Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Molecular Phylogenetics and Evolution

Volumn 50, Issue 1, 2009, Pages 31-43

  Torres Carvajal, Omar ^a,b   de Queiroz, Kevin ^a  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

^b PONTIFICIA UNIVERSIDAD CATÓLICA DEL ECUADOR   (Ecuador)

Author keywords

Andes; Chronophylogenetic; Hoplocercinae; Iguanidae; Neotropical; Phylogenetics; Relative divergence times

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; GENETICS; LIZARD; NUCLEIC ACID DATABASE; PHYLOGENY; SOUTH AMERICA; TIME;

ANIMALS; DATABASES, NUCLEIC ACID; LIZARDS; PHYLOGENY; SOUTH AMERICA; TIME FACTORS;

ENYALIOIDES; HOPLOCERCINAE; HOPLOCERCUS; HOPLOCERCUS SPINOSUS; IGUANIA; IGUANIDAE; MORUNASAURUS; MORUNASAURUS ANNULARIS; SQUAMATA;

EID: 57749209369     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.10.002     Document Type: Article

References (68)

1. Aleman A., and Ramos V.A. Northern Andes. In: Cordani U.G., Milani E.J., Thomaz-Filho A., and Campos D.A. (Eds). Tectonic Evolution of South America (2000), Brazilian Academy of Science, Rio de Janeiro 453-480
2. Avila-Pires T.C.S. Lizards of Brazilian Amazonia (Reptilia: Squamata). Natl. Nat. Mus. Zool. Verh. 299 (1995) 1-706
3. Bocourt M.F. Notes sur quelques sauriens de l'Amerique tropicale. Ann. Sci. Nat. Paris 19 (1874) 1-2
4. Boulenger G.A. Description of a new species of Enyalius in the Brussels museum. Proc. Zool. Soc. Lond. 1 (1881) 246-247
5. Boulenger G.A. Description of a new species of lizard of the genus Enyalius. Proc. Zool. Soc. Lond. 1 (1883) 46
6. Boulenger G.A. Catalogue of the lizards in the British Museum (Natural History) II (1885), Taylor and Francis, London
7. Burnham K.P., and Anderson D.R. Multimodel inference. Understanding AIC and BIC in model selection. Sociol. Methods Res. 33 (2004) 261-304
8. Cantino, P.D., de Queiroz, K., 2007. PhyloCode: A Phylogenetic Code of Biological Nomenclature. Version 4b. Available from: .
9. de Queiroz K., and Gauthier J. Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names. Syst. Zool. 39 (1990) 307-322
10. de Queiroz K., and Gauthier J. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23 (1992) 449-480
11. de Queiroz K., and Gauthier J. Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9 (1994) 27-31
12. de Queiroz K., and Good D.A. Phenetic clustering in biology: a critique. Q. Rev. Biol. 72 (1997) 3-30
13. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
14. Drummond A.J., Ho S.Y.W., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLOS Biol. 4 (2006) 699-710
15. Duellman W.E. Descriptions of new lizards from the upper Amazon basin. Herpetologica 29 (1973) 228-231
16. Dunn E.R. Amphibians and reptiles from El Valle de Anton, Panama. Occas. Pap. Boston Soc. Nat. Hist. 8 (1933) 65-79
17. Estes R., and Price L.I. Iguanid lizard from the Upper Cretaceous of Brazil. Science 180 (1973) 748-751
18. Etheridge R. A review of the iguanid lizard genus Enyalius. Bull. Brit. Mus. Nat. Hist. (Zool.) 18 (1969) 231-260
19. Etheridge R., and de Queiroz K. A phylogeny of Iguanidae. In: Estes R., and Pregill G. (Eds). Phylogenetic Relationships of the Lizard Families (1988), Stanford University Press, Stanford 283-367
20. Fitzinger L.I. Systema Reptilium, Fasciculus Primus, Amblyglossae (1843), Baumüller und Seidel, Wien
21. Frost D.R., and Etheridge R. A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata). Misc. Pub. Univ. Kans. Nat. Hist. Mus. 81 (1989) 1-65
22. Gelman A., and Rubin D.B. Inference from iterative simulation using multiple sequences. Stat. Sci. 7 (1992) 457-511
23. Gregory-Wodzicki K.M. Uplift history of the central and northern Andes: a review. Geol. Soc. Am. Bull. 112 (2000) 1091-1105
24. Guichenot, A., 1855. Reptiles. In: de Castelnau F. (Ed.), Animaux nouveaux ou rares recueillis pendant l'expédition dans les parties centrales de l'Amérique du Sud, de Rio de Janeiro a Lima, et de Lima au Para; exécutée par ordre du gouvernement français pendant les années 1843 a 1847, sous la direction du Comte Francis de Castelnau. Chez P. Bertrand, Libraire-Éditeur, Paris, pp. 1-95.
25. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
26. Huelsenbeck J.P., Larget B., and Alfaro M.E. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21 (2004) 1123-1133
27. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
28. Köhler G., Seipp R., Moya S., and Almendáriz A. Zur Kenntnis von Morunasaurus annularis (O'Shaughnessy, 1881). Salamandra 35 (1999) 181-190
29. Köhler G. A new species of Morunasaurus from Peru (Reptilia, Squamata, Hoplocercidae). Senckenb. Biol. 82 (2003) 235-241
30. Kumazawa Y., and Nishida M. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37 (1993) 380-398
31. Leaché A.D., and McGuire J.A. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree. Mol. Phylogenet. Evol. 39 (2006) 628-644
32. Leviton A.E., Gibbs R.H., Heal E., and Dawson C.E. Standards in herpetology and ichthyology: part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985 (1985) 802-832
33. Macey J.R., Larson A., Ananjeva N.B., and Papenfuss T.J. Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards. J. Mol. Evol. 44 (1997) 660-674
34. Macey J.R., Larson A., Ananjeva N.B., Fang Z., and Papenfuss T.J. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14 (1997) 91-104
35. Macey J.R., Schulte II J.A., Ananjeva N.B., Larson A., Rastegar-Pouyani N., Shammakov S.M., and Papenfuss T.J. Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau. Mol. Phylogenet. Evol. 10 (1998) 118-131
36. Macey J.R., Schulte II J.A., Larson A., Tuniyev B.S., Orlov N., and Papenfuss T.J. Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families. Mol. Phylogenet. Evol. 12 (1999) 250-272
37. Macey J.R., and Verma A. Re: homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Mol. Phylogenet. Evol. 7 (1997) 272-279
38. Maddison, D.R., Maddison, W.P., 2001. MacClade: Analysis of Phylogeny and Character Evolution. Version 4.03. Sinauer Associates, Sunderland.
39. Noonan B.P., and Chippindale P.T. Vicariant origin of Malagasy reptiles supports late cretaceous Antarctic land bridge. Am. Nat. 168 (2006) 730-741
40. O'Shaughnessy A.W.E. An account of the collection of lizards made by Mr. Buckley in Ecuador, and now in the British Museum, with descriptions of the new species. Proc. Zool. Soc. Lond. 1881 (1881) 227-245
41. Pagel M., and Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53 (2004) 571-581
42. Pagel M., and Meade A. Mixture models in phylogenetic inference. In: Gascuel O. (Ed). Mathematics of Evolution and Phylogeny (2005), Clarendon Press, Oxford 1-22
43. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
44. Raftery A.E. Hypothesis testing and model selection. In: Gilks W.R., Richardson S., and Spiegelhalter D.J. (Eds). Markov Chain Monte Carlo in Practice (1996), Chapman and Hall, London 163-187
45. Rambaut, A., Drummond, A.J., 2007. Tracer. Version 1.4. Available from: .
46. Ripplinger J., and Sullivan J. Does choice in model selection affect maximum likelihood analysis?. Syst. Biol. 57 (2008) 76-85
47. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
48. Schulte J.A., and de Queiroz K. Phylogenetic relationships and heterogeneous evolutionary processes among phrynosomatine sand lizards (Squamata, Iguanidae) revisited. Mol. Phylogenet. Evol. 47 (2008) 700-716
49. Schulte II J.A., Macey J.R., Larson A., and Papenfuss T.J. Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae. Mol. Phylogenet. Evol. 10 (1998) 367-376
50. Schulte II J.A., Macey J.R., Espinoza R.E., and Larson A. Phylogenetic relationships in the iguanid lizard genus Liolaemus: multiple origins of viviparous reproduction and evidence for recurring Andean vicariance and dispersal. Biol. J. Linn. Soc. 69 (2000) 75-102
51. Schulte II J.A., Valladares J.P., and Larson A. Phylogenetic relationships within Iguanidae inferred using molecular and morphological data and a phylogenetic taxonomy of iguanian lizards. Herpetologica 59 (2003) 399-419
52. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
53. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
54. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
55. Simpson B.B. Quaternary biogeography of the high montane regions of South America. In: Duellman W.E. (Ed). The South American Herpetofauna: Its Origin, Evolution and Dispersal (1979), University of Kansas Natural History Museum, Lawrence 157-188
56. Smith H.M., Sinelnik G., Fawcett J.D., and Jones R.E. A survey of the chronology of ovulation in anoline lizard genera. Trans. Kans. Acad. Sci. 75 (1973) 107-120
57. Sullivan J., Abdo Z., Joyce P., and Swofford D.L. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol. Biol. Evol. 22 (2005) 1386-1392
58. Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony* (and other methods). Version 4.0. Sinauer Associates, Sunderland.
59. Swofford D.L., Olsen G.J., Waddell P.J., and Hillis D.M. Phylogenetic inference. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics. second ed. (1996), Sinauer Associates, Sunderland 407-543
60. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
61. Torres-Carvajal O., Schulte II J.A., and Cadle J.E. Phylogenetic relationships of South American lizards of the genus Stenocercus (Squamata: Iguania): a new approach using a general mixture model for gene sequence data. Mol. Phylogenet. Evol. 39 (2006) 171-185
62. Torres-Carvajal O., Almendáriz A., Valencia J., Yánez-Muñoz M., and Reyes J.P. A new species of Enyalioides (Iguanidae: Hoplocercinae). Pap. Avul. Zool. 48 (2008) 227-235
63. Townsend T., Larson A., Louis E., and Macey J.R. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 53 (2004) 735-757
64. Van der Hammen T., Werner J.H., and Van Dommelen H. Palynological record of the upheaval of the northern Andes: a study of the Pliocene and lower quaternary of the Colombian eastern Cordillera and the early evolution of its high-Andean biota. Rev. Palaeobot. Palynol. 16 (1973) 1-122
65. Vitt L.J., and de la Torre S. Guía para la investigación de las lagartijas de Cuyabeno. A research guide to the lizards of Cuyabeno. Museo de Zoología (QCAZ), Centro de Biodiversidad y Ambiente, Pontificia Universidad Católica del Ecuador. Monografía 1 (1996) 1-165
66. Weisrock D.W., Macey J.R., Ugurtas I.H., Larson A., and Papenfuss T.J. Molecular phylogenetics and historical biogeography among salamandrids of the "true" salamander clade: rapid branching of numerous highly divergent lineages in Mertensiella luschani associated with the rise of Anatolia. Mol. Phylogenet. Evol. 18 (2001) 434-448
67. Wiens J.J., and Etheridge R.E. Phylogenetic relationships of hoplocercid lizards: coding and combining meristic, morphometric, and polymorphic data using step matrices. Herpetologica 59 (2003) 375-398
68. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum likelihood Criterion. Ph.D. Dissertation. The University of Texas at Austin.