Phylogenetic relationships and heterogeneous evolutionary processes among phrynosomatine sand lizards (Squamata, Iguanidae) revisited

Molecular Phylogenetics and Evolution

Volumn 47, Issue 2, 2008, Pages 700-716

  Schulte II, James A ^a   de Queiroz, Kevin ^a  

^a SMITHSONIAN INSTITUTION   (United States)

Author keywords

Callisaurus; Cophosaurus; Holbrookia; Mitochondrial DNA; Mixed models; Mixture models; Phrynosomatinae; Phylogeny; Process heterogeneity; Uma

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; GENETIC VARIABILITY; GENETICS; LIZARD; MOLECULAR EVOLUTION; NONPARAMETRIC TEST; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; LIZARDS; MODELS, GENETIC; PHYLOGENY; STATISTICS, NONPARAMETRIC; VARIATION (GENETICS);

CALLISAURUS; COPHOSAURUS; HOLBROOKIA; IGUANIDAE; PHRYNOSOMATINAE; SQUAMATA;

EID: 42749094398     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.01.010     Document Type: Article

References (68)

1. Adest, G.A., 1978. The relationships of the sand lizards Uma, Callisaurus, and Holbrookia (Sauria: Iguanidae): an electrophoretic study. Unpublished Ph.D. dissertation, University of California, Los Angeles.
2. Alfaro M.E., Zoller S., and Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20 (2003) 255-266
3. Anderson S., Bankier A.T., Barrell B.G., De Bruijn M.H.L., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., Schreier P.H., Smith A.J.H., Staden R., and Young I.G. Sequence and organization of the human mitochondrial genome. Nature 290 (1981) 457-465
4. Axtell, R.W., 1958. A monographic revision of the iguanid genus Holbrookia. Ph.D. dissertation, University of Texas, Austin.
5. Brandley M.C., Schmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54 (2005) 373-390
6. Castoe T.A., Doan T.M., and Parkinson C.L. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Syst. Biol. 53 (2004) 448-469
7. Castoe T.A., Sasa M.M., and Parkinson C.L. Modeling nucleotide evolution at the mesoscale: the phylogeny of the Neotropical pitvipers of the Porthidium group (Viperidae: Crotalinae). Mol. Phylogenet. Evol. 37 (2005) 881-898
8. Castoe T.A., and Parkinson C.L. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Mol. Phylogenet. Evol. 39 (2006) 91-110
9. ChangChien, L.-L., 1996. A phylogenetic study of sceloporine lizards and their relationships with other iguanid lizards based on DNA/DNA hybridization. Ph.D. dissertation, University of Wisconsin, Madison.
10. Clarke R.F. An ethological study of the iguanid lizard genera Callisaurus, Cophosaurus, and Holbrookia. Emporia St. Res. Stud. 13 (1965) 1-66
11. Cox D.C., and Tanner W.W. Osteology and myology of the head and neck regions of Callisaurus, Cophosaurus, Holbrookia, and Uma (Reptilia: Iguanidae). Great Basin Nat. 37 (1977) 35-56
12. Crother, B.I., 2000. Scientific and standard English names of amphibians and reptiles of North America north of Mexico, with comments regarding confidence in our understanding. Herpetolog. Circ. 29, Society for the Study of Amphibians and Reptiles.
13. Crother B.I. Scientific and standard English names of amphibians and reptiles of North America north of Mexico: update. Herpetol. Rev. 34 (2003) 196-203
14. de Queiroz, K., 1989. Morphological and biochemical evolution in the sand lizards. Ph.D. dissertation, University of California, Berkeley.
15. de Queiroz K. Phylogenetic relationship and rates of allozyme evolution among the lineages of sceloporine sand lizards. Biol. J. Linn. Soc. 45 (1992) 333-362
16. Douady C.J., Delsuc F., Boucher Y., Doolittle W.F., and Douzery E.J.P. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20 (2003) 248-254
17. Earle A.M. The middle ear of Holbrookia and Callisaurus. Copeia 1961 (1961) 405-410
18. Earle A.M. The middle ear of the genus Uma compared to those of the other sand lizards. Copeia 1962 (1962) 185-188
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 Univ. Press, Stanford, California 283-367
20. Felsenstein J. Confidence limits on phylogenies an approach using the bootstrap. Evolution 39 (1985) 783-791
21. Felsenstein J. Confidence limits on phylogenies with a molecular clock. Syst. Zool. 34 (1985) 152-161
22. Felsenstein J., and Kishino H. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42 (1993) 193-200
23. Fu, J., 1999. Phylogeny of Lacertid Lizards (Squamata: Lacertidae) and the Evolution of Unisexuality, Ph.D. dissertation. University of Toronto, Toronto.
24. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652-670
25. Huelsenbeck J.P., and Nielsen R. The effect of non-independent substitution on phylogenetic accuracy. Syst. Biol. 48 (1999) 317-328
26. Huelsenbeck J.P., Larget B., Miller R.E., and Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51 (2002) 673-688
27. 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
28. Jeffreys H. Some tests of significance, treated by the theory of probability. Proc. Camb. Phil. Soc. 31 (1935) 203-222
29. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
30. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Paabo S., Villablanca F.X., and Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86 (1989) 6196-6200
31. Kumazawa Y., and Nishida M. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37 (1993) 380-398
32. Kumazawa Y., Ota H., Nishida M., and Ozawa T. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150 (1998) 313-329
33. 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
34. Lewis P.O., Holder M.T., and Holsinger K.E. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54 (2005) 241-253
35. Macey J.R., and Verma A. Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Mol. Phylogenet. Evol. 7 (1997) 272-279
36. 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
37. Macey J.R., Schulte II J.A., Larson A., Fang Z., Wang Y., Tuniyev B.S., and Papenfuss T.J. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: a case of vicariance and dispersal. Mol. Phylogenet. Evol. 9 (1998) 80-87
38. 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
39. Maddison, D.R., Maddison, W.P., 2003. MacClade: Analysis of Phylogeny and Character Evolution. Version 4.08. Sinauer Associates, Sunderland, MA.
40. Mittleman M.B. A summary of the iguanid genus Urosaurus. Bull. Mus. Comp. Zool. Harvard Univ. 91 (1942) 106-176
41. Naylor G.J.P., Collins T.M., and Wesley M.B. Hydrophobicity and phylogeny. Nature 373 (1995) 565-566
42. Norris K.S. The evolution and systematics of the iguanid genus Uma and its relation to the evolution of other North American desert reptiles. Bull. Am. Mus. Nat. Hist. 114 (1958) 253-326
43. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
44. 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
45. Pagel M., and Meade A. Mixture models in phylogenetic inference. In: Gascuel O. (Ed). Mathematics of Evolution and Phylogeny (2005), Clarendon Press, Oxford 121-142
46. Pagel M., and Meade A. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. Am. Nat. 167 (2006) 808-825
47. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
48. 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 & Hall, London 163-187
49. Rambaut, A., Drummond, A.J., 2005. Tracer. Version 1.3, Available from: http://tree.bio.ed.ac.uk/software/tracer/.
50. Reeder T.W., and Wiens J.J. Evolution of the lizard family Phrynosomatidae as inferred from diverse types of data. Herpetol. Monogr. 10 (1996) 43-84
51. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
52. Savolainen V., Chase M.W., Salamin N., Soltis D.E., Soltis P.S., López A.J., Fédrigo O., and Naylor G.J.P. Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion. Syst. Biol. 51 (2002) 638-647
53. Savage J.M. The iguanid lizard genera Urosaurus and Uta, with remarks on related groups. Zoologica 43 (1958) 41-54
54. 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
55. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
56. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
57. Shimodaira H., and Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
58. Smith H.M. Handbook of lizards (1946), Comstock, Ithaca, NY
59. Strugnell J., Norman M., Jackson J., Drummond A.J., and Cooper A. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol. Phylogenet. Evol. 37 (2005) 426-441
60. 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
61. * (and other methods). Version 4.0. Sinauer Associates, Sunderland, MA.
62. 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. 2nd ed. (1996), Sinauer Associates, Sunderland, MA 407-543
63. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lec. Math. Life Sci. 17 (1986) 57-86
64. Templeton A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37 (1983) 221-244
65. 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
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. Wilgenbusch J., and de Queiroz K. Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Syst. Biol. 49 (2000) 592-612
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.