Abstract
Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNALeu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.
Similar content being viewed by others
References
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
S Asakawa Y Kumazawa T Araki H Himeno K Miura K Watanabe (1991) ArticleTitleStrand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes J Mol Evol 32 511–520 Occurrence Handle1908022
JL Boore (1999) ArticleTitleAnimal mitochondrial genomes Nucleic Acids Res 27 1767–1780 Occurrence Handle10.1093/nar/27.8.1767 Occurrence Handle10101183
WM Brown EM Prager A Wang AC Wilson (1982) ArticleTitleMitochondrial DNA sequences of primates: tempo and mode of evolution J Mol Evol 18 225–239 Occurrence Handle10.1007/BF01734101 Occurrence Handle6284948
JE Cadle (1988) ArticleTitlePhylogenetic relationship among advanced snakes: a molecular perspective Univ Calif Publ Zool 119 1–77
DA Clayton (1992) ArticleTitleTranscription and replication of animal mitochondrial DNAs Int Rev Cytol 141 217–232 Occurrence Handle1452432
J Felsenstein (1981) ArticleTitleEvolutionary trees from DNA sequences: a maximum likelihood approach J Mol Evol 17 368–376 Occurrence Handle10.1007/BF01734359 Occurrence Handle7288891
MRJ Forstner SK Davis E Arévalo (1995) ArticleTitleSupport for the hypothesis of anguimorph ancestry for the suborder serpentes from phylogenetic analysis of mitochondrial DNA sequences Mol Phylogenet Evol 4 93–102 Occurrence Handle10.1006/mpev.1995.1010 Occurrence Handle7620640
PJ Heise LR Maxson HG Dowling SB Hedges (1995) ArticleTitleHigher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes Mol Biol Evol 12 259–265 Occurrence Handle7700153
DM Hillis C Moritz (1990) An overview of applications of molecular systematics DM Hillis C Moritz (Eds) Molecular systematics Sinauer Associates Sunderland, MA
R Hoffstetter (1955) Squamates de type moderne J Piveteau (Eds) Traité de Paléontologie 5 Masson Paris 606–662
JP Huelsenbeck FR Ronquist (2001) ArticleTitleMRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 754–755 Occurrence Handle10.1093/bioinformatics/17.8.754 Occurrence Handle11524383
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
A Janke D Erpenbeck M Nilsson U Arnason (2001) ArticleTitleThe mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny Proc R Soc Lond B 268 623–631 Occurrence Handle10.1098/rspb.2000.1402
H Kishino M Hasegawa (1989) ArticleTitleEvaluation 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 Occurrence Handle2509717
Y Kumazawa (2004) ArticleTitleMitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes DNA Res 11 137–144 Occurrence Handle15449546
Y Kumazawa H Endo (2004) ArticleTitleMitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements DNA Res 11 115–125 Occurrence Handle15449544
Y Kumazawa M Nishida (1993) ArticleTitleSequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics J Mol Evol 37 380–398 Occurrence Handle10.1007/BF00178868 Occurrence Handle7508516
Y Kumazawa M Nishida (1995) ArticleTitleVariations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers Mol Biol Evol 12 759–772 Occurrence Handle7476123
Y Kumazawa H Ota M Nishida T Ozawa (1996) ArticleTitleGene 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 Occurrence Handle8896377
Y Kumazawa H Ota M Nishida T Ozawa (1998) ArticleTitleThe complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions Genetics 150 313–329 Occurrence Handle9725849
MSY Lee (2000) ArticleTitleSoft anatomy, diffuse homoplasy, and the relationship of lizards and snakes Zool Scripta 29 101–130 Occurrence Handle10.1046/j.1463-6409.2000.00035.x
MSY Lee JD Scanlon (2002) ArticleTitleSnake phylogeny based on osteology, soft anatomy and ecology Biol Rev 77 333–401 Occurrence Handle10.1017/S1464793102005924 Occurrence Handle12227520
G Levinson GA Gutman (1987) ArticleTitleSlipped-strand mispairing: a major mechanism for DNA sequence evolution Mol Biol Evol 4 203–221 Occurrence Handle3328815
SB McDowell CM Bogert (1954) ArticleTitleThe systematic position of Lantltanotus and the affinities of the anguimorphan lizards Bull Am Mus Nat Hist 105 1–142
S Pääbo DM Irwin AC Wilson (1990) ArticleTitleDNA damage promotes jumping between templates during enzymatic amplification J Biol Chem 265 4718–4721 Occurrence Handle2307682
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
D Posada KA Crandall (1998) ArticleTitleModeltest: testing the model of DNA substitution Bioinformatics 14 817–818 Occurrence Handle10.1093/bioinformatics/14.9.817 Occurrence Handle9918953
JC Rage (1987) Fossil history RA Seigel JT Collins SS Novak (Eds) Snakes: Ecology and evolutionary biology Macmillan New York 51–76
JS Rest JC Ast CC Austin PJ Waddell EA Tibbetts JM Hay DP Mindell (2003) ArticleTitleMolecular systematics of primary reptilian lineages and the tuatara mitochondrial genome Mol Phylogenet Evol 29 289–297 Occurrence Handle10.1016/S1055-7903(03)00108-8 Occurrence Handle13678684
O Rieppel (1979) ArticleTitleA cladistic classification of primitive snakes based on skull structure Z Zool Syst Evolforsch 17 140–150
O Rieppel H Zaher E Tchernov MJ Polcyn (2003) ArticleTitleThe 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
C Saccone C Gissi A Reyes A Larizza E Sbisà G Pesole (2002) ArticleTitleMitochondrial DNA in metazoa: degree of freedom in a frozen event Gene 286 3–12 Occurrence Handle10.1016/S0378-1119(01)00807-1 Occurrence Handle11943454
N Saitou M Nei (1987) ArticleTitleThe neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406–425 Occurrence Handle3447015
H Shimodaira M Hasegawa (1999) ArticleTitleMultiple comparisons of log-likelihoods with applications to phylogenetic inference Mol Biol Evol 16 1114–1116
JB Slowinski R Lawson (2002) ArticleTitleSnake phylogeny: evidence from nuclear and mitochondrial genes Mol Phylogenet Evol 24 194–202 Occurrence Handle10.1016/S1055-7903(02)00239-7 Occurrence Handle12144756
K Strimmer A Haeseler Particlevon (1996) ArticleTitleQuartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies Mol Biol Evol 13 964–969
DL Swofford (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4 Sinauer Associates Sunderland, MA
JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 4876–4882 Occurrence Handle10.1093/nar/25.24.4876 Occurrence Handle9396791
Uetz P (2003) The EMBL reptile database: http://www.embl-heidelberg.de/uetz/Living Reptiles.html
Underwood G (1967) A contribution to the classification of snakes. British Museum of Natural History, London
G Underwood (1976) A systematic analysis of boid snakes Ad’’A Bellairs CB Cox (Eds) Morphology and biology of reptiles. Linn Soc Symp Ser No. 3 Academic Press London 151–175
N Vidal P David (2004) ArticleTitleNew insights into the early history of snakes inferred from two nuclear genes Mol Phylogenet Evol 31 783–787 Occurrence Handle10.1016/j.ympev.2004.01.001 Occurrence Handle15062811
N Vidal SB Hedges (2002) ArticleTitleHigher-level relationships of snakes inferred from four nuclear and mitochondrial genes CR Biologies 325 977–985 Occurrence Handle10.1016/S1631-0691(02)01510-X
TP Wilcox DJ Zwickl TA Heath DM Hillis (2002) ArticleTitlePhylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Mol Phylogenet Evol 25 361–371 Occurrence Handle10.1016/S1055-7903(02)00244-0 Occurrence Handle12414316
DR Wolstenholme (1992) ArticleTitleAnimal mitochondrial DNA: structure and evolution Int Rev Cytol 141 173–216 Occurrence Handle1452431
R Zardoya A Meyer (2000) ArticleTitleMitochondrial evidence on the phylogenetic position of caecilians (Amphibia: Gymnophiona) Genetics 155 765–775 Occurrence Handle10835397
GR Zug LJ Vitt JP Caldwell (2001) Herpetology Academic Press San Diego
Acknowledgments
We thank Mr. K. Yagi, Drs. M. Nishida and D. Wake, Remix Peponi Co., and the Museum of Vertebrate Zoology, University of California at Berkeley, for providing animal samples. We also thank Dr. T. Nishikawa and Nagoya University Museum for the curation of our specimens and Ms. C. Aoki for her excellent experimental assistance. Gratitude is extended to Dr. H. Shimodaira, two anonymous reviewers, and the Associate Editor for valuable comments on the phylogenetic tests. This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan (Nos. 12640680 and 14540641).
Author information
Authors and Affiliations
Corresponding author
Additional information
[Reviewing Editor: Dr. Bill Ballard]
Appendix
Appendix
Complete mtDNA Sequencing for Six Snakes
We employed an efficient and accurate method for sequencing reptile mtDNAs using the long-and-accurate polymerase chain reaction (LA-PCR) amplification of mtDNAs followed by sequencing and assembling nested PCR products with a number of reptile-oriented primers (Kumazawa and Endo 2004). Using the LA-PCR technology, we amplified mtDNA segments for each taxon with the combinations of primers shown in the note to Table A1. Because snake mtDNAs typically contain two CRs, inclusion of two CRs in the same PCR target may cause the jumping PCR (Pääbo et al. 1990) to give rise to artifactually shorter products. This problem was carefully avoided in this study by separating mtDNA sequences into three to five portions for the amplification targets.
More than 85% of the whole mtDNA sequences for the six snakes were successfully amplified and sequenced with the reptile-oriented primers (Kumazawa and Endo 2004). In general, primers designed for some extremely variable regions (e.g., CRs and 3′ end portion of ND5 gene to ND6 gene) were less effective in the PCR amplification. These gaps could be readily filled by the primer walking strategy. The boa constrictor and the sunbeam snake had long tandem repeats within CRs and sequencing from surrounding primers did not extend over the repeated region. We estimated the length of the repeated region from the size of an amplified product using these primers and then carefully assembled sequences obtained from these primers in light of the length of a repeat unit.
Rights and permissions
About this article
Cite this article
Dong, S., Kumazawa, Y. Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features. J Mol Evol 61, 12–22 (2005). https://doi.org/10.1007/s00239-004-0190-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00239-004-0190-9