes ⊞ (snakes) Scolecophidia Leptotyphlopidae Stejneger 1892 Gerrhopilidae Vidal et al. 2010 Xenotyphlopidae Vidal et al. 2010 Typhlopidae Merrem 1820 Anomalepididae Alethinophidia Amerophidia Aniliidae Tropidophiidae Brongersma 1951 Afrophidia Booidea Uropeltidae Anomochilidae Cylindrophiidae Xenopeltidae Bonaparte 1845 Loxocemidae Pythonidae Fitzinger 1826 Calabariidae Boidae Xenophidiidae Bolyeriidae Hoffstetter 1946 Caenophidia Acrochordidae Bonaparte 1831 Xenodermidae Colubroidea Pareidae Viperidae Proteroglypha Homalopsidae Colubridae Lamprophiidae Elapidae ⊟

Note that the above has three hidden clades that can be expanded and collapsed. The interactive elements can be eliminated with the parameter |nohidden=, as shown in the following example:

{{Phylogeny/Squamata|label=Gekkota|wrap=|nohidden=}}

Gekkota	Pygopodomorpha Diplodactylidae Underwood 1954 Pygopodidae Boulenger 1884 Carphodactylidae Gekkomorpha Eublepharidae Gekkonoidea Sphaerodactylidae Underwood 1954 Phyllodactylidae Gekkonidae

The above examples used parameter |wrap= to add an outer clade and label, which defaults to the name of the label or subtree selected. Omitting |wrap= allows a custom cladogram to be build around the selection from the template. .

{{clade |style=background-color:#eeeeff;
|label1=[[Laterata]]
|1={{Phylogeny/Squamata|label=LATERATA|nohidden=}}
}}

Laterata	Teiformata Gymnophthalmidae Merrem 1820 Teiidae Gray 1827 Lacertibaenia Lacertiformata Lacertidae Amphisbaenia Rhineuridae Vanzolini 1951 Bipedidae Taylor 1951 Blanidae Kearney & Stuart 2004 Cadeidae Vidal & Hedges 2008 Trogonophiidae Gray 1865 Amphisbaenidae Gray 1865

References

Some useful references:

• Zheng & Wiens (2016))^[1]
• Pyron et al (2013)^[2]
• Vidal & Hedges (2009)^[3]
• Reptile Database: Higher Taxa in Extant Reptiles^[4]
• Reeder et al (2015).^[5]
• Hedges 2014 (skinks)^[6]
• Fry al al (2006) (evolution of venom) ^[7]
• Snakes
  • Figueroa et al (2016) ^[8]
  • Reynolds et al (2014) (boas and pythons)^[9]
  • Zaher et al (2019) (advanced caenophidian snakes)^[10]

1. Zheng, Yuchi; Wiens, John J. (2016). "Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species". Molecular Phylogenetics and Evolution. 94 (Pt B): 537–547. doi:10.1016/j.ympev.2015.10.009. PMID 26475614.
2. Pyron, R; Burbrink, Frank T; Wiens, John J (2013). "A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes". BMC Evolutionary Biology. 13 (1): 93. Bibcode:2013BMCEE..13...93P. doi:10.1186/1471-2148-13-93. ISSN 1471-2148. PMC 3682911. PMID 23627680.
3. Vidal, N; Hedges, SB (2009). "The molecular evolutionary tree of lizards, snakes, and amphisbaenians". Comptes Rendus Biologies. 332 (2–3): 129–39. doi:10.1016/j.crvi.2008.07.010. PMID 19281946. S2CID 23137302.
4. Uetz, P.; et al. (eds.). "Higher Taxa in Extant Reptiles". The Reptile Database. Retrieved 12 October 2019.
5. Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J. (2015). "Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa". PLOS ONE. 10 (3): e0118199. Bibcode:2015PLoSO..1018199R. doi:10.1371/journal.pone.0118199. PMC 4372529. PMID 25803280.
6. Hedges, SB (2014). "The high-level classification of skinks (Reptilia, Squamata, Scincomorpha)". Zootaxa. 3765 (4): 317–338. doi:10.11646/zootaxa.3765.4.2. PMID 24870904.
7. Fry, Brian G.; et al. (February 2006). "Early evolution of the venom system in lizards and snakes" (PDF). Nature. 439 (7076): 584–588. Bibcode:2006Natur.439..584F. doi:10.1038/nature04328. PMID 16292255. S2CID 4386245.
8. Figueroa, Alex; McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P. (2016). Parmakelis, Aristeidis (ed.). "A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus". PLOS ONE. 11 (9): e0161070. Bibcode:2016PLoSO..1161070F. doi:10.1371/journal.pone.0161070. ISSN 1932-6203. PMC 5014348. PMID 27603205.
9. R. Graham Reynolds; Matthew L. Niemiller; Liam J. Revell (2014). "Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling". Molecular Phylogenetics and Evolution. 71: 201–213. doi:10.1016/j.ympev.2013.11.011. PMID 24315866.
10. Zaher, Hussam; Murphy, Robert W.; Arredondo, Juan Camilo; Graboski, Roberta; Machado-Filho, Paulo Roberto; Mahlow, Kristin; Montingelli, Giovanna G.; Quadros, Ana Bottallo; Orlov, Nikolai L.; Wilkinson, Mark; Zhang, Ya-Ping; Grazziotin, Felipe G. (2019). Joger, Ulrich (ed.). "Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)". PLOS ONE. 14 (5): e0216148. Bibcode:2019PLoSO..1416148Z. doi:10.1371/journal.pone.0216148. ISSN 1932-6203. PMC 6512042. PMID 31075128.