Kumazawa Y, Ota H, Nishida M, Ozawa T: 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. 1996, 13 (9): 1242-1254.
Article
CAS
PubMed
Google Scholar
Kumazawa Y, Ota H, Nishida M, Ozawa T: The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics. 1998, 150: 313-329.
CAS
PubMed Central
PubMed
Google Scholar
Jiang ZJ, Castoe TA, Austin CC, Burbrink FT, Herron MD, McGuire JA, Parkinson CL, Pollock DD: Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. BMC Evol Biol. 2007, 7: 123-10.1186/1471-2148-7-123.
Article
PubMed Central
PubMed
Google Scholar
Yan J, Li H, Zhou K: Evolution of the mitochondrial genome in snakes: gene rearrangements and phylogenetic relationships. BMC Genomics. 2008, 9: 569-10.1186/1471-2164-9-569.
Article
PubMed Central
PubMed
Google Scholar
Dong S, Kumazawa Y: Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features. J Mol Evol. 2005, 61 (1): 12-22. 10.1007/s00239-004-0190-9.
Article
CAS
PubMed
Google Scholar
Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD: Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS ONE. 2008, 3 (5): e2201-10.1371/journal.pone.0002201.
Article
PubMed Central
PubMed
Google Scholar
Lee MSY, Hugall AF, Lawson R, Scanlon JD: Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses. Systematics and Biodiversity. 2007, 5 (4): 371-389. 10.1017/S1477200007002290.
Article
Google Scholar
Kumazawa Y: Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes. DNA Res. 2004, 11: 137-144. 10.1093/dnares/11.2.137.
Article
CAS
PubMed
Google Scholar
Douglas DA, Janke A, Arnason U: A mitogenomic study on the phylogenetic position of snakes. Zool Scr. 2006, 35 (6): 545-558. 10.1111/j.1463-6409.2006.00257.x.
Article
Google Scholar
Castoe TA, de Koning APJ, Kim H, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD: Evidence for an ancient adaptive episode of convergent molecular evolution. PNAS. 2009, 106 (22): 8986-8991. 10.1073/pnas.0900233106.
Article
CAS
PubMed Central
PubMed
Google Scholar
McDiarmid RW, Campbell JA, Toure TA: Snake species of the world: a taxonomic and geographic reference. 1999, Herpetologists' League, 1:
Google Scholar
Greene H, Cundall D: Limbless tetrapods and snakes with legs. Science. 2000, 287: 1939-1941. 10.1126/science.287.5460.1939.
Article
CAS
PubMed
Google Scholar
Vidal N, Hedges SB: The molecular evolutionary tree of lizards, snakes and amphisbaenians. CR Biol. 2008, doi: 101016/jcrvi200807010
Google Scholar
Albert EM, San Mauro D, García-París M, Rüber L, Zardoya R: Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data. Gene. 2008, 441 (1-2): 12-21. 10.1016/j.gene.2008.05.014.
Article
PubMed
Google Scholar
Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW, Townsend TM, Reeder TW: Branch lengths, support and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst Biol. 2008, 57 (3): 420-431. 10.1080/10635150802166053.
Article
PubMed
Google Scholar
Wilcox TP, Zwickl DJ, Heath TA, Hillis DM: Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol. 2002, 25: 361-371. 10.1016/S1055-7903(02)00244-0.
Article
CAS
PubMed
Google Scholar
Vidal N, Hedges SB: Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes. CR Biol. 2002, 325: 977-985. 10.1016/S1631-0691(02)01510-X.
Article
CAS
Google Scholar
Vidal N, Hedges SB: Molecular evidence for a terrestrial origin of snakes. Proc R Soc Lond B. 2004, 271 (suppl 4): 226-229. 10.1098/rsbl.2003.0151.
Article
Google Scholar
Noonan BP, Chippendale PT: Dispersal and vicariance: the complex evolutionary history of boid snakes. Mol Phylogenet Evol. 2006, 40 (2): 347-358. 10.1016/j.ympev.2006.03.010.
Article
CAS
PubMed
Google Scholar
Vidal N, Delmas A, Hedges SB: The higher-level relationships of alethinophidian snakes inferred from seven nuclear and mitochondrial genes. Biology of the Boas and Pythons. Edited by: Henderson RW, Powell R. 2007, Eagle Mountain Publishing, Eagle Mountain, Utah
Google Scholar
Kley NJ, Breinerd EL: Feeding by mandibular raking in a snake. Nature. 1999, 402: 369-370. 10.1038/46460.
Article
CAS
Google Scholar
Kumazawa Y, Endo H: Mitochondrial genome of the Komodo dragon, efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res. 2004, 11: 115-125. 10.1093/dnares/11.2.115.
Article
CAS
PubMed
Google Scholar
Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nuc Acids Res. 2005, 33: 511-518. 10.1093/nar/gki198.
Article
CAS
Google Scholar
Notredame C, Higgins DG, Heringa J: T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Evol. 2000, 302 (1): 205-217.
CAS
Google Scholar
Cannone JJ, Subramanian S, Schnare MN, Collet JR, D'Souza LM, Du Y, Feng B, Lin , Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR: The comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinf. 2002, 3: 15-10.1186/1471-2105-3-15.
Article
Google Scholar
Swofford DL: Phylogenetic analysis using parsimony (*and other methods), version 4[computer software and manual]. 2002, Sunderland, MA: Sinauer Associates
Google Scholar
Brown JM, Lemmon AR: The importance of data partitioning and the utility of Bayes Factors in Bayesian phylogenetics. Syst Biol. 56 (4): 643-655. 10.1080/10635150701546249.
Kass RE, Raftery AE: Bayes Factors. J Am Stat Assoc. 1995, 90 (430): 773-795. 10.2307/2291091.
Article
Google Scholar
Posada D, Crandall KA: Modeltest, testing the model of DNA substitution. Bioinf. 1998, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817.
Article
CAS
Google Scholar
Lanave C, Preparata G, Saccone C, Serio G: A new method for calculating evolutionary substitution rates. J Mol Evol. 1984, 20 (1): 86-93. 10.1007/BF02101990.
Article
CAS
PubMed
Google Scholar
Gu X, Fu Y, Li W: Maximum likelihood estimation of heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 1995, 12 (4): 546-557.
CAS
PubMed
Google Scholar
Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993, 10: 512-526.
CAS
PubMed
Google Scholar
Adachi J, Hasegawa M: Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 1996, 42: 459-468. 10.1007/BF02498640.
Article
CAS
PubMed
Google Scholar
Lartillot N, Philippe H: A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004, 21 (6): 1095-1109. 10.1093/molbev/msh112.
Article
CAS
PubMed
Google Scholar
Lartillot N, Brinkmann H, Philippe H: Suppression of long-branch attraction artifacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 2007, 7 (suppl 1): S4-10.1186/1471-2148-7-S1-S4.
Article
PubMed Central
PubMed
Google Scholar
Jobb G: TREEFINDER. version of January 2008 [Computer software and manual] Munich, Germany Distributed by the author at. 2008, [http://www.treefinder.de]January [Computer software and manual] Munich, Germany Distributed by the author at
Google Scholar
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP: Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001, 294: 2310-2314. 10.1126/science.1065889.
Article
CAS
PubMed
Google Scholar
Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinf. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.
Article
CAS
Google Scholar
University of Oslo Bioportal. [http://www.bioportal.uio.no]
Tchernov E, Rieppel O, Zaher H, Polcyn MJ, Jacobs LL: A fossil snake with limbs. Science. 2000, 287: 2010-2012. 10.1126/science.287.5460.2010.
Article
CAS
PubMed
Google Scholar
Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981, 17: 368-376. 10.1007/BF01734359.
Article
CAS
PubMed
Google Scholar
Strimmer K, Rambaut A: Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond B. 2002, 269: 137-142. 10.1098/rspb.2001.1862.
Article
Google Scholar
Kishino H, Hasegawa M: Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea. J Mol Evol. 1989, 29: 170-179. 10.1007/BF02100115.
Article
CAS
PubMed
Google Scholar
Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999, 16: 1114-1116.
Article
CAS
Google Scholar
Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002, 51 (3): 492-508. 10.1080/10635150290069913.
Article
PubMed
Google Scholar
Vidal N, Hedges SB: The phylogeny of squamate reptiles (lizards, snakes and amphisbaenians) inferred from nine nuclear protein-coding genes. CR Biol. 2005, 328: 1000-1008.
Article
CAS
Google Scholar
Kumazawa Y: Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene. 2007, 388: 19-26. 10.1016/j.gene.2006.09.026.
Article
CAS
PubMed
Google Scholar