Complete mitochondrial DNA sequences of six snakes: Phylogenetic relationships and molecular evolution of genomic features

Journal of Molecular Evolution

Volumn 61, Issue 1, 2005, Pages 12-22

  Dong, Songyu ^a   Kumazawa, Yoshinori ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Concerted evolution; Control region; Gene rearrangement; Mitochondrial genome; Molecular phylogeny; Polymerase chain reaction; Reptilia; Serpentes; Squamata; tRNA gene

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; DNA SEQUENCE; GENE CONTROL; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC CODE; GENOMICS; MOLECULAR EVOLUTION; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SNAKE;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; RNA, TRANSFER; SEQUENCE HOMOLOGY, NUCLEIC ACID; SNAKES;

ACROCHORDIDAE; ANILIUS SCYTALE; BOA CONSTRICTOR; BOIDAE; COLUBRIDAE; CYLINDROPHIIDAE; LEPTOTYPHLOPIDAE; OVOPHIS OKINAVENSIS; PYTHONIDAE; REPTILIA; SERPENTES; SQUAMATA; VIPERIDAE; XENOPELTIDAE;

EID: 23944461017     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0190-9     Document Type: Article

References (48)

1. Adachi J, Hasegawa M (1996) MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs, No 28. Institute of Statistical Mathematics, Tokyo
2. S Asakawa Y Kumazawa T Araki H Himeno K Miura K Watanabe 1991 Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes J Mol Evol 32 511 520
3. JL Boore 1999 Animal mitochondrial genomes Nucleic Acids Res 27 1767 1780
4. WM Brown EM Prager A Wang AC Wilson 1982 Mitochondrial DNA sequences of primates: tempo and mode of evolution J Mol Evol 18 225 239
5. JE Cadle 1988 Phylogenetic relationship among advanced snakes: a molecular perspective Univ Calif Publ Zool 119 1 77
6. DA Clayton 1992 Transcription and replication of animal mitochondrial DNAs Int Rev Cytol 141 217 232
7. J Felsenstein 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach J Mol Evol 17 368 376
8. MRJ Forstner SK Davis E Arévalo 1995 Support for the hypothesis of anguimorph ancestry for the suborder serpentes from phylogenetic analysis of mitochondrial DNA sequences Mol Phylogenet Evol 4 93 102
9. PJ Heise LR Maxson HG Dowling SB Hedges 1995 Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes Mol Biol Evol 12 259 265
10. DM Hillis C Moritz 1990 An overview of applications of molecular systematics DM Hillis C Moritz Molecular systematics Sinauer Associates Sunderland, MA
11. R Hoffstetter 1955 Squamates de type moderne J Piveteau Traité de Paléontologie 5 Masson Paris 606 662
12. JP Huelsenbeck FR Ronquist 2001 MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 754 755
13. Iwabe N, Hara Y, Kumazawa Y, Shibamoto K, Saito Y, Miyata T, Katoh K (2005) Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins. Mol Biol Evol 22:810-813
14. A Janke D Erpenbeck M Nilsson U Arnason 2001 The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny Proc R Soc Lond B 268 623 631
15. H Kishino M Hasegawa 1989 Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea J Mol Evol 29 170 179
16. Y Kumazawa 2004 Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes DNA Res 11 137 144
17. Y Kumazawa H Endo 2004 Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements DNA Res 11 115 125
18. Y Kumazawa M Nishida 1993 Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics J Mol Evol 37 380 398
19. Y Kumazawa M Nishida 1995 Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers Mol Biol Evol 12 759 772
20. Y Kumazawa H Ota M Nishida T Ozawa 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 1242 1254
21. Y Kumazawa H Ota M Nishida T Ozawa 1998 The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions Genetics 150 313 329
22. MSY Lee 2000 Soft anatomy, diffuse homoplasy, and the relationship of lizards and snakes Zool Scripta 29 101 130
23. MSY Lee JD Scanlon 2002 Snake phylogeny based on osteology, soft anatomy and ecology Biol Rev 77 333 401
24. G Levinson GA Gutman 1987 Slipped-strand mispairing: a major mechanism for DNA sequence evolution Mol Biol Evol 4 203 221
25. SB McDowell CM Bogert 1954 The systematic position of Lantltanotus and the affinities of the anguimorphan lizards Bull Am Mus Nat Hist 105 1 142
26. S Pääbo DM Irwin AC Wilson 1990 DNA damage promotes jumping between templates during enzymatic amplification J Biol Chem 265 4718 4721
27. Palumbi S, Martin A, Romano S, McMillan WO, Stice L, Grabowskl G (1991) The simple fool's guide to PCR. Version 2.0. Department of Zoology and Kewalo Marine Laboratory. University of Hawaii, Honolulu
28. D Posada KA Crandall 1998 Modeltest: testing the model of DNA substitution Bioinformatics 14 817 818
29. JC Rage 1987 Fossil history RA Seigel JT Collins SS Novak Snakes: Ecology and evolutionary biology Macmillan New York 51 76
30. JS Rest JC Ast CC Austin PJ Waddell EA Tibbetts JM Hay DP Mindell 2003 Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome Mol Phylogenet Evol 29 289 297
31. O Rieppel 1979 A cladistic classification of primitive snakes based on skull structure Z Zool Syst Evolforsch 17 140 150
32. O Rieppel H Zaher E Tchernov MJ Polcyn 2003 The anatomy and relationships of Haasiophis terrasanctus, a fossil snake with well-developed hind limbs from the mid-Cretaceous of the Middle East J Paleont 77 536 558
33. C Saccone C Gissi A Reyes A Larizza E Sbisà G Pesole 2002 Mitochondrial DNA in metazoa: degree of freedom in a frozen event Gene 286 3 12
34. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
35. H Shimodaira M Hasegawa 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol Biol Evol 16 1114 1116
36. JB Slowinski R Lawson 2002 Snake phylogeny: evidence from nuclear and mitochondrial genes Mol Phylogenet Evol 24 194 202
37. K Strimmer A von Haeseler 1996 Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies Mol Biol Evol 13 964 969
38. DL Swofford 2003 PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4 Sinauer Associates Sunderland, MA
39. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876 4882
40. Uetz P (2003) The EMBL reptile database: http://www.embl-heidelberg.de/ uetz/Living Reptiles.html
41. Underwood G (1967) A contribution to the classification of snakes. British Museum of Natural History, London
42. G Underwood 1976 A systematic analysis of boid snakes Ad''A Bellairs CB Cox Morphology and biology of reptiles. Linn Soc Symp Ser No. 3 Academic Press London 151 175
43. N Vidal P David 2004 New insights into the early history of snakes inferred from two nuclear genes Mol Phylogenet Evol 31 783 787
44. N Vidal SB Hedges 2002 Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes CR Biologies 325 977 985
45. TP Wilcox DJ Zwickl TA Heath DM Hillis 2002 Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Mol Phylogenet Evol 25 361 371
46. DR Wolstenholme 1992 Animal mitochondrial DNA: structure and evolution Int Rev Cytol 141 173 216
47. R Zardoya A Meyer 2000 Mitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona) Genetics 155 765 775
48. GR Zug LJ Vitt JP Caldwell 2001 Herpetology Academic Press San Diego