Skip to main content
Log in

Current State of the Problems in the Phylogeny of Squamate Reptiles (Squamata, Reptilia)

  • Published:
Biology Bulletin Reviews Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1.
Fig. 2.

Similar content being viewed by others

REFERENCES

  1. 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.

  2. 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.

    Google Scholar 

  3. 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.

    Google Scholar 

  4. Ananjeva, N.B., Modern phylogeny of iguanomorphic lizards (Sauria, Reptilia), Pr. Ukr. Gerpetol. Tov., 2013, no. 3, pp. 3–12.

  5. 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.

    Google Scholar 

  6. 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.

    Google Scholar 

  7. 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.

    Google Scholar 

  8. 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.

    Article  Google Scholar 

  9. 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.

    Article  PubMed  Google Scholar 

  10. 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.

    Google Scholar 

  11. 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.

    Article  PubMed  Google Scholar 

  12. Camp, C.L. Classification of the lizards, Bull. Am. Mus. Nat. Hist., 1923, vol. 48, no. 11, pp. 289–481.

    Google Scholar 

  13. 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.

    Article  PubMed  PubMed Central  Google Scholar 

  14. 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.

    Article  PubMed  PubMed Central  Google Scholar 

  15. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. De Queiroz, K. and Gauthier, J., Phylogenetic taxonomy, Ann. Rev. Ecol. Syst., 1992, vol. 23, pp. 449–480.

    Article  Google Scholar 

  17. De Queiroz, K. and Gauthier, J., Toward a phylogenetic system of biological nomenclature, Trends Ecol. Evol., 1994, vol. 9, pp. 27–31.

    Article  CAS  PubMed  Google Scholar 

  18. 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.

    Article  PubMed  Google Scholar 

  19. 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.

    Article  Google Scholar 

  20. 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.

    Article  CAS  PubMed  Google Scholar 

  21. Edwards, S.V., Is a new and general theory of molecular systematics emerging? Evolution. 2009a, vol. 63, pp. 1–19.

    Article  CAS  PubMed  Google Scholar 

  22. Edwards, S.V., Natural selection and phylogenetic analysis, Proc. Natl. Acad. Sci. U.S.A., 2009b, vol. 106, pp. 8799–8800.

    Article  PubMed  PubMed Central  Google Scholar 

  23. 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.

    Google Scholar 

  24. 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.

    Article  Google Scholar 

  25. 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.

  26. 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.

    Google Scholar 

  27. 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.

    Article  CAS  PubMed  Google Scholar 

  28. 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.

    Article  Google Scholar 

  29. Greer, A.E., Facial tongue-wiping in xantusiid lizards: its systematic implications, J. Herpetol., 1985, vol. 19, pp. 174–175.

    Article  Google Scholar 

  30. 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.

    Article  Google Scholar 

  31. 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.

    Article  Google Scholar 

  32. 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.

    Article  Google Scholar 

  33. Hedges, S.B. and Poling, L.L., A molecular phylogeny of reptiles, Science, 1999, vol. 283, no. 5404, pp. 998–1001.

    Article  CAS  PubMed  Google Scholar 

  34. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 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.

    Article  PubMed  Google Scholar 

  36. Kocot, K.M., Cannon, J.T., Todt, C., et al., Phylogenomics reveals deep molluscan relationships, Nature, 2011, vol. 477, pp. 452–456.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kumazawa, Y., Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations, Gene, 2007, vol. 388, pp. 19–26.

    Article  CAS  PubMed  Google Scholar 

  38. Lee, M.S.Y., Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes, Zool. Scr., 2000, vol. 29, pp. 101–130.

    Article  Google Scholar 

  39. Losos, J.B., Hillis, D.M., and Greene, H.W., Who speaks with a forked tongue? Science, 2012, vol. 338, pp. 1428–1429.

    Article  CAS  PubMed  Google Scholar 

  40. 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.

    Article  CAS  PubMed  Google Scholar 

  41. 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.

    Article  Google Scholar 

  42. 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.

  43. Neimark, E., Iguanas against molecular phylogenetics, Elementy, 2012. http://elementy.ru/news/431954.

  44. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. 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.

    PubMed  Google Scholar 

  46. 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.

    Article  PubMed  Google Scholar 

  47. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. 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.

    Article  PubMed  Google Scholar 

  49. 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.

    Article  PubMed  Google Scholar 

  50. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. 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.

    Article  CAS  PubMed  Google Scholar 

  52. 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.

    Article  CAS  PubMed  Google Scholar 

  53. 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.

    Article  CAS  PubMed  Google Scholar 

  54. 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.

    Article  Google Scholar 

  55. Schwenk, K., Systematics and subjectivity: the phylogeny and classification of iguanian lizards revisited, Herpetol. Rev., 1994, vol. 25, pp. 53–57.

    Google Scholar 

  56. 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.

    Google Scholar 

  57. 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

  58. 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.

    Article  Google Scholar 

  59. 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.

    Article  PubMed  PubMed Central  Google Scholar 

  60. Struck, T.H., Paul, C., Hill, N., et al., Phylogenomic analyses unravel annelid evolution, Nature, 2011, vol. 471, pp. 95–98.

    Article  CAS  PubMed  Google Scholar 

  61. Sukhanov, V.B., Phylogeny and Lacertilia system (s. Sauria), Zool. Zh., 1961, vol. 40, no. 1, pp. 73–83.

    Google Scholar 

  62. The reptile database, 2018. http://www.reptile-database.org.

  63. 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.

    Article  PubMed  Google Scholar 

  64. 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.

    Google Scholar 

  65. 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.

    Article  CAS  PubMed  Google Scholar 

  66. Vidal, N. and Hedges, S.B., The molecular evolutionary tree of lizards, snakes, and amphisbaenians, C.R. Biol., 2009, vol. 332, pp. 129–139.

    Article  CAS  PubMed  Google Scholar 

  67. 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.

    Article  CAS  Google Scholar 

  68. 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.

    Article  CAS  PubMed  Google Scholar 

  69. 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.

    Article  PubMed  Google Scholar 

  70. 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.

    Article  CAS  PubMed  Google Scholar 

  71. 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.

    Article  PubMed  PubMed Central  Google Scholar 

  72. 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.

    Article  PubMed  Google Scholar 

Download references

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

Authors

Corresponding author

Correspondence to N. B. Ananjeva.

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

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

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

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S2079086419020026

Navigation