Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Molecular Phylogenetics and Evolution

Volumn 61, Issue 2, 2011, Pages 400-412

  Guo, Xianguang ^a   Dai, Xin ^b   Chen, Dali ^c   Papenfuss, Theodore J ^d   Ananjeva, Natalia B ^e   Melnikov, Daniel A ^e   Wang, Yuezhao ^a  

^a CHENGDU INSTITUTE OF BIOLOGY   (China)

^b YANGZHOU UNIVERSITY   (China)

^c SICHUAN UNIVERSITY   (China)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e ZOOLOGICAL INSTITUTE   (Russian Federation)

Author keywords

16S rRNA; Eremias; Phylogeny; Relaxed molecular clock

Indexed keywords

MITOCHONDRIAL DNA; RNA 16S;

ANIMAL; ARTICLE; ASIA; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; EUROPE; GENETICS; LIZARD; MOLECULAR EVOLUTION; PHYLOGENY; RNA GENE;

ANIMALS; ASIA; BAYES THEOREM; DNA, MITOCHONDRIAL; EUROPE; EVOLUTION, MOLECULAR; GENES, RRNA; LIZARDS; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

ACANTHODACTYLUS; EREMIAS; EREMIAS ARGUS; EREMIAS BRENCHLEYI; LACERTIDAE; LATASTIA; SQUAMATA; TEIIDAE;

EID: 80052747840     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.06.022     Document Type: Article

References (85)

1. Ababneh F., Jermiin L.S., Ma C., Robinson J. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics 2006, 22:1225-1231.
2. Akaike H. A new look at the statistical model identification. IEEE Transactions on Automatic Control 1974, 19:716-723.
3. Aljanabi S.M., Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research 1997, 25:4692-4693.
4. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402.
5. An Z., Kutzbach J.E., Prell W.L., Porter S.C. Evolution of Asian monsoons and phased uplift of the Himalaya-Tibet plateau since late Miocene times. Nature 2001, 411:62-66.
6. Arnold E.N. The hemipenis of lacertid lizards (Reptilia: Lacertidae): structure, variation and systematic implications. Journal of Natural History 1986, 20:1221-1257.
7. Arnold E.N. Towards the phylogeny and biogeography of the Lacertidae: relationships within an Old-World family of lizards derived from morphology. Bulletin of the British Museum (Natural History) Zoology 1989, 55:209-257.
8. Arnold E.N. Overview of morphological evolution and radiation in the Lacertidae. The Biology of Lacertid Lizards: Evolutionary and Ecological Perspectives 2004, 11-36. Institut Menorquí d'Estudis, Recerca, 8. Maá, Menorca. V. Pérez-Mellado, N. Riera, A. Perera (Eds.).
9. Arnold E.N., Arribas O., Carranza S. Systematics of the Palaearctic and Oriental lizard tribe Lacertini (Squamata: Lacertidae: Lacertinae), with descriptions of eight new genera. Zootaxa 2007, 1430:1-86.
10. Barabnov A.V. Aspidorhinus Eichwald, 1841 as a valid subgeneric name for Eremias velox species group (Sauria, Lacertidae). Current Studies in Herpetology 2009, 9:59-61. (in Russian with English abstract).
11. Böhme, M., 2007. Herpetofauna (Anura, Squamata) and palaeoclimatic implications: preliminary results. In: Daxner-Höck, G. (Ed.), Oligocene-Miocene Vertebrates from the Valley of Lakes (Central Mongolia): Morphology, Phylogenetic and Stratigraphic Implications. Ann. Naturhist. Mus. Wien. 108A, pp. 43-52.
12. Boulenger G.A. A synopsis of the lizards of the genus Eremias. Journal of Zoological Research, 1918, 3:1-12.
13. Boulenger G.A. Monograph of the Lacertidae 1921, vol. II. Trustees of the British Museum of Natural History, London.
14. Brandley M.C., Schmitz A., Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic Biology 2005, 54:373-390.
15. Brown R.P. Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages. Journal of Molecular Evolution 2005, 60:45-56.
16. Caetano-Anollés G. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Research 2002, 30:2575-2587.
17. Carstens B.C., Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology 2007, 56:400-411.
18. Dessimoz C., Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biology 2010, 11:R37.
19. Eremchenko V. Nomenclature of Asian racerunner Eremias Wiegmann, 1834 in connection with procedure following designation monotype (Sauria: Lacertidae). Proceedings of the National Academy of Sciences of Kyrgyz Republic 1999, 1:72-73. (in Russian).
20. Eremchenko V., Panfilov A. Taxonomic situation of multiocellated racerunner of the " multiocellata" -complex of Kyrghyzstan and neighbour China (Sauria: Lacertidae: Eremias). Science and New Technologies 1999, 4:112-124. (in Russian with English abstract).
21. Felsenstein J.P. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
22. Fitzinger L. Eremias. Herpetologica Mexicana, seu Descriptio Amphibiorum Novae Hispaniae, Pars prima. Saurorum Species 1834, 9. Lüderitz, Berolini. A.F.A. Wiegmann (Ed.).
23. Fitzinger, L., 1843. Systema Reptilium. 21. Fasciculus Primus. Vienna, p. 21.
24. FitzSimons, V.M., 1943. The lizards of South Africa. Memoirs of the Transvaal Museum 1, xv+528 pp., XXIV pls., 1 folding map.
25. Fu J. Toward the phylogeny of the family Lacertidae-why 4708 base pairs of mtDNA sequences cannot draw the picture?. Biological Journal of the Linnean Society 2000, 71:203-217.
26. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics 2003, 34:397-423.
27. Gelman A., Rubin D.B. Inference from iterative simulation using multiple sequences. Statistical Science 1992, 7:457-511.
28. Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 2010, 27:221-224.
29. Guo X.-G., Wang Y.-Z. Partitioned Bayesian analyses, dispersal-vicariance analysis, and the biogeography of Chinese toad-headed lizards (Agamidae: Phrynocephalus): a re-evaluation. Molecular Phylogenetics and Evolution 2007, 45:643-662.
30. Guo X.-G., Chen D.-L., Wan H.-F., Wang Y.-Z. Review of systematics of the racerunner lizard (Lacertidae: Eremias). Sichuan Journal of Zoology 2010, 29:665-672. (in Chinese with English abstract).
31. Harris D.J., Batista V., Carretero M.A. Assessment of genetic diversity within Acanthodactylus erythrurus (Reptilia: Lacertidae) in Morocco and the Iberian Peninsula using mitochondrial DNA sequence data. Amphibia-Reptilia 2004, 25:227-232.
32. Harrison T.M., Copeland P., Kidd W.S.F., Yin A. Raising Tibet. Science 1992, 255:1663-1670.
33. Harrison T.M., Copeland P., Kidd W.S.F., Loevera O.M. Activation of the Nyainqentanghla shear zone: implications for uplift of the southern Tibetan Plateau. Tectonics 1995, 14:658-676.
34. Ho J.W.K., Adams C.E., Lew J.B., Matthews T.J., Ng C.C., Shahabi-Sirjan A., Tan L.H., Zhao Y., Easteal S., Wilson S.R., Jermiin L.S. SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides. Bioinformatics 2006, 22:2162-2163.
35. Huelsenbeck J.P., Crandall K.A. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics 1997, 28:437-466.
36. Huelsenbeck J.P., Larget B., Miller R.E., Ronquist F. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 2002, 51:673-688.
37. Jermiin L.S., Jayaswal V., Ababneh F., Robinson J. Phylogenetic model evaluation. Data, Sequences Analysis and Evolution 2008, vol. I:331-363. Humana Press, Totowa. J. Keith (Ed.).
38. Jermiin L.S., Ho J.W.K., Lau K.W., Jayaswal V. SeqVis: a tool for detecting compositional heterogeneity among aligned nucleotide sequences. Bioinformatics for DNA Sequence Analysis 2009, 65-91. Humana Press, Totowa, NJ. D. Posada (Ed.).
39. Kass R.E., Raftery A.E. Bayes factors. Journal of the American Statistical Association 1995, 90:773-795.
40. Kishino H., Thorne J.L., Bruno W.J. Performance of divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution 2001, 18:352-361.
41. Knowles L.L., Carstens B.C. Delimiting species without monophyletic gene trees. Systematic Biology 2007, 56:887-895.
42. Lavine M., Schervish M.J. Bayes factors: what they are and what they are not. American Statistician 1999, 53:119-122.
43. Lewis P.O. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 2001, 50:913-925.
44. Li Y.-X., Xue X.-X., Liu H.-J. Fossil lizards of Qinling Mountains. Vertebrata Palasiatica 2004, 42:171-176. (in Chinese with English abstract).
45. Mayer W., Benyr G. Albumin-evolution und phylogenese in der Familie Lacertidae (Reptilia: Sauria). Annalen des Naturhistorischen Museums Wien 1994, 96B:621-648.
46. Mayer W., Pavlicev M. The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae. Molecular Phylogenetics and Evolution 2007, 44:1155-1163.
47. Molnar P. Mio-Pliocene growth of the Tibetan Plateau and evolution of East Asian climate. Palaeontologia Electronica 2005, 8:1-23.
48. Müller K. SeqState: primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 2005, 4:65-69.
49. Newton M.A., Raftery A.E. Approximate Bayesian inference by the weighted likelihood bootstrap (with discussion). Journal of the Royal Statistical Society Series B - Methodological 1994, 56:3-48.
50. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogeneitc analysis of combined data. Systematic Biology 2004, 53:47-67.
51. Orlov, V.F., 2008. Taxonomical diversity of the Eremias Lizards: history and recent state of problem. In: Ananjeva, N.B., Danilov, I.G., Dunayev, E.A. (Eds.), The Problems of Herpetology, Proceedings of the 3th Meeting of the Nikolsky Herpetological Society, St. Petersburg, pp. 328-336.
52. Palumbi S.R. Nucleic acids II: the polymerase chain reaction. Molecular Systematics 1996, 205-247. Sinauer Associates, Sunderland, MA. second ed. D.M. Hillis, C. Moritz, B.K. Mable (Eds.).
53. Pavlicev M., Mayer W. Fast radiation of the subfamily Lacertinae (Reptilia: Lacertidae): history or methodical artefact?. Molecular Phylogenetics and Evolution 2009, 52:727-734.
54. Pollock D.D., Zwickl D.J., Mccguire J.A., Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Systematic Biology 2002, 51:664-671.
55. Posada D. JModelTest: phylogenetic model averaging. Molecular Biology and Evolution 2008, 25:1253-1256.
56. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approach. Systematic Biology 2004, 53:793-808.
57. Raftery A.E. Hypothesis testing and model selection. Markov Chain Monte Carlo in Practice 1996, 163-188. Chapman and Hall, London, UK. W.R. Gilks, D.J. Spiegelhalter, S. Richardson (Eds.).
58. Rambaut, A., Drummond, A.J., 2009. Tracer v1.5.0, http://beast.bio.ed.ac.uk/Tracer.
59. Rastegar-Pouyani E., Rastegar-Pouyani N., Kazemi-Noureini S., Joger U., Wink M. Molecular phylogeny of the Eremias persica complex of the Iranian plateau (Reptilia: Lacertidae), based on mtDNA sequences. Zoological Journal of the Linnean Society 2010, 158:641-660.
60. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
61. Rui J.-L., Wang Y.-T., Nie L.-W. The complete mitochondrial DNA genome of Eremias brenchleyi (Reptilia: Lacertidae) and its phylogeny position within Squamata Reptiles. Amphibia-Reptilia 2009, 30:25-35.
62. Savill N.J., Hoyle D.C., Higgs P.G. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics 2001, 157:399-411.
63. Shine R. The evolution of viviparity in reptiles: an ecological analysis. Development 1985, vol. 15:605-694. John Wiley and Sons, Inc New York. B.C. Gans, F. Billet (Eds.).
64. Simmons M.P., Ochoterena H. Gaps as characters in sequence based phylogenetic analysis. Systematic Biology 2000, 49:369-381.
65. Sites J.W., Marshall J.C. Operational criteria for delimiting species. Annual Review of Ecology, Evolution, and Systematics 2004, 35:199-227.
66. Suchard M.A., Weiss R.E., Sinsheimer J.S. Bayesian selection of continuous time Markov chain evolutionary models. Molecular Biology and Evolution 2001, 18:1001-1013.
67. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4 2002, Sinauer, Sunderland, MA.
68. Szczerbak N.N. Taxonomy of the genus Eremias (Sauria, Reptilia) in connection with the focuses of the desert-steppe fauna development in Paleoarctic. Vestnik Zoologii 1971, 2:48-55. (in Russian with English abstract).
69. Szczerbak, N.N., 1974. Yashchurki Palearktiki (Eremias lizards of the Palearctic). Axadeimiya Nauk Ukrainskoi USSR Institut Zoologii. Naukova Dumka, Kiev (in Russian), 296 pp.
70. Szczerbak N.N. Guide to the Reptiles of the Eastern Palearctic 2003, Krieger Publishing Company, Malabar, Florida, USA, 350 pp.
71. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997, 25:4876-4882.
72. Thorne J.L., Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 2002, 51:689-702.
73. Wan, L.-X., 2006. Molecular Phylogeography of the Chinese Lacertids of the Genus Eemias. Ph. D. Thesis. Lanzhou University, 90 pp (in Chinese with English abstract).
74. Wan L.-X., Sun S.-H., Jin Y.-T., Yan Y.-F., Liu N.-F. Molecular phylogeography of the Chinese lacertids of the genus Eremias (Lacertidae) based on 16S rRNA mitochondrial DNA sequences. Amphibia-Reptilia 2007, 28:33-41.
75. Welch K.R.G. Herpetology of Europe and Southwest Asia: A Checklist and Bibliography of the Orders Gymnophiona and Urodela 1983, Robert E. Krieger Publishing Co., Malabar, Florida, 135 pp.
76. Welch K.R.G., Cooke P.S., Wright A.S. Lizards of the Orient: A Checklist 1990, Robert E. Krieger Publishing Co., Malabar, Florida, 162 pp.
77. Whiting A.S., Bauer A.M., Sites J.W. Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae). Molecular Phylogenetics and Evolution 2003, 29:582-598.
78. Xia X., Lemey P. Assessing substitution saturation with DAMBE. The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny 2009, 615-630. Cambridge University Press. second ed. M. Salemi, A.-M. Vandamme (Eds.).
79. Xia X., Xie Z. DAMBE: data analysis in molecular biology and evolution. Journal of Heredity 2001, 92:371-373.
80. Xia X., Xie Z., Kjer K.M. 18S Ribosomal ribosomal RNA and tetrapod phylogeny. Systematic Biology 2003, 52:283-295.
81. Xia X., Xie Z., Salemi M., Chen L., Wang Y. An index of substitution saturation and its application. Molecular Phylogenetics and Evolution 2003, 26:1-7.
82. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 1997, 13:555-556.
83. Zhao K.-T. Lacertidae. Fauna 3 Sinica, Reptilia (Squamata: Lacertilia) 1999, vol. 2:219-242. Science Press, Beijing, (in Chinese).
84. Zhao Q., Liu H.-X., Luo L.-G., Ji X. Comparative population genetics and phylogeography of two lacertid lizards (Eremias argus and E. brenchleyi) from China. Molecular Phylogenetics and Evolution 2011, 58:478-491.
85. Zwickl D.J., Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 2002, 51:588-598.