Journal of Molecular Evolution

, Volume 61, Issue 1, pp 12–22 | Cite as

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features



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.


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



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).


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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  1. 1.Department of Biological Science, School of ScienceNagoya UniversityNagoya Japan
  2. 2.Division of Material Science, Graduate School of ScienceNagoya UniversityNagoya Japan

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