The complete mitochondrial genome of the Sichuan hot-spring keel-back (Thermophis zhaoermii; Serpentes: Colubridae) and a mitogenomic phylogeny of the snakes

Mitochondrial DNA

Volumn 21, Issue 1, 2010, Pages 8-18

  He, Miao ^a,b   Feng, Jinchao ^c   Zhao, Ermi ^a,d  

^a SICHUAN UNIVERSITY   (China)

^b INSTITUTE OF BLOOD TRANSFUSION   (China)

^c MINZU UNIVERSITY OF CHINA   (China)

^d CHENGDU INSTITUTE OF BIOLOGY   (China)

Author keywords

Hot spring keel back; Mitochondrial genome; Phylogeny; Thermophis zhaoermii

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BAYES THEOREM; CLADISTICS; CRETACEOUS; DNA REPLICATION ORIGIN; DNA SEQUENCE; DNA STRAND; GENE CONSTRUCT; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC CODE; GENETIC VARIABILITY; MAXIMUM LIKELIHOOD METHOD; MITOCHONDRIAL GENOME; MOLECULAR BIOLOGY; MOLECULAR PHYLOGENY; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAPHYLY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SNAKE; THERMAL SPRING; THERMOPHIS ZHAOERMII;

ANIMALS; CHINA; COLUBRIDAE; DNA, INTERGENIC; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, RRNA; GENETIC SPECIATION; GENOME, MITOCHONDRIAL; LOCUS CONTROL REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TIME FACTORS;

ACROCHORDUS; ALETHINOPHIDIA; COLUBRIDAE; COLUBRINAE; COLUBROIDEA; HENOPHIDIA; HOMALOPSINAE; SERPENTES;

EID: 76649129000     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/19401730903505867     Document Type: Article

References (53)

1. Akaike H. 1974. A new look at the statistical identification model. IEEE Trans Autom Contr 19:716-723.
2. Burbrink FT, Pyron RA. 2008. The taming of the skew: Estimating proper confidence intervals for divergence dates. Syst Biol 57: 317-328.
3. Cadle JE. 1987. Geographic distribution: Problems in phylogeny and zoogeography. In: Seigel RA, Collins JT, Novak SS, editors. Snakes: Ecology and evolutionary biology. New York: McGraw-Hill. p 77-105.
4. Castoe TA, Parkinson CL. 2006. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Mol Phylogenet Evol 39:91-110.
5. Castoe TA, Jiang ZJ, Gu WJ, Wang ZYO, Pollock DD. 2008. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS ONE 3(5):e2201.
6. Chen N, Zhao SJ. 2009. New progress in snake mitochondrial gene rearrangement. Mitochondrial DNA 20(4):69-71.
7. Dong S, Kumazawa Y. 2005. Complete mitochondrial DNA sequences of six snakes: Phylogenetic relationships and molecular evolution of genomic features. J Mol Evol 61(1):12-22.
8. Douglas D, Janke A, Arnason U. 2006. A mitogenomic study on the phylogenetic position of snakes. Zool Scr 35(6):545-558.
9. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
10. Guo P, Liu SY, Feng JC, He M. 2008. The description of a new species of Thermophis (Serpentes; Colubridae). Sichuan J Zool 27:321.
11. Harrison TM, Copeland P, Kidd WSF, Yin A. 1992. Raising Tibet. Science 255:1663-1670.
12. He M, Feng JC, Liu SY, Guo P, Zhao EM. 2009. The phylogenetic position of Thermophis (Serpentes: Colubridae), an endemic snake from the Qinghai-Xizang Plateau, China. J Nat Hist 43: 479-488.
13. Head JJ, Holroyd PA, Hutchison JH, Ciochon RL. 2005. First report of snakes (Serpentes) from the Late Middle Eocene of the Ponduang Formation, Myanmar. J Vert Paleontol 25:246-250.
14. Heise PJ, Maxson LR, Dowling HG, Hedges SB. 1995. Higherlevel snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes. Mol Biol Evol 12:259-265.
15. Holman JA. 2000. Fossil snakes of North America: Origin, evolution, distribution, paleoecology. Bloomington: Indiana University Press.
16. Huang S, Liu SY, Guo P, Zhang YP, Zhao EM. 2009. What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau?Mol Phylogenet Evol 51:438-446.
17. Janke A, Erpenbeck D, Nilsson M, Arnason U. 2001. The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): Implications for amniote phylogeny. Proceedings of the Royal Society of London Series B-Biological Sciences 268(1467):623-631.
18. Jiang ZJ, Castoe TA, Austin CC, Burbrink FT, Herron MD, McGuire JA, Parkinson CL, Pollock DD. 2007. Comparative mitochondrial genomics of snakes: Extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC Evol Biol 7(1):123.
19. Kelly CMR, Barker NP, Villet MH. 2003. Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes. Syst Biol 52:439-459.
20. Keogh JS. 1998. Molecular phylogeny of elapid snakes and a consideration of their biogeographic history. Biol J Linn Soc 63: 177-203.
21. Kumazawa Y, Ota H, Nishida M, Ozawa T. 1996. Gene rearrangements in snake mitochondrial genomes: Highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Mol Biol Evol 13(9): 1242-1254.
22. Kumazawa Y, Ota H, Nishida M, Ozawa T. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150(1): 313-329.
23. Kumazawa Y. 2004. Mitochondrial DNA sequences of five squamates: Phylogenetic affiliation of snakes. DNA Res 11(2): 137-144.
24. Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
25. Lawson R, Slowinski JB, Crother BI, Burbrink FT. 2005. Phylogeny of the Colubroidea (Serpentes): New evidence from mitochondrial and nuclear genes. Mol Phylogenet Evol 37:581-601.
26. Lowe TM, Eddy SR. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955-964.
27. Malnate EV. 1953. The taxonomic status of the Tibetan colubrid snake Natrix baileyi. Copeia 1953:92-96.
28. Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
29. Parkinson CL. 1999. Molecular systematics and biogeographical history of pitvipers as determined by mitochondrial ribosomal DNA sequences. Copeia 1999:576-586.
30. Pope KO, D'Hondt SL, Marshall CR. 1998. Meteorite impact and the mass extinction of species at the Cretaceous/Tertiary boundary. Proc Natl Acad Sci USA 95:11028-11029.
31. Rage JC. 1987. Fossil record. In: Seigel RA, Collins JT, Novak SS, editors. Snakes: Ecology and evolutionary biology. New York: McGraw-Hill Publishing. p 51-76.
32. Rage JC, Werner C. 1999. Mid-Cretaceous (Cenomanian) snakes from Wadi Abu Hashim, Sudan: The earliest snake assemblage. Palaeontol Afr 35:85-110.
33. Rage JC, Buffetaut E, BuVetaut-Tong H, Chaimanee Y, Ducrocq S, Jaeger JJ, Suteethorn V. 1992. A colubrid snake in the late Eocene of Thailand: The oldest known Colubridae (Reptilia, Serpentes). C R Biol 2314:1085-1089.
34. Rage JC, Bajpai S, Thewissen JGM, Tiwari BN. 2003. Early Eocene snakes from Kutch, Western India, with a review of the Palaeophiidae. Geodiversitas 25:695-716.
35. Rambaut A, Drummond AJ. 2007. Tracer v1.4. Available online at: http://beast.bio.ed.ac.uk/Tracer. Accessed: Dec. 28, 2007
36. Ronquist FR, Huelsenbeck JP. 2003. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 19:1572-1574.
37. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press.
38. Slowinski JB, Lawson R. 2002. Snake phylogeny: Evidence from nuclear and mitochondrial genes. Mol Phylogenet Evol 23: 194-202.
39. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RaxML web-servers. Syst Biol 75(5):758-771.
40. Szyndlar Z, Rage JC. 1990.West Palearctic cobras of the genus Naja (Serpentes: Elapidae): Interrelationships among extinct and extant species. Amphibia-Reptilia 11:385-400.
41. Szyndlar Z, Rage JC. 2002. Fossil record of the true vipers. In: Schuett GW, Höggren M, Douglas ME, Greene HW, editors. Biology of the vipers. Eagle Mountain, Colorado: Eagle Mountain Press. p 419-444.
42. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins D. 1997. The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876-4882.
44. Vidal N, Hedges SB. 2002. Higher-level relationships of caenophidian snakes inferred from four nuclear and mitochondrial genes. C R Biol 325:987-995. (Pubitemid 35428761)
45. Vidal N, Delmas A, David P, Cruaud C, Couloux A, Hedges SB. 2007. The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes. C R Biol 330: 182-187.
46. Vidal N, Rage J-C, Couloux A, Hedges SB. 2009. Snakes (Serpentes). In: Hedges SB, Kumar S, editors. The timetree of life. Oxford: Oxford University Press. p 390-397.
47. Wall F. 1907. Some new Asian snakes. J Bombay Nat Hist Soc 17: 612-618.
48. Wang GL, He SP, Huang S, He M, Zhao EM. 2009. The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata). Chin Sci Bull 54(10): 1713-1724.
49. Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW Jr, Townsend TM, Reeder TW. 2008. Branch lengths, support, and congruence: Testing the phylogenomic approach with 20 nuclear loci in snakes. Syst Biol 57(3):420-431.
50. Wüster W, Peppin L, Pook CE, Walker DE. 2008. A nesting of vipers: Phylogeny and historical biogeography of the Viperidae (Squamata: Serpentes). Mol Phylogenet Evol 49:445-459.
51. Yan J, Li HD, Zhou KY. 2008. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships. BMC Genomics 9:569.
52. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314.
53. Zaher H. 1999. Hemipenial morphology of the South American xenodontine snakes, with a proposal for a monophyletic Xenodontinae and a reappraisal of colubroid hemipenes. Bull Am Mus Nat Hist 240:1-168.