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Volumn 21, Issue 3-4, 2010, Pages 138-146

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

Author keywords

Mitochondrial DNA; Molecular clock; Rate heterogeneity; Whales

Indexed keywords

MITOCHONDRIAL DNA;

EID: 77956087396     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/19401736.2010.494727     Document Type: Article
Times cited : (66)

References (42)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
    • (1974) IEEE Trans Automat Contr , vol.19 , pp. 716-723
    • Akaike, H.1
  • 2
    • 0036804729 scopus 로고    scopus 로고
    • Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    • Aris-Brosou S, Yang Z. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol 51: 703-714.
    • (2002) Syst Biol , vol.51 , pp. 703-714
    • Aris-Brosou, S.1    Yang, Z.2
  • 4
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
    • (2007) BMC Evol Biol , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 6
    • 41549084082 scopus 로고    scopus 로고
    • A Bayesian evaluation of human mitochondrial substitution rates
    • Endicott P, Ho SYW. 2008. A Bayesian evaluation of human mitochondrial substitution rates. AmJ Hum Genet 82:895-902.
    • (2008) AmJ Hum Genet , vol.82 , pp. 895-902
    • Endicott, P.1    Syw, H.2
  • 7
    • 68949086557 scopus 로고    scopus 로고
    • Evaluating the mitochondrial timescale of human evolution
    • Endicott P, Ho SYW,Metspalu M, Stringer C. 2009. Evaluating the mitochondrial timescale of human evolution. Trends Ecol Evol 24:515-521.
    • (2009) Trends Ecol Evol , vol.24 , pp. 515-521
    • Endicott, P.1    Ho Sywmetspalu, M.2    Stringer, C.3
  • 8
    • 70350771134 scopus 로고    scopus 로고
    • Mitochondrial DNA as a marker of molecular diversity: A reappraisal
    • Galtier N, Nabholz B, Glemin S, Hurst GD. 2009. Mitochondrial DNA as a marker of molecular diversity: A reappraisal. Mol Ecol 18:4541-4550.
    • (2009) Mol Ecol , vol.18 , pp. 4541-4550
    • Galtier, N.1    Nabholz, B.2    Glemin, S.3    Hurst, G.D.4
  • 9
    • 8744259620 scopus 로고    scopus 로고
    • Is there a universal mtDNA clock for birds?
    • García-Moreno J. 2004. Is there a universal mtDNA clock for birds? J Avian Biol 35:465-468.
    • (2004) J Avian Biol , vol.35 , pp. 465-468
    • García-Moreno, J.1
  • 10
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11:725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 11
    • 67649133122 scopus 로고    scopus 로고
    • An examination of phylogenetic models of substitution rate variation among lineages
    • Ho SYW. 2009. An examination of phylogenetic models of substitution rate variation among lineages. Biol Lett 5:421-424.
    • (2009) Biol Lett , vol.5 , pp. 421-424
    • Syw, H.1
  • 12
    • 70350103638 scopus 로고    scopus 로고
    • Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
    • Ho SYW, Phillips MJ. 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58:367-380.
    • (2009) Syst Biol , vol.58 , pp. 367-380
    • Syw, H.1    Phillips, M.J.2
  • 13
    • 20444427160 scopus 로고    scopus 로고
    • Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
    • Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005a. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22: 1561-1568.
    • (2005) Mol Biol Evol , vol.22 , pp. 1561-1568
    • Syw, H.1    Phillips, M.J.2    Cooper, A.3    Drummond, A.J.4
  • 14
    • 17744387938 scopus 로고    scopus 로고
    • Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
    • Ho SYW, Phillips MJ, Drummond AJ, Cooper A. 2005b. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol Biol Evol 22:1355-1363.
    • (2005) Mol Biol Evol , vol.22 , pp. 1355-1363
    • Syw, H.1    Phillips, M.J.2    Drummond, A.J.3    Cooper, A.4
  • 16
    • 0035103260 scopus 로고    scopus 로고
    • Performance of a divergence time estimation method under a probabilistic model of rate evolution
    • Kishino H, Thorne JL, Bruno WJ. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18:352-361.
    • (2001) Mol Biol Evol , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 18
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
    • (1984) J Mol Evol , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 21
    • 37549001784 scopus 로고    scopus 로고
    • A general comparison of relaxed molecular clock models
    • Lepage T, Bryant D, Philippe H, Lartillot N. 2007. A general comparison of relaxed molecular clock models. Mol Biol Evol 24:2699-12680
    • (2007) Mol Biol Evol , vol.24 , pp. 2699-12680
    • Lepage, T.1    Bryant, D.2    Philippe, H.3    Lartillot, N.4
  • 22
    • 0036134757 scopus 로고    scopus 로고
    • Heterotachy, an important process of protein evolution
    • Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol 19:1-7.
    • (2002) Mol Biol Evol , vol.19 , pp. 1-7
    • Lopez, P.1    Casane, D.2    Philippe, H.3
  • 23
    • 70349665848 scopus 로고    scopus 로고
    • Divergence date estimation and a comprehensive molecular tree of extant cetaceans
    • McGowen MR, Spaulding M, Gatesy J. 2009. Divergence date estimation and a comprehensive molecular tree of extant cetaceans. Mol Phylogenet Evol 53:891-906.
    • (2009) Mol Phylogenet Evol , vol.53 , pp. 891-906
    • McGowen, M.R.1    Spaulding, M.2    Gatesy, J.3
  • 24
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 25
    • 63049112416 scopus 로고    scopus 로고
    • The erratic mitochondrial clock: Variations of mutation rate, not population size, affect mtDNAdiversity across birds andmammals
    • Nabholz B, Glemin S, Galtier N. 2009. The erratic mitochondrial clock: Variations of mutation rate, not population size, affect mtDNAdiversity across birds andmammals.BMCEvol Biol 9:54.
    • (2009) BMCEvol Biol , vol.9 , pp. 54
    • Nabholz, B.1    Glemin, S.2    Galtier, N.3
  • 26
    • 0015162354 scopus 로고
    • On the constancy of the evolutionary rate of cistrons
    • Ohta T, Kimura M. 1971. On the constancy of the evolutionary rate of cistrons. J Mol Evol 1:18-25.
    • (1971) J Mol Evol , vol.1 , pp. 18-25
    • Ohta, T.1    Kimura, M.2
  • 27
    • 77953775759 scopus 로고    scopus 로고
    • Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration
    • Papadopoulou A, Anastasiou I, Vogler AP. 2010. Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration. Mol Biol Evol 27:1659-1672.
    • (2010) Mol Biol Evol , vol.27 , pp. 1659-1672
    • Papadopoulou, A.1    Anastasiou, I.2    Vogler, A.P.3
  • 29
    • 34548556039 scopus 로고    scopus 로고
    • Inferring speciation times under an episodic molecular clock
    • Rambaut A, Drummond AJ. 2007. Tracer. Oxford: University of Oxford. Rannala B, Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Syst Biol 56:453-466.
    • (2007) Syst Biol , vol.56 , pp. 453-466
    • Rannala, B.1    Yang, Z.2
  • 30
    • 0030773749 scopus 로고    scopus 로고
    • A nonparametric approach to estimating divergence times in the absence of rate constancy
    • Sanderson MJ. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy.Mol Biol Evol 14:1218-1231.
    • (1997) Mol Biol Evol , vol.14 , pp. 1218-1231
    • Sanderson, M.J.1
  • 31
    • 3042548848 scopus 로고    scopus 로고
    • Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
    • Seo TK, Kishino H, Thorne JL. 2004. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol Biol Evol 21:1201-1213.
    • (2004) Mol Biol Evol , vol.21 , pp. 1201-1213
    • Seo, T.K.1    Kishino, H.2    Thorne, J.L.3
  • 32
    • 28944450584 scopus 로고    scopus 로고
    • Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
    • Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23:7-9.
    • (2006) Mol Biol Evol , vol.23 , pp. 7-9
    • Shapiro, B.1    Rambaut, A.2    Drummond, A.J.3
  • 33
    • 33845385936 scopus 로고    scopus 로고
    • Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
    • Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Ann Rev Ecol Syst 37: 545-579.
    • (2006) Ann Rev Ecol Syst , vol.37 , pp. 545-579
    • Simon, C.1    Buckley, T.R.2    Frati, F.3    Stewart, J.B.4    Beckenbach, A.T.5
  • 34
    • 53349160132 scopus 로고    scopus 로고
    • Rates of molecular evolution are linked to life history in flowering plants
    • Smith SA, Donoghue MJ. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322:86-89.
    • (2008) Science , vol.322 , pp. 86-89
    • Smith, S.A.1    Donoghue, M.J.2
  • 37
    • 65649118549 scopus 로고    scopus 로고
    • Many-core algorithms for statistical phylogenetics
    • Suchard MA, Rambaut A. 2009. Many-core algorithms for statistical phylogenetics. Bioinformatics 25:1370-1376.
    • (2009) Bioinformatics , vol.25 , pp. 1370-1376
    • Suchard, M.A.1    Rambaut, A.2
  • 38
    • 0034983646 scopus 로고    scopus 로고
    • Bayesian selection of continuous-time Markov chain evolutionary models
    • Suchard MA, Weiss RE, Sinsheimer JS. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18:1001-1013.
    • (2001) Mol Biol Evol , vol.18 , pp. 1001-1013
    • Suchard, M.A.1    Weiss, R.E.2    Sinsheimer, J.S.3
  • 39
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15: 1647-1657.
    • (1998) Mol Biol Evol , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 40
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314.
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 41
    • 70349733063 scopus 로고    scopus 로고
    • Bayesian inference of cetacean phylogeny based on mitochondrial genomes
    • Yang X-G. 2009. Bayesian inference of cetacean phylogeny based on mitochondrial genomes. Biologia 64:811-818.
    • (2009) Biologia , vol.64 , pp. 811-818
    • Yang, X.-G.1
  • 42
    • 42449136665 scopus 로고    scopus 로고
    • Mitochondrial DNA under siege in avian phylogeography
    • Zink RM, Barrowclough GF. 2008. Mitochondrial DNA under siege in avian phylogeography. Mol Ecol 17:2107-2121.
    • (2008) Mol Ecol , vol.17 , pp. 2107-2121
    • Zink, R.M.1    Barrowclough, G.F.2


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