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Volumn 11, Issue 1, 2010, Pages

Snake mitochondrial genomes: Phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

EID: 76749085724     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-14     Document Type: Article
Times cited : (31)

References (47)
  • 1
    • 0029909927 scopus 로고    scopus 로고
    • Gene rearrangements in snake mitochondrial genomes, highly concerted evolution of control region-like sequences duplicated and inserted into a tRNA gene cluster
    • 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.
    • (1996) Mol Biol Evol , vol.13 , Issue.9 , pp. 1242-1254
    • Kumazawa, Y.1    Ota, H.2    Nishida, M.3    Ozawa, T.4
  • 2
    • 0031696736 scopus 로고    scopus 로고
    • The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions
    • 1460336, 9725849
    • 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. 1460336, 9725849.
    • (1998) Genetics , vol.150 , pp. 313-329
    • Kumazawa, Y.1    Ota, H.2    Nishida, M.3    Ozawa, T.4
  • 3
    • 34548136104 scopus 로고    scopus 로고
    • Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region
    • 10.1186/1471-2148-7-123, 1950710, 17655768
    • 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, 1950710, 17655768.
    • (2007) BMC Evol Biol , vol.7 , pp. 123
    • Jiang, Z.J.1    Castoe, T.A.2    Austin, C.C.3    Burbrink, F.T.4    Herron, M.D.5    McGuire, J.A.6    Parkinson, C.L.7    Pollock, D.D.8
  • 4
    • 60849122547 scopus 로고    scopus 로고
    • Evolution of the mitochondrial genome in snakes: gene rearrangements and phylogenetic relationships
    • 10.1186/1471-2164-9-569, 2632649, 19038056
    • 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, 2632649, 19038056.
    • (2008) BMC Genomics , vol.9 , pp. 569
    • Yan, J.1    Li, H.2    Zhou, K.3
  • 5
    • 23944461017 scopus 로고    scopus 로고
    • Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features
    • 10.1007/s00239-004-0190-9, 16007493
    • 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, 16007493.
    • (2005) J Mol Evol , vol.61 , Issue.1 , pp. 12-22
    • Dong, S.1    Kumazawa, Y.2
  • 6
    • 48249140650 scopus 로고    scopus 로고
    • Adaptive evolution and functional redesign of core metabolic proteins in snakes
    • 10.1371/journal.pone.0002201, 2376058, 18493604
    • 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, 2376058, 18493604.
    • (2008) PLoS ONE , vol.3 , Issue.5
    • Castoe, T.A.1    Jiang, Z.J.2    Gu, W.3    Wang, Z.O.4    Pollock, D.D.5
  • 7
    • 35948935045 scopus 로고    scopus 로고
    • Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood, Bayesian and parsimony analyses
    • 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.
    • (2007) Systematics and Biodiversity , vol.5 , Issue.4 , pp. 371-389
    • Lee, M.S.Y.1    Hugall, A.F.2    Lawson, R.3    Scanlon, J.D.4
  • 8
    • 11144311319 scopus 로고    scopus 로고
    • Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes
    • 10.1093/dnares/11.2.137, 15449546
    • Kumazawa Y. Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes. DNA Res 2004, 11:137-144. 10.1093/dnares/11.2.137, 15449546.
    • (2004) DNA Res , vol.11 , pp. 137-144
    • Kumazawa, Y.1
  • 9
    • 33750308129 scopus 로고    scopus 로고
    • A mitogenomic study on the phylogenetic position of snakes
    • Douglas DA, Janke A, Arnason U. A mitogenomic study on the phylogenetic position of snakes. Zool Scr 2006, 35(6):545-558.
    • (2006) Zool Scr , vol.35 , Issue.6 , pp. 545-558
    • Douglas, D.A.1    Janke, A.2    Arnason, U.3
  • 10
    • 67049119180 scopus 로고    scopus 로고
    • Evidence for an ancient adaptive episode of convergent molecular evolution
    • 10.1073/pnas.0900233106, 2690048, 19416880
    • 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, 2690048, 19416880.
    • (2009) PNAS , vol.106 , Issue.22 , pp. 8986-8991
    • Castoe, T.A.1    de Koning, A.P.J.2    Kim, H.3    Gu, W.4    Noonan, B.P.5    Naylor, G.6    Jiang, Z.J.7    Parkinson, C.L.8    Pollock, D.D.9
  • 12
    • 0034677743 scopus 로고    scopus 로고
    • Limbless tetrapods and snakes with legs
    • 10.1126/science.287.5460.1939, 10755945
    • Greene H, Cundall D. Limbless tetrapods and snakes with legs. Science 2000, 287:1939-1941. 10.1126/science.287.5460.1939, 10755945.
    • (2000) Science , vol.287 , pp. 1939-1941
    • Greene, H.1    Cundall, D.2
  • 13
    • 60149087446 scopus 로고    scopus 로고
    • The molecular evolutionary tree of lizards, snakes and amphisbaenians
    • doi: 101016/jcrvi200807010
    • Vidal N, Hedges SB. The molecular evolutionary tree of lizards, snakes and amphisbaenians. CR Biol 2008, doi: 101016/jcrvi200807010.
    • (2008) CR Biol
    • Vidal, N.1    Hedges, S.B.2
  • 14
    • 67349091702 scopus 로고    scopus 로고
    • Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data
    • 10.1016/j.gene.2008.05.014, 18639394
    • 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, 18639394.
    • (2008) Gene , vol.441 , Issue.1-2 , pp. 12-21
    • Albert, E.M.1    San Mauro, D.2    García-París, M.3    Rüber, L.4    Zardoya, R.5
  • 15
    • 43749109878 scopus 로고    scopus 로고
    • Branch lengths, support and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes
    • 10.1080/10635150802166053, 18570036
    • 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, 18570036.
    • (2008) Syst Biol , vol.57 , Issue.3 , pp. 420-431
    • Wiens, J.J.1    Kuczynski, C.A.2    Smith, S.A.3    Mulcahy, D.G.4    Sites, J.W.5    Townsend, T.M.6    Reeder, T.W.7
  • 16
    • 0036431235 scopus 로고    scopus 로고
    • Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
    • 10.1016/S1055-7903(02)00244-0, 12414316
    • 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, 12414316.
    • (2002) Mol Phylogenet Evol , vol.25 , pp. 361-371
    • Wilcox, T.P.1    Zwickl, D.J.2    Heath, T.A.3    Hillis, D.M.4
  • 17
    • 0036760668 scopus 로고    scopus 로고
    • Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes
    • Vidal N, Hedges SB. Higher-level relationships of snakes inferred from four nuclear and mitochondrial genes. CR Biol 2002, 325:977-985.
    • (2002) CR Biol , vol.325 , pp. 977-985
    • Vidal, N.1    Hedges, S.B.2
  • 18
    • 2342633801 scopus 로고    scopus 로고
    • Molecular evidence for a terrestrial origin of snakes
    • Vidal N, Hedges SB. Molecular evidence for a terrestrial origin of snakes. Proc R Soc Lond B 2004, 271(suppl 4):226-229.
    • (2004) Proc R Soc Lond B , vol.271 , Issue.SUPPL. 4 , pp. 226-229
    • Vidal, N.1    Hedges, S.B.2
  • 19
    • 33745861739 scopus 로고    scopus 로고
    • Dispersal and vicariance: the complex evolutionary history of boid snakes
    • 10.1016/j.ympev.2006.03.010, 16624591
    • 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, 16624591.
    • (2006) Mol Phylogenet Evol , vol.40 , Issue.2 , pp. 347-358
    • Noonan, B.P.1    Chippendale, P.T.2
  • 20
    • 45849138251 scopus 로고    scopus 로고
    • The higher-level relationships of alethinophidian snakes inferred from seven nuclear and mitochondrial genes
    • Eagle Mountain Publishing, Eagle Mountain, Utah, Henderson RW, Powell R
    • 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 2007, Eagle Mountain Publishing, Eagle Mountain, Utah, Henderson RW, Powell R.
    • (2007) Biology of the Boas and Pythons
    • Vidal, N.1    Delmas, A.2    Hedges, S.B.3
  • 21
    • 0033604606 scopus 로고    scopus 로고
    • Feeding by mandibular raking in a snake
    • Kley NJ, Breinerd EL. Feeding by mandibular raking in a snake. Nature 1999, 402:369-370.
    • (1999) Nature , vol.402 , pp. 369-370
    • Kley, N.J.1    Breinerd, E.L.2
  • 22
    • 11144329138 scopus 로고    scopus 로고
    • Mitochondrial genome of the Komodo dragon, efficient sequencing method with reptile-oriented primers and novel gene rearrangements
    • 10.1093/dnares/11.2.115, 15449544
    • 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, 15449544.
    • (2004) DNA Res , vol.11 , pp. 115-125
    • Kumazawa, Y.1    Endo, H.2
  • 23
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • 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.
    • (2005) Nuc Acids Res , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 24
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: a novel method for fast and accurate multiple sequence alignment
    • 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.
    • (2000) J Mol Evol , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 26
    • 0004248459 scopus 로고    scopus 로고
    • Phylogenetic analysis using parsimony (*and other methods), version 4[computer software and manual]
    • Sunderland, MA: Sinauer Associates
    • Swofford DL. Phylogenetic analysis using parsimony (*and other methods), version 4[computer software and manual]. 2002, Sunderland, MA: Sinauer Associates.
    • (2002)
    • Swofford, D.L.1
  • 27
    • 37249003697 scopus 로고    scopus 로고
    • The importance of data partitioning and the utility of Bayes Factors in Bayesian phylogenetics
    • 10.1080/10635150701546249, 17661232
    • 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, 17661232.
    • Syst Biol , vol.56 , Issue.4 , pp. 643-655
    • Brown, J.M.1    Lemmon, A.R.2
  • 29
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest, testing the model of DNA substitution
    • Posada D, Crandall KA. Modeltest, testing the model of DNA substitution. Bioinf 1998, 14(9):817-818.
    • (1998) Bioinf , vol.14 , Issue.9 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 30
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • 10.1007/BF02101990, 6429346
    • 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, 6429346.
    • (1984) J Mol Evol , vol.20 , Issue.1 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 31
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of heterogeneity of substitution rate among nucleotide sites
    • 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.
    • (1995) Mol Biol Evol , vol.12 , Issue.4 , pp. 546-557
    • Gu, X.1    Fu, Y.2    Li, W.3
  • 32
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • 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.
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 33
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • 10.1007/BF02498640, 8642615
    • 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, 8642615.
    • (1996) J Mol Evol , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 34
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • 10.1093/molbev/msh112, 15014145
    • 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, 15014145.
    • (2004) Mol Biol Evol , vol.21 , Issue.6 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 35
    • 34248159030 scopus 로고    scopus 로고
    • Suppression of long-branch attraction artifacts in the animal phylogeny using a site-heterogeneous model
    • 10.1186/1471-2148-7-S1-S4, 1796613, 17288577
    • 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, 1796613, 17288577.
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 1
    • Lartillot, N.1    Brinkmann, H.2    Philippe, H.3
  • 37
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • 10.1126/science.1065889, 11743192
    • 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, 11743192.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 38
    • 0041386108 scopus 로고    scopus 로고
    • MRBAYES 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinf 2003, 19:1572-1574.
    • (2003) Bioinf , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 39
    • 51349166052 scopus 로고    scopus 로고
    • University of Oslo Bioportal
    • University of Oslo Bioportal. , http://www.bioportal.uio.no
  • 40
    • 0034677761 scopus 로고    scopus 로고
    • A fossil snake with limbs
    • 10.1126/science.287.5460.2010, 10720326
    • 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, 10720326.
    • (2000) Science , vol.287 , pp. 2010-2012
    • Tchernov, E.1    Rieppel, O.2    Zaher, H.3    Polcyn, M.J.4    Jacobs, L.L.5
  • 41
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • 10.1007/BF01734359, 7288891
    • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17:368-376. 10.1007/BF01734359, 7288891.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 42
    • 41049111540 scopus 로고    scopus 로고
    • Inferring confidence sets of possibly misspecified gene trees
    • Strimmer K, Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond B 2002, 269:137-142.
    • (2002) Proc R Soc Lond B , vol.269 , pp. 137-142
    • Strimmer, K.1    Rambaut, A.2
  • 43
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea
    • 10.1007/BF02100115, 2509717
    • 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, 2509717.
    • (1989) J Mol Evol , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 44
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999, 16:1114-1116.
    • (1999) Mol Biol Evol , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 45
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • 10.1080/10635150290069913, 12079646
    • Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51(3):492-508. 10.1080/10635150290069913, 12079646.
    • (2002) Syst Biol , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 46
    • 28044466648 scopus 로고    scopus 로고
    • The phylogeny of squamate reptiles (lizards, snakes and amphisbaenians) inferred from nine nuclear protein-coding genes
    • 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.
    • (2005) CR Biol , vol.328 , pp. 1000-1008
    • Vidal, N.1    Hedges, S.B.2
  • 47
    • 33845787944 scopus 로고    scopus 로고
    • Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations
    • 10.1016/j.gene.2006.09.026, 17118581
    • 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, 17118581.
    • (2007) Gene , vol.388 , pp. 19-26
    • Kumazawa, Y.1


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