Abstract—The results of recent phylogenetic studies of the main groups of squamate reptiles are summarized. The contributions of various methodological approaches to modern patterns in the analysis of these vertebrates, including the positions of different groups on the phylogenetic tree of reptiles, are considered. Modern patterns in the integrated analysis of the structure of phylogenetic and taxonomic diversity and ecogeographical patterns in its formation are discussed.
Similar content being viewed by others
REFERENCES
Albert, E.M., Sanmauro, D., Garcia-Paris, M., et al., Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data, Gene, 2009, vol. 441, nos. 1–2, pp. 12–21.
Ananjeva, N.B., Phylogeny and biogeography of agamid lizards (Agamidae, Lacertilia, Reptilia): review of modern concepts and results of molecular and morphological studies, Usp. Sovrem. Biol., 2004, vol. 124, no. 1, pp. 44–56.
Ananjeva, N.B., Taxonomic diversity and phylogenetic relations of Palearctic agamids (Agaminae, Agamidae, Sauria), Usp. Sovrem. Biol., 2011, vol. 131, no. 6, pp. 578–586.
Ananjeva, N.B., Modern phylogeny of iguanomorphic lizards (Sauria, Reptilia), Pr. Ukr. Gerpetol. Tov., 2013, no. 3, pp. 3–12.
Ananjeva, N.B. and Orlov, N.L., Agamid lizards (Agamidae, Acrodonta, Sauria) of Vietnam. 1. Annotated list, Zool. Zh., 2008a, vol. 87, no. 3, pp. 306–318.
Ananjeva, N.B. and Orlov, N.L., Agamid lizards (Agamidae, Acrodonta, Sauria) of Vietnam. 2. Key identification tables. Distribution analysis in the Southeastern Asia, Zool. Zh., 2008b, vol. 87, no. 4, pp. 436–445.
Ananjeva, N.B. and Orlov, N.L., Egg teeth of Squamata reptiles and their phylogenetic significance, Zool. Zh., 2012, vol. 91, no. 11, pp. 1351–1357.
Ananjeva, N.B., Guo, X., and Wang, Y., Taxonomic diversity of agamid lizards (Reptilia, Sauria, Acrodonta, Agamidae) from China: a comparative analysis, Asiat. Herpetol. Res., 2011, vol. 2, no. 3, pp. 117–128.
Bansal, R. and Karanth, P., Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos, Mol. Phylogenet. Evol., 2010, vol. 57, pp. 459–465.
Barabanov, A.V. and Litvinchuk, S.N., A new record of the Kurdistan newt (Neurergus derjugini) in Iran and potential distribution modeling for the species, Russ. J. Herpetol., 2015, vol. 22, no. 2, pp. 107–115.
Bars-Closel, M., Kohlsdorf, T., Moen, D.S., and Wiens, J.J., Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes), Evolution, 2017, vol. 71, no. 9, pp. 2243–2261.
Camp, C.L. Classification of the lizards, Bull. Am. Mus. Nat. Hist., 1923, vol. 48, no. 11, pp. 289–481.
Castoe, T.A., De Koning, A.P.J., Kim, H.-M., et al., Evidence for an ancient adaptive episode of convergent molecular evolution, Proc. Natl. Acad. Sci. U.S.A., 2009, vol. 106, pp. 8986–8991.
Chiari, Y., Cahais, V., Galtier, N., and Delsuc, F., Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria), BMC Biol., 2012, vol. 10, p. 65.
Cornetti, L., Ficetola, G.F., Hoban, S., and Vernesi, C., Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages, Heredity, 2015, vol. 115, no. 6, pp. 517–526.
De Queiroz, K. and Gauthier, J., Phylogenetic taxonomy, Ann. Rev. Ecol. Syst., 1992, vol. 23, pp. 449–480.
De Queiroz, K. and Gauthier, J., Toward a phylogenetic system of biological nomenclature, Trends Ecol. Evol., 1994, vol. 9, pp. 27–31.
Douglas, M.E., Douglas, M.R., Schuett, G.W., et al., Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach, Mol. Phylogenet. Evol., 2010, vol. 55, pp. 153–167.
Dujsevayeva, T.N., Ananjeva, N.B., and Miroshnichenko, L.V., Studies on spezialized epidermal derivatives in iguanian lizards. I. Gross morphology, topography and histology of callose scales in the Asian rock Agama, Laudakia himalayana (Steindachner, 1869) (Squamata: Agamidae), Amphib.-Reptilia, 2007, vol. 28, no. 4, pp. 537–546.
Dunn, C.W., Hejnol, A., Matus, D.Q., et al., Broad phylogenomic sampling improves resolution of the animal tree of life, Nature, 2008, vol. 452, pp. 745–749.
Edwards, S.V., Is a new and general theory of molecular systematics emerging? Evolution. 2009a, vol. 63, pp. 1–19.
Edwards, S.V., Natural selection and phylogenetic analysis, Proc. Natl. Acad. Sci. U.S.A., 2009b, vol. 106, pp. 8799–8800.
Estes, R., Gauthier, J., and De Queiroz, K., Phylogenetic relationships within Squamata, in Phylogenetic Relationships of the Lizard Families, Estes, R. and Pregill, G., Eds., Stanford: Stanford Univ. Press, 1988, pp. 119–281.
Ficetola, G.F. and Stöck, M., Do hybrid-origin polyploidy amphibians occupy transgressive or intermediate ecological niches compared to their diploid ancestors? J. Biogeogr., 2016, vol. 43, pp. 703–715.
Ficetola, G.F., Mazel, F., and Thuiller, W., Global determnants of zoogeographical boundaries, Nat. Ecol. Evol., 2017, vol. 1, art. ID. 0089, pp. 1–7.
Frost, D. and Etheridge, R., A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata), Misc. Publ.-Univ. Kans. Mus. Nat. Hist., 1989, vol. 81, pp. 1–65.
Fry, B.G., Vidal, N., Norman, J.A., et al., Early evolution of the venom system in lizards and snakes, Nature, 2006, vol. 439, pp. 584–588.
Gauthier, J.A., Kearney, M., Maisano, J.A., et al., Assembling the squamate tree of life: perspectives from the phenotype and the fossil record, Bull. Peabody Mus. Nat. Hist., 2012, vol. 53, no. 1, pp. 3–308.
Greer, A.E., Facial tongue-wiping in xantusiid lizards: its systematic implications, J. Herpetol., 1985, vol. 19, pp. 174–175.
Grismer, L.L. and Grismer, J.L., A re-evaluation of the phylogenetic relationships of the Cyrtodactylus condorensis group (Squamata; Gekkonidae) and a suggested protocol for the characterization of rock-dwelling ecomorphology in Cyrtodactylus, Zootaxa, 2017, vol. 4300, no. 4, pp. 486–504.
Grismer, L.L., Wood, P.L., Jr., Thura, M.K., et al., Twelve new species of Cyrtodactylus Gray (Squamata: Gekkonidae) from isolated limestone habitats in east-central and southern Myanmar demonstrate high localized diversity and unprecedented microendemism, Zool. J. Linn. Soc., 2017, vol. 182, pp. 862–959.
Harrington, S.M., Leavitt, D.H., and Reeder, T.W., Squamate phylogenetics, molecular branch lengths, and molecular apomorphies: a response to McMahan et al., Copeia, 2016, vol. 104, pp. 702–707.
Hedges, S.B. and Poling, L.L., A molecular phylogeny of reptiles, Science, 1999, vol. 283, no. 5404, pp. 998–1001.
Jarvis, E.D., Mirarab, S., Aberer, J., et al., Whole-genome analyses resolves early branches in the tree of life of modern birds, Science, 2014, vol. 346, pp. 1320–1331.
Jombart, T., Pavoine, S., Devillard, S., and Pontier, D., Putting phylogeny into the analysis of biological traits: a methodological approach, J. Theor. Biol., 2010, vol. 264, pp. 693–701.
Kocot, K.M., Cannon, J.T., Todt, C., et al., Phylogenomics reveals deep molluscan relationships, Nature, 2011, vol. 477, pp. 452–456.
Kumazawa, Y., Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations, Gene, 2007, vol. 388, pp. 19–26.
Lee, M.S.Y., Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes, Zool. Scr., 2000, vol. 29, pp. 101–130.
Losos, J.B., Hillis, D.M., and Greene, H.W., Who speaks with a forked tongue? Science, 2012, vol. 338, pp. 1428–1429.
Macey, J., Schulte, J.A., Larson, A., et al., Evaluating trans-tethis migration: an example using Acrodont lizard, Syst. Biol., 2000, vol. 49, pp. 233–256.
McMahan, C.D., Freeborn, L.R., Wheeler, W.C., and Crother, B.I., Forked tongues revisited: molecular apomorphies support morphological hypotheses of squamate evolution, Copeia, 2015, vol. 103, pp. 525–529.
Moody, S., Phylogenetic and historical biogeopraphic relationships of the genera in the family Agamidae (Reptilia, Lacertilia), PhD Thesis, Ann Arbor, MI: Univ. of Michigan, 1980.
Neimark, E., Iguanas against molecular phylogenetics, Elementy, 2012. http://elementy.ru/news/431954.
Pincheira-Donoso, D., Bauer, A.M., Meiri, S., et al., Global taxonomic diversity of living reptiles, PLoS One, 2013, vol. 8, no. 3, p. e59741. https://doi.org/10.1371/journal.pone.0059741
Pyron, R.A., Novel approaches for phylogenetic inference from morphological data and total-evidence dating in squamate reptiles (lizards, snakes, and amphisbaenians), Syst. Biol., 2017, vol. 66, no. 1, pp. 38–56.
Pyron, R.A., Burbrink, F.T., Colli, G.R., et al., The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees, Mol. Phylogenet. Evol., 2011, vol. 58, pp. 329–342.
Pyron, R.A., Burbrink, F.T., and Wiens, J.J., A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes, BMC Evol. Biol., 2013, vol. 13, p. 93. https://doi.org/.https://doi.org/10.1186/1471-2148-13-93.
Pyron, R.A., Hendry, C.R., Chou, V.M., et al., Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia), Mol. Phylogenet. Evol., 2014, vol. 81, pp. 221–231.
Raxworthy, C.J., Ingram, C.M., Rabibiso, N., and Pearson, R.G., Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar, Syst. Biol., 2007, vol. 56, pp. 907–923.
Reeder, T.W., Townsend, T.M., Mulcahy, D.G., et al., Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa, PLoS One, 2015, vol. 10, no. 3, p. e0118199.
Regier, J.C., Shultz, J.W., Zwick, A., et al., Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences, Nature, 2010, vol. 463, pp. 1079–1083.
Ricklefs, R.E., Losos, J.B., and Townsend, T.M., Evolutionary diversification of clades of squamate reptiles, J. Evol. Biol., 2007, vol. 20, pp. 1751–1762.
Schulte, J.A., Macey, J.R., Larson, A., and Papenfuss, T.J., Testing the monophyly of four iguanid subfamilies: a comparison of molecular and morphological data, Mol. Phylogenet. Evol., 1998, vol. 10, pp. 367–376.
Schulte, J.A., Valladares, J.P., and Larson, A., Phylogenetic relationships within Iguanidae inferred using molecular and morphological data and phylogenetic taxonomy of iguanian lizards, Herpetologica, 2003, vol. 59, no. 3, pp. 399–419.
Schwenk, K., Systematics and subjectivity: the phylogeny and classification of iguanian lizards revisited, Herpetol. Rev., 1994, vol. 25, pp. 53–57.
Sergeev, A.M., Phylogeny of some reptile embryonic adaptations. II. Phylogeny of embryonic adaptations correlatively related with hard egg shells, Izv. Akad. Nauk SSSR, Otd. Biol. Nauk, 1940, pp. 3–30.
Skawiń ski, T. and Borczyk, B., Evolution of developmental sequences in lepidosaurs, PeerJ, 2017, no. 5, p. e3262. https://doi.org/10.7717/peerj.3262
Smirina, E.M. and Ananjeva, N.B., Growth layers in different bones and acrodont teeth of the agamid lizard Laudakia stoliczkana (Blanford, 1875) (Agamidae, Sauria), Amphib.-Reptilia, 2007, vol. 28, no. 2, pp. 193–204.
Streicher, J.W. and Wiens, J.J., Phylogenomic analyses of more than 4,000 nuclear loci resolve the origin of snakes among lizard families, Biol. Lett., 2017, vol. 13, p. 20170393.
Struck, T.H., Paul, C., Hill, N., et al., Phylogenomic analyses unravel annelid evolution, Nature, 2011, vol. 471, pp. 95–98.
Sukhanov, V.B., Phylogeny and Lacertilia system (s. Sauria), Zool. Zh., 1961, vol. 40, no. 1, pp. 73–83.
The reptile database, 2018. http://www.reptile-database.org.
Townsend, T., Larson, A., Louis, E.J., and Macey, J.R., Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree, Syst. Biol., 2004, vol. 53, pp. 735–757.
Underwood, G. and Lee, M.S.Y., The egg teeth of Dibamus and their bearing on possible relationships with gekkotan lizards, Amphib.-Reptilia, 2000, vol. 21, pp. 507–511.
Vidal, N. and Hedges, S.B., The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes, C.R. Biol., 2005, vol. 328, pp. 1000–1008.
Vidal, N. and Hedges, S.B., The molecular evolutionary tree of lizards, snakes, and amphisbaenians, C.R. Biol., 2009, vol. 332, pp. 129–139.
Voronov, A.S., Shibalev, D.A., and Kupriyanova, N.S., Evolutionary relationships between reptiles inferred from the comparison of their ITS2 sequences, Russ. J. Genet., 2011, vol. 47, pp. 864–873.
Weigert, A., Helm, C., Meyer, M., et al., Illuminating the base of the annelid tree using transcriptomics, Mol. Biol. Evol., 2014, vol. 31, pp. 1391–1400.
Wiens, J.J. and Morrill, M.C., Missing data in phylogenetic analysis: reconciling results from simulations and empirical data, Syst. Biol., 2011, vol. 60, pp. 719–731.
Wiens, J.J., Kuczynski, C.A., Townsend, T., and Reeder, T.W., Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa, Syst. Biol., 2010, vol. 59, no. 6, pp. 674–688.
Wiens, J.J., Hutter, C.R., Mulcahy, D.G., et al., Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species, Biol. Lett., 2012, vol. 8, pp. 1043–1046.
Zheng, Y. and Wiens, J.J., Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species, Mol. Phylogenet. Evol., 2016, vol. 94, pp. 537–547.
ACKNOWLEDGMENTS
The work was supported by the Russian Foundation for Basic Research (grant no. 18-04-00040) and Zoological Institute, Russian Academy of Sciences, project no. АААА-А19-119020590095-9.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.
Additional information
Translated by G. Chirikova
Rights and permissions
About this article
Cite this article
Ananjeva, N.B. Current State of the Problems in the Phylogeny of Squamate Reptiles (Squamata, Reptilia). Biol Bull Rev 9, 119–128 (2019). https://doi.org/10.1134/S2079086419020026
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S2079086419020026