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Volumn 23, Issue 24, 2014, Pages 5947-5965

Molecular-clock methods for estimating evolutionary rates and timescales

Author keywords

Bayesian phylogenetics; calibration; lineage effects; local clock; rate variation; relaxed clock

Indexed keywords

BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; FOSSIL; MOLECULAR EVOLUTION; MUTATION RATE; PHYLOGENY; STATISTICAL MODEL;

EID: 84919772565     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12953     Document Type: Article
Times cited : (241)

References (166)
  • 1
    • 41149141772 scopus 로고    scopus 로고
    • Dating phylogenies with hybrid local molecular clocks
    • Aris-Brosou S, (2007) Dating phylogenies with hybrid local molecular clocks. PLoS ONE, 2, e879.
    • (2007) PLoS ONE , vol.2 , pp. e879
    • Aris-Brosou, S.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. Systematic Biology, 51, 703-714.
    • (2002) Systematic Biology , vol.51 , pp. 703-714
    • Aris-Brosou, S.1    Yang, Z.2
  • 3
    • 0347356457 scopus 로고    scopus 로고
    • Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa
    • Aris-Brosou S, Yang Z, (2003) Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Molecular Biology and Evolution, 20, 1947-1954.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 1947-1954
    • Aris-Brosou, S.1    Yang, Z.2
  • 4
    • 84865475040 scopus 로고    scopus 로고
    • Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
    • Baele G, Lemey P, Bedford T, et al,. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution, 29, 2157-2167.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 2157-2167
    • Baele, G.1    Lemey, P.2    Bedford, T.3
  • 6
    • 77951997517 scopus 로고    scopus 로고
    • Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals
    • Battistuzzi FU, Filipski A, Hedges SB, Kumar S, (2010) Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Molecular Biology and Evolution, 27, 1289-1300.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 1289-1300
    • Battistuzzi, F.U.1    Filipski, A.2    Hedges, S.B.3    Kumar, S.4
  • 8
    • 73349098709 scopus 로고    scopus 로고
    • Timing of morphological and ecological innovations in the cyanobacteria-A key to understanding the rise in atmospheric oxygen
    • Blank CE, Sánchez-Baracaldo P, (2010) Timing of morphological and ecological innovations in the cyanobacteria-a key to understanding the rise in atmospheric oxygen. Geobiology, 8, 1-23.
    • (2010) Geobiology , vol.8 , pp. 1-23
    • Blank, C.E.1    Sánchez-Baracaldo, P.2
  • 11
    • 79961055146 scopus 로고    scopus 로고
    • The genome as a life-history character: Why rate of molecular evolution varies between mammal species
    • Bromham L, (2011) The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philosophical Transactions of the Royal Society of London B, 366, 2503-2513.
    • (2011) Philosophical Transactions of the Royal Society of London B , vol.366 , pp. 2503-2513
    • Bromham, L.1
  • 13
    • 84879052543 scopus 로고    scopus 로고
    • Parasitic plants have increased rates of molecular evolution across all three genomes
    • Bromham L, Cowman PF, Lanfear R, (2013) Parasitic plants have increased rates of molecular evolution across all three genomes. BMC Evolutionary Biology, 13, 126.
    • (2013) BMC Evolutionary Biology , vol.13 , pp. 126
    • Bromham, L.1    Cowman, P.F.2    Lanfear, R.3
  • 14
    • 80053362389 scopus 로고    scopus 로고
    • Rate variation and estimation of divergence times using strict and relaxed clocks
    • Brown RP, Yang Z, (2011) Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evolutionary Biology, 11, 271.
    • (2011) BMC Evolutionary Biology , vol.11 , pp. 271
    • Brown, R.P.1    Yang, Z.2
  • 16
    • 0025779286 scopus 로고
    • Synonymous nucleotide substitution rates in mammalian genes: Implications for the molecular clock and the relationship of mammalian orders
    • Bulmer M, Wolfe KH, Sharp PM, (1991) Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proceedings of the National Academy of Sciences of the USA, 88, 5974-5978.
    • (1991) Proceedings of the National Academy of Sciences of the USA , vol.88 , pp. 5974-5978
    • Bulmer, M.1    Wolfe, K.H.2    Sharp, P.M.3
  • 18
    • 0037565011 scopus 로고    scopus 로고
    • Extracting time from phylogenies: Positive interplay between fossil and genetic data
    • Conroy CJ, van Tuinen M, (2003) Extracting time from phylogenies: Positive interplay between fossil and genetic data. Journal of Mammalogy, 84, 444-455.
    • (2003) Journal of Mammalogy , vol.84 , pp. 444-455
    • Conroy, C.J.1    Van Tuinen, M.2
  • 19
    • 84855882440 scopus 로고    scopus 로고
    • Expansion dating: Calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum
    • Crandall ED, Sbrocco EJ, DeBoer TS, Barber PH, Carpenter KE, (2012) Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum. Molecular Biology and Evolution, 29, 707-719.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 707-719
    • Crandall, E.D.1    Sbrocco, E.J.2    Deboer, T.S.3    Barber, P.H.4    Carpenter, K.E.5
  • 20
    • 0034100202 scopus 로고    scopus 로고
    • Understanding the overdispersed molecular clock
    • Cutler DJ, (2000) Understanding the overdispersed molecular clock. Genetics, 154, 1403-1417.
    • (2000) Genetics , vol.154 , pp. 1403-1417
    • Cutler, D.J.1
  • 21
    • 0015162882 scopus 로고
    • The structures of cytochrome c and the rates of molecular evolution
    • Dickerson RE, (1971) The structures of cytochrome c and the rates of molecular evolution. Journal of Molecular Evolution, 1, 26-45.
    • (1971) Journal of Molecular Evolution , vol.1 , pp. 26-45
    • Dickerson, R.E.1
  • 23
    • 0001423985 scopus 로고
    • Amino-acid sequence investigations of fibrinopeptides from various mammals: Evolutionary implications
    • Doolittle RF, Blombäck B, (1964) Amino-acid sequence investigations of fibrinopeptides from various mammals: evolutionary implications. Nature, 202, 147-152.
    • (1964) Nature , vol.202 , pp. 147-152
    • Doolittle, R.F.1    Blombäck, B.2
  • 24
    • 0030023247 scopus 로고    scopus 로고
    • Determining divergence times of the major kingdoms of living organisms with a protein clock
    • Doolittle RF, Feng D-F, Tsang S, Cho G, Little E, (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science, 271, 470-477.
    • (1996) Science , vol.271 , pp. 470-477
    • Doolittle, R.F.1    Feng, D.-F.2    Tsang, S.3    Cho, G.4    Little, E.5
  • 25
    • 79959483593 scopus 로고    scopus 로고
    • Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation
    • Dornburg A, Beaulieu JM, Oliver JC, Near TJ, (2011) Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation. Systematic Biology, 60, 519-527.
    • (2011) Systematic Biology , vol.60 , pp. 519-527
    • Dornburg, A.1    Beaulieu, J.M.2    Oliver, J.C.3    Near, T.J.4
  • 26
    • 77956488734 scopus 로고    scopus 로고
    • Bayesian random local clocks, or one rate to rule them all
    • Drummond AJ, Suchard MA, (2010) Bayesian random local clocks, or one rate to rule them all. BMC Biology, 8, 114.
    • (2010) BMC Biology , vol.8 , pp. 114
    • Drummond, A.J.1    Suchard, M.A.2
  • 28
    • 17744381574 scopus 로고    scopus 로고
    • Bayesian coalescent inference of past population dynamics from molecular sequences
    • Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 1185-1192
    • Drummond, A.J.1    Rambaut, A.2    Shapiro, B.3    Pybus, O.G.4
  • 31
    • 84899622654 scopus 로고    scopus 로고
    • Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
    • Duchêne S, Ho SYW, (2014) Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data. Molecular Phylogenetics and Evolution, 77, 65-70.
    • (2014) Molecular Phylogenetics and Evolution , vol.77 , pp. 65-70
    • Duchêne, S.1    Ho, S.Y.W.2
  • 32
    • 84904666887 scopus 로고    scopus 로고
    • The impact of calibration and clock-model choice on molecular estimates of divergence times
    • Duchêne S, Lanfear R, Ho SYW, (2014a) The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phlyogenetics and Evolution, 78, 277-289.
    • (2014) Molecular Phlyogenetics and Evolution , vol.78 , pp. 277-289
    • Duchêne, S.1    Lanfear, R.2    Ho, S.Y.W.3
  • 33
    • 84897460299 scopus 로고    scopus 로고
    • ClockstaR: Choosing the number of relaxed-clock models in molecular phylogenetic analysis
    • Duchêne S, Molak M, Ho SYW, (2014b) ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics, 30, 1017-1019.
    • (2014) Bioinformatics , vol.30 , pp. 1017-1019
    • Duchêne, S.1    Molak, M.2    Ho, S.Y.W.3
  • 34
    • 0034496840 scopus 로고    scopus 로고
    • Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • Edwards SV, Beerli P, (2000) Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
    • (2000) Evolution , vol.54 , pp. 1839-1854
    • Edwards, S.V.1    Beerli, P.2
  • 35
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 36
    • 70349599032 scopus 로고    scopus 로고
    • Calibrating the Tree of Life: Fossils, molecules and evolutionary timescales
    • Forest F, (2009) Calibrating the Tree of Life: fossils, molecules and evolutionary timescales. Annals of Botany, 104, 789-794.
    • (2009) Annals of Botany , vol.104 , pp. 789-794
    • Forest, F.1
  • 37
    • 84905373684 scopus 로고    scopus 로고
    • Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data
    • Fourment M, Holmes EC, (2014) Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology, 14, 163.
    • (2014) BMC Evolutionary Biology , vol.14 , pp. 163
    • Fourment, M.1    Holmes, E.C.2
  • 40
    • 0000736067 scopus 로고    scopus 로고
    • Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
    • Gelman A, Meng X-L, (1998) Simulating normalizing constants: from importance sampling to bridge sampling to path sampling. Statistical Science, 13, 163-185.
    • (1998) Statistical Science , vol.13 , pp. 163-185
    • Gelman, A.1    Meng, X.-L.2
  • 41
    • 0024767023 scopus 로고
    • Lineage effects and the index of dispersion of molecular evolution
    • Gillespie JH, (1989) Lineage effects and the index of dispersion of molecular evolution. Molecular Biology and Evolution, 6, 636-647.
    • (1989) Molecular Biology and Evolution , vol.6 , pp. 636-647
    • Gillespie, J.H.1
  • 44
    • 77954967444 scopus 로고    scopus 로고
    • Bayesian estimation of divergence times from large sequence alignments
    • Guindon S, (2010) Bayesian estimation of divergence times from large sequence alignments. Molecular Biology and Evolution, 27, 1768-1781.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 1768-1781
    • Guindon, S.1
  • 45
    • 84871837020 scopus 로고    scopus 로고
    • From trajectories to averages: An improved description of the heterogeneity of substitution rates along lineages
    • Guindon S, (2013) From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages. Systematic Biology, 62, 22-34.
    • (2013) Systematic Biology , vol.62 , pp. 22-34
    • Guindon, S.1
  • 46
    • 38249007654 scopus 로고
    • Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea
    • Hasegawa M, Kishino H, Yano T, (1989) Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea. Journal of Human Evolution, 18, 461-476.
    • (1989) Journal of Human Evolution , vol.18 , pp. 461-476
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 47
    • 79951565662 scopus 로고    scopus 로고
    • Old taxa on young islands: A critique of the use of island age to date island-endemic clades and calibrate phylogenies
    • Heads M, (2011) Old taxa on young islands: a critique of the use of island age to date island-endemic clades and calibrate phylogenies. Systematic Biology, 60, 204-218.
    • (2011) Systematic Biology , vol.60 , pp. 204-218
    • Heads, M.1
  • 48
    • 84865256173 scopus 로고    scopus 로고
    • A hierarchical Bayesian model for calibrating estimates of species divergence times
    • Heath TA, (2012) A hierarchical Bayesian model for calibrating estimates of species divergence times. Systematic Biology, 61, 793-809.
    • (2012) Systematic Biology , vol.61 , pp. 793-809
    • Heath, T.A.1
  • 49
    • 84919710270 scopus 로고    scopus 로고
    • Bayesian inference of species divergence times
    • (eds Chen M-H, Kuo L. Lewis P.O.), CRC Press, Boca Raton, Florida
    • Heath TA, Moore BR, (2014) Bayesian inference of species divergence times. In: Bayesian Phylogenetics: Methods Algorithms, and Applications (eds, Chen M-H, Kuo L, Lewis PO,), pp. 277-318. CRC Press, Boca Raton, Florida.
    • (2014) Bayesian Phylogenetics: Methods Algorithms, and Applications , pp. 277-318
    • Heath, T.A.1    Moore, B.R.2
  • 50
    • 84857198898 scopus 로고    scopus 로고
    • A Dirichlet process prior for estimating lineage-specific substitution rates
    • Heath TA, Holder MT, Huelsenbeck JP, (2012) A Dirichlet process prior for estimating lineage-specific substitution rates. Molecular Biology and Evolution, 29, 939-955.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 939-955
    • Heath, T.A.1    Holder, M.T.2    Huelsenbeck, J.P.3
  • 52
    • 84555188625 scopus 로고    scopus 로고
    • Calibrated tree priors for relaxed phylogenetics and divergence time estimation
    • Heled J, Drummond AJ, (2012) Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Systematic Biology, 61, 138-149.
    • (2012) Systematic Biology , vol.61 , pp. 138-149
    • Heled, J.1    Drummond, A.J.2
  • 53
    • 68149148249 scopus 로고    scopus 로고
    • TreeTime: An extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
    • Himmelmann L, Metzler D, (2009) TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration. Bioinformatics, 25, 2440-2441.
    • (2009) Bioinformatics , vol.25 , pp. 2440-2441
    • Himmelmann, L.1    Metzler, D.2
  • 54
    • 84905638405 scopus 로고    scopus 로고
    • Beyond fossil calibrations: Realities of molecular clock practices in evolutionary biology
    • Hipsley CA, Müller J, (2014) Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Frontiers in Genetics, 5, 138.
    • (2014) Frontiers in Genetics , vol.5 , pp. 138
    • Hipsley, C.A.1    Müller, J.2
  • 55
    • 34347329101 scopus 로고    scopus 로고
    • Calibrating molecular estimates of substitution rates and divergence times in birds
    • Ho SYW, (2007) Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38, 409-414.
    • (2007) Journal of Avian Biology , vol.38 , pp. 409-414
    • Ho, S.Y.W.1
  • 56
    • 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. Biology Letters, 5, 421-424.
    • (2009) Biology Letters , vol.5 , pp. 421-424
    • Ho, S.Y.W.1
  • 57
    • 84906066883 scopus 로고    scopus 로고
    • The changing face of the molecular clock
    • Ho SYW, (2014) The changing face of the molecular clock. Trends in Ecology and Evolution, 29, 496-503.
    • (2014) Trends in Ecology and Evolution , vol.29 , pp. 496-503
    • Ho, S.Y.W.1
  • 58
    • 77956087396 scopus 로고    scopus 로고
    • Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
    • Ho SYW, Lanfear R, (2010) Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA, 21, 138-146.
    • (2010) Mitochondrial DNA , vol.21 , pp. 138-146
    • Ho, S.Y.W.1    Lanfear, R.2
  • 59
    • 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. Systematic Biology, 58, 367-380.
    • (2009) Systematic Biology , vol.58 , pp. 367-380
    • Ho, S.Y.W.1    Phillips, M.J.2
  • 60
    • 79954569160 scopus 로고    scopus 로고
    • Skyline-plot methods for estimating demographic history from nucleotide sequences
    • Ho SYW, Shapiro B, (2011) Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources, 11, 423-434.
    • (2011) Molecular Ecology Resources , vol.11 , pp. 423-434
    • Ho, S.Y.W.1    Shapiro, B.2
  • 61
    • 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, (2005) Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution, 22, 1355-1363.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 1355-1363
    • Ho, S.Y.W.1    Phillips, M.J.2    Drummond, A.J.3    Cooper, A.4
  • 62
    • 79960629871 scopus 로고    scopus 로고
    • Time-dependent rates of molecular evolution
    • Ho SYW, Lanfear R, Bromham L, et al,. (2011) Time-dependent rates of molecular evolution. Molecular Ecology, 20, 3087-3101.
    • (2011) Molecular Ecology , vol.20 , pp. 3087-3101
    • Ho, S.Y.W.1    Lanfear, R.2    Bromham, L.3
  • 63
    • 84919710269 scopus 로고    scopus 로고
    • Simulating and detecting autocorrelation in molecular evolutionary rates among lineages
    • in press
    • Ho SYW, Duchêne S, Duchêne D, (2014) Simulating and detecting autocorrelation in molecular evolutionary rates among lineages. Molecular Ecology Resources, in press.
    • (2014) Molecular Ecology Resources
    • Ho, S.Y.W.1    Duchêne, S.2    Duchêne, D.3
  • 64
    • 0034077901 scopus 로고    scopus 로고
    • A compound poisson process for relaxing the molecular clock
    • Huelsenbeck JP, Larget B, Swofford D, (2000) A compound poisson process for relaxing the molecular clock. Genetics, 154, 1879-1892.
    • (2000) Genetics , vol.154 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.3
  • 65
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP, (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310-2314.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 66
    • 2442671519 scopus 로고    scopus 로고
    • Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    • Huelsenbeck JP, Larget B, Alfaro ME, (2004) Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution, 21, 1123-1133.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 1123-1133
    • Huelsenbeck, J.P.1    Larget, B.2    Alfaro, M.E.3
  • 67
    • 72049121650 scopus 로고    scopus 로고
    • The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
    • Inoue J, Donoghue PC, Yang Z, (2010) The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology, 59, 74-89.
    • (2010) Systematic Biology , vol.59 , pp. 74-89
    • Inoue, J.1    Donoghue, P.C.2    Yang, Z.3
  • 68
    • 33846432342 scopus 로고
    • Some tests of significance, treated by the theory of probability
    • Jeffreys H, (1935) Some tests of significance, treated by the theory of probability. Proceedings of the Cambridge Philosophical Society, 31, 203-222.
    • (1935) Proceedings of the Cambridge Philosophical Society , vol.31 , pp. 203-222
    • Jeffreys, H.1
  • 74
    • 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. Molecular Biology and Evolution, 18, 352-361.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 75
    • 78651433454 scopus 로고    scopus 로고
    • Tectonic calibrations in molecular dating
    • Kodandaramaiah U, (2011) Tectonic calibrations in molecular dating. Current Zoology, 57, 116-124.
    • (2011) Current Zoology , vol.57 , pp. 116-124
    • Kodandaramaiah, U.1
  • 76
    • 22944437097 scopus 로고    scopus 로고
    • Molecular clocks: Four decades of evolution
    • Kumar S, (2005) Molecular clocks: four decades of evolution. Nature Reviews Genetics, 6, 654-662.
    • (2005) Nature Reviews Genetics , vol.6 , pp. 654-662
    • Kumar, S.1
  • 77
    • 79251494453 scopus 로고    scopus 로고
    • The local-clock permutation test: A simple test to compare rates of molecular evolution on phylogenetic trees
    • Lanfear R, (2011) The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees. Evolution, 65, 606-611.
    • (2011) Evolution , vol.65 , pp. 606-611
    • Lanfear, R.1
  • 78
    • 84861380450 scopus 로고    scopus 로고
    • Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
    • Lanfear R, Calcott B, Ho SYW, Guindon S, (2012) Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695-1701.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 1695-1701
    • Lanfear, R.1    Calcott, B.2    Ho, S.Y.W.3    Guindon, S.4
  • 79
    • 0016155942 scopus 로고
    • An examination of the constancy of the rate of molecular evolution
    • Langley CH, Fitch WM, (1974) An examination of the constancy of the rate of molecular evolution. Journal of Molecular Evolution, 3, 161-177.
    • (1974) Journal of Molecular Evolution , vol.3 , pp. 161-177
    • Langley, C.H.1    Fitch, W.M.2
  • 80
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • Lartillot N, Philippe H, (2006) Computing Bayes factors using thermodynamic integration. Systematic Biology, 55, 195-207.
    • (2006) Systematic Biology , vol.55 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 81
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N, Lepage T, Blanquart S, (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 25, 2286-2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 82
    • 32044457409 scopus 로고    scopus 로고
    • Continuous and tractable models for the variation of evolutionary rates
    • Lepage T, Lawi S, Tupper P, Bryant D, (2006) Continuous and tractable models for the variation of evolutionary rates. Mathematic Biosciences, 199, 216-233.
    • (2006) Mathematic Biosciences , vol.199 , pp. 216-233
    • Lepage, T.1    Lawi, S.2    Tupper, P.3    Bryant, D.4
  • 84
    • 84862908923 scopus 로고    scopus 로고
    • Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics
    • Li WL, Drummond AJ, (2012) Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Molecular Biology and Evolution, 29, 751-761.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 751-761
    • Li, W.L.1    Drummond, A.J.2
  • 85
    • 79955364420 scopus 로고    scopus 로고
    • Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence
    • Linder M, Britton T, Sennblad B, (2011) Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence. Systematic Biology, 60, 329-342.
    • (2011) Systematic Biology , vol.60 , pp. 329-342
    • Linder, M.1    Britton, T.2    Sennblad, B.3
  • 86
    • 84555194967 scopus 로고    scopus 로고
    • Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: A comparison of three approaches
    • Lukoschek V, Keogh JS, Avise JC, (2012) Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches. Systematic Biology, 61, 22-43.
    • (2012) Systematic Biology , vol.61 , pp. 22-43
    • Lukoschek, V.1    Keogh, J.S.2    Avise, J.C.3
  • 88
    • 43949092742 scopus 로고    scopus 로고
    • A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points
    • Marshall CR, (2008) A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. American Naturalist, 171, 726-742.
    • (2008) American Naturalist , vol.171 , pp. 726-742
    • Marshall, C.R.1
  • 89
    • 84901486419 scopus 로고    scopus 로고
    • A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models
    • Matari NH, Blair JE, (2014) A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models. BMC Evolutionary Biology, 14, 101.
    • (2014) BMC Evolutionary Biology , vol.14 , pp. 101
    • Matari, N.H.1    Blair, J.E.2
  • 91
    • 45849122039 scopus 로고    scopus 로고
    • Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics
    • Minin VN, Bloomquist EW, Suchard MA, (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution, 25, 1459-1471.
    • (2008) Molecular Biology and Evolution , vol.25 , pp. 1459-1471
    • Minin, V.N.1    Bloomquist, E.W.2    Suchard, M.A.3
  • 92
    • 84876022648 scopus 로고    scopus 로고
    • Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages
    • Molak M, Lorenzen ED, Shapiro B, Ho SYW, (2013) Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Molecular Biology and Evolution, 30, 253-262.
    • (2013) Molecular Biology and Evolution , vol.30 , pp. 253-262
    • Molak, M.1    Lorenzen, E.D.2    Shapiro, B.3    Ho, S.Y.W.4
  • 93
    • 84940262984 scopus 로고    scopus 로고
    • Empirical calibrated radiocarbon sampler: A tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA
    • in press
    • Molak M, Suchard MA, Ho SYW, Beilman DW, Shapiro B, (2014) Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA. Molecular Ecology Resources, in press.
    • (2014) Molecular Ecology Resources
    • Molak, M.1    Suchard, M.A.2    Ho, S.Y.W.3    Beilman, D.W.4    Shapiro, B.5
  • 94
    • 0028932702 scopus 로고
    • Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions
    • Mouchiroud D, Gautier C, Bernardi G, (1995) Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. Journal of Molecular Evolution, 40, 107-113.
    • (1995) Journal of Molecular Evolution , vol.40 , pp. 107-113
    • Mouchiroud, D.1    Gautier, C.2    Bernardi, G.3
  • 96
    • 0030984551 scopus 로고    scopus 로고
    • Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test
    • Muse SV, Gaut BS, (1997) Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genetics, 146, 393-399.
    • (1997) Genetics , vol.146 , pp. 393-399
    • Muse, S.V.1    Gaut, B.S.2
  • 97
    • 0026670564 scopus 로고
    • Testing for equality of evolutionary rates
    • Muse SV, Weir BS, (1992) Testing for equality of evolutionary rates. Genetics, 132, 269-276.
    • (1992) Genetics , vol.132 , pp. 269-276
    • Muse, S.V.1    Weir, B.S.2
  • 101
    • 84878758292 scopus 로고    scopus 로고
    • A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses
    • Nowak MD, Smith AB, Simpson C, Zwickl DJ, (2013) A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLOS ONE, 8, e66245.
    • (2013) PLOS ONE , vol.8 , pp. e66245
    • Nowak, M.D.1    Smith, A.B.2    Simpson, C.3    Zwickl, D.J.4
  • 102
    • 84877929456 scopus 로고    scopus 로고
    • Molecular dating of phylogenies by likelihood methods: A comparison of models and a new information criterion
    • Paradis E, (2013) Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Molecular Phylogenetics and Evolution, 67, 436-444.
    • (2013) Molecular Phylogenetics and Evolution , vol.67 , pp. 436-444
    • Paradis, E.1
  • 103
    • 84863116561 scopus 로고    scopus 로고
    • Best practices for justifying fossil calibrations
    • Parham JF, Donoghue PC, Bell CJ, et al,. (2012) Best practices for justifying fossil calibrations. Systematic Biology, 61, 346-359.
    • (2012) Systematic Biology , vol.61 , pp. 346-359
    • Parham, J.F.1    Donoghue, P.C.2    Bell, C.J.3
  • 104
    • 33750562341 scopus 로고    scopus 로고
    • Application of molecular clocks in ornithology revisited
    • Peterson AT, (2006) Application of molecular clocks in ornithology revisited. Journal of Avian Biology, 37, 541-544.
    • (2006) Journal of Avian Biology , vol.37 , pp. 541-544
    • Peterson, A.T.1
  • 105
    • 73349140515 scopus 로고    scopus 로고
    • Quantitative prediction of molecular clock and ka/ks at short timescales
    • Peterson GI, Masel J, (2009) Quantitative prediction of molecular clock and ka/ks at short timescales. Molecular Biology and Evolution, 26, 2595-2603.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 2595-2603
    • Peterson, G.I.1    Masel, J.2
  • 106
    • 79959381301 scopus 로고    scopus 로고
    • Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia
    • Pyron RA, (2011) Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466-481.
    • (2011) Systematic Biology , vol.60 , pp. 466-481
    • Pyron, R.A.1
  • 107
    • 0034044313 scopus 로고    scopus 로고
    • Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies
    • Rambaut A, (2000) Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics, 16, 395-399.
    • (2000) Bioinformatics , vol.16 , pp. 395-399
    • Rambaut, A.1
  • 108
    • 0036803348 scopus 로고    scopus 로고
    • Identifiability of parameters in MCMC Bayesian inference of phylogeny
    • Rannala B, (2002) Identifiability of parameters in MCMC Bayesian inference of phylogeny. Systematic Biology, 51, 754-760.
    • (2002) Systematic Biology , vol.51 , pp. 754-760
    • Rannala, B.1
  • 109
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B, Yang Z, (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 43, 304-311.
    • (1996) Journal of Molecular Evolution , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 110
    • 34548556039 scopus 로고    scopus 로고
    • Inferring speciation times under an episodic molecular clock
    • Rannala B, Yang Z, (2007) Inferring speciation times under an episodic molecular clock. Systematic Biology, 56, 453-466.
    • (2007) Systematic Biology , vol.56 , pp. 453-466
    • Rannala, B.1    Yang, Z.2
  • 111
    • 79959462209 scopus 로고    scopus 로고
    • Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
    • dos Reis M, Yang Z, (2011) Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Molecular Biology and Evolution, 28, 2161-2172.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2161-2172
    • Dos Reis, M.1    Yang, Z.2
  • 112
    • 84873505893 scopus 로고    scopus 로고
    • The unbearable uncertainty of Bayesian divergence time estimation
    • dos Reis M, Yang Z, (2013) The unbearable uncertainty of Bayesian divergence time estimation. Journal of Systematics and Evolution, 51, 30-43.
    • (2013) Journal of Systematics and Evolution , vol.51 , pp. 30-43
    • Dos Reis, M.1    Yang, Z.2
  • 113
    • 84864346710 scopus 로고    scopus 로고
    • Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
    • dos Reis M, Inoue J, Hasegawa M, et al,. (2012) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proceedings of the Royal Society of London B, 279, 3491-3500.
    • (2012) Proceedings of the Royal Society of London B , vol.279 , pp. 3491-3500
    • Dos Reis, M.1    Inoue, J.2    Hasegawa, M.3
  • 114
    • 84902457782 scopus 로고    scopus 로고
    • The impact of the rate prior on Bayesian estimation of divergence times with multiple loci
    • dos Reis M, Zhu T, Yang Z, (2014) The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Systematic Biology, 63, 555-565.
    • (2014) Systematic Biology , vol.63 , pp. 555-565
    • Dos Reis, M.1    Zhu, T.2    Yang, Z.3
  • 115
    • 84860159826 scopus 로고    scopus 로고
    • A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera
    • Ronquist F, Klopfstein S, Vilhelmsen L, et al,. (2012a) A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Systematic Biology, 61, 973-999.
    • (2012) Systematic Biology , vol.61 , pp. 973-999
    • Ronquist, F.1    Klopfstein, S.2    Vilhelmsen, L.3
  • 116
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F, Teslenko M, van der Mark P, et al,. (2012b) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539-542.
    • (2012) Systematic Biology , vol.61 , pp. 539-542
    • Ronquist, F.1    Teslenko, M.2    Van Der Mark, P.3
  • 117
    • 0020386088 scopus 로고
    • A molecular-clock date for the origin of the animal phyla
    • Runnegar B, (1982) A molecular-clock date for the origin of the animal phyla. Lethaia, 15, 199-205.
    • (1982) Lethaia , vol.15 , pp. 199-205
    • Runnegar, B.1
  • 118
    • 33645030825 scopus 로고    scopus 로고
    • Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times
    • Rutschmann F, (2006) Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions, 12, 35-48.
    • (2006) Diversity and Distributions , vol.12 , pp. 35-48
    • Rutschmann, F.1
  • 119
    • 34547468349 scopus 로고    scopus 로고
    • Assessing calibration uncertainty in molecular dating: The assignment of fossils to alternative calibration points
    • Rutschmann F, Eriksson T, Salim KA, Conti E, (2007) Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points. Systematic Biology, 56, 591-608.
    • (2007) Systematic Biology , vol.56 , pp. 591-608
    • Rutschmann, F.1    Eriksson, T.2    Salim, K.A.3    Conti, E.4
  • 120
    • 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. Molecular Biology and Evolution, 14, 1218-1231.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 1218-1231
    • Sanderson, M.J.1
  • 121
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • Sanderson MJ, (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101-109.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 122
    • 0037314098 scopus 로고    scopus 로고
    • R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson MJ, (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19, 301-302.
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 123
    • 84887774902 scopus 로고    scopus 로고
    • A practical guide to molecular dating
    • Sauquet H, (2013) A practical guide to molecular dating. Comptes Rendus Palevol, 12, 355-367.
    • (2013) Comptes Rendus Palevol , vol.12 , pp. 355-367
    • Sauquet, H.1
  • 124
    • 84863116093 scopus 로고    scopus 로고
    • Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of Nothofagus (Fagales)
    • Sauquet H, Ho SYW, Gandolfo MA, et al,. (2012) Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Systematic Biology, 61, 289-313.
    • (2012) Systematic Biology , vol.61 , pp. 289-313
    • Sauquet, H.1    Ho, S.Y.W.2    Gandolfo, M.A.3
  • 125
    • 78751478795 scopus 로고    scopus 로고
    • A Bayesian phylogenetic method to estimate unknown sequence ages
    • Shapiro B, Ho SYW, Drummond AJ, et al,. (2011) A Bayesian phylogenetic method to estimate unknown sequence ages. Molecular Biology and Evolution, 28, 879-887.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 879-887
    • Shapiro, B.1    Ho, S.Y.W.2    Drummond, A.J.3
  • 126
    • 0037227363 scopus 로고    scopus 로고
    • Partitioning the variation in mammalian substitution rates
    • Smith NG, Eyre-Walker A, (2003) Partitioning the variation in mammalian substitution rates. Molecular Biology and Evolution, 20, 10-17.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 10-17
    • Smith, N.G.1    Eyre-Walker, A.2
  • 127
    • 84870458929 scopus 로고    scopus 로고
    • TreePL: Divergence time estimation using penalized likelihood for large phylogenies
    • Smith SA, O'Meara BC, (2012) treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics, 28, 2689-2690.
    • (2012) Bioinformatics , vol.28 , pp. 2689-2690
    • Smith, S.A.1    O'Meara, B.C.2
  • 129
    • 77958152206 scopus 로고    scopus 로고
    • Sampling-through-time in birth-death trees
    • Stadler T, (2010) Sampling-through-time in birth-death trees. Journal of Theoretical Biology, 267, 396-404.
    • (2010) Journal of Theoretical Biology , vol.267 , pp. 396-404
    • Stadler, T.1
  • 130
    • 84882808862 scopus 로고    scopus 로고
    • Dating phylogenies with sequentially sampled tips
    • Stadler T, Yang Z, (2013) Dating phylogenies with sequentially sampled tips. Systematic Biology, 62, 674-688.
    • (2013) Systematic Biology , vol.62 , pp. 674-688
    • Stadler, T.1    Yang, Z.2
  • 131
    • 84865146139 scopus 로고    scopus 로고
    • RAxML-Light: A tool for computing terabyte phylogenies
    • Stamatakis A, Aberer AJ, Goll C, et al,. (2012) RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics, 28, 2064-2066.
    • (2012) Bioinformatics , vol.28 , pp. 2064-2066
    • Stamatakis, A.1    Aberer, A.J.2    Goll, C.3
  • 132
    • 19444384196 scopus 로고    scopus 로고
    • Should phylogenetic models be trying to 'fit an elephant'?
    • Steel M, (2005) Should phylogenetic models be trying to 'fit an elephant'? Trends in Genetics, 21, 307-309.
    • (2005) Trends in Genetics , vol.21 , pp. 307-309
    • Steel, M.1
  • 135
    • 65349177267 scopus 로고    scopus 로고
    • Microsatellites are molecular clocks that support accurate inferences about history
    • Sun JX, Mullikin JC, Patterson N, Reich DE, (2009) Microsatellites are molecular clocks that support accurate inferences about history. Molecular Biology and Evolution, 26, 1017-1027.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 1017-1027
    • Sun, J.X.1    Mullikin, J.C.2    Patterson, N.3    Reich, D.E.4
  • 136
    • 0023337434 scopus 로고
    • On the overdispersed molecular clock
    • Takahata N, (1987) On the overdispersed molecular clock. Genetics, 116, 169-179.
    • (1987) Genetics , vol.116 , pp. 169-179
    • Takahata, N.1
  • 139
    • 0036803223 scopus 로고    scopus 로고
    • Divergence time and evolutionary rate estimation with multilocus data
    • Thorne JL, Kishino H, (2002) Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology, 51, 689-702.
    • (2002) Systematic Biology , vol.51 , pp. 689-702
    • Thorne, J.L.1    Kishino, H.2
  • 140
    • 30144435978 scopus 로고    scopus 로고
    • Estimation of divergence times from molecular sequence data
    • (ed. Nielsen R.), Springer Verlag, New York
    • Thorne JL, Kishino H, (2005) Estimation of divergence times from molecular sequence data. In: Statistical Methods in Molecular Evolution (ed., Nielsen R,), pp. 235-256. Springer Verlag, New York.
    • (2005) Statistical Methods in Molecular Evolution , pp. 235-256
    • Thorne, J.L.1    Kishino, H.2
  • 141
    • 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. Molecular Biology and Evolution, 15, 1647-1657.
    • (1998) Molecular Biology and Evolution , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 142
    • 84857233832 scopus 로고    scopus 로고
    • Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae
    • Thornhill AH, Popple LW, Carter RJ, Ho SYW, Crisp MD, (2012) Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Molecular Phylogenetics and Evolution, 63, 15-27.
    • (2012) Molecular Phylogenetics and Evolution , vol.63 , pp. 15-27
    • Thornhill, A.H.1    Popple, L.W.2    Carter, R.J.3    Ho, S.Y.W.4    Crisp, M.D.5
  • 143
    • 78650476811 scopus 로고    scopus 로고
    • A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
    • Wang M, Jiang YY, Kim KM, et al,. (2011) A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Molecular Biology and Evolution, 28, 567-582.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 567-582
    • Wang, M.1    Jiang, Y.Y.2    Kim, K.M.3
  • 144
    • 84863012163 scopus 로고    scopus 로고
    • Exploring uncertainty in the calibration of the molecular clock
    • Warnock RC, Yang Z, Donoghue PC, (2012) Exploring uncertainty in the calibration of the molecular clock. Biology Letters, 8, 156-159.
    • (2012) Biology Letters , vol.8 , pp. 156-159
    • Warnock, R.C.1    Yang, Z.2    Donoghue, P.C.3
  • 146
    • 25144502293 scopus 로고    scopus 로고
    • Molecular dates for the "cambrian explosion": The influence of prior assumptions
    • Welch JJ, Fontanillas E, Bromham L, (2005) Molecular dates for the "Cambrian explosion": the influence of prior assumptions. Systematic Biology, 54, 672-678.
    • (2005) Systematic Biology , vol.54 , pp. 672-678
    • Welch, J.J.1    Fontanillas, E.2    Bromham, L.3
  • 147
    • 69149111299 scopus 로고    scopus 로고
    • As time goes by: A simple fool's guide to molecular clock approaches in invertebrates
    • Wilke T, Schultheiss R, Albrecht C, (2009) As time goes by: a simple fool's guide to molecular clock approaches in invertebrates. American Malacological Bulletin, 27, 25-45.
    • (2009) American Malacological Bulletin , vol.27 , pp. 25-45
    • Wilke, T.1    Schultheiss, R.2    Albrecht, C.3
  • 148
    • 79952158855 scopus 로고    scopus 로고
    • Dating primate divergences through an integrated analysis of palaeontological and molecular data
    • Wilkinson RD, Steiper ME, Soligo C, et al,. (2011) Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology, 60, 16-31.
    • (2011) Systematic Biology , vol.60 , pp. 16-31
    • Wilkinson, R.D.1    Steiper, M.E.2    Soligo, C.3
  • 149
    • 84891687862 scopus 로고    scopus 로고
    • Stability along with extreme variability in core genome evolution
    • Wolf YI, Snir S, Koonin EV, (2013) Stability along with extreme variability in core genome evolution. Genome Biology and Evolution, 5, 1393-1402.
    • (2013) Genome Biology and Evolution , vol.5 , pp. 1393-1402
    • Wolf, Y.I.1    Snir, S.2    Koonin, E.V.3
  • 150
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe KH, Li WH, Sharp PM, (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the USA, 84, 9054-9058.
    • (1987) Proceedings of the National Academy of Sciences of the USA , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.H.2    Sharp, P.M.3
  • 151
    • 84900337125 scopus 로고    scopus 로고
    • A synchronized global sweep of the internal genes of modern avian influenza virus
    • Worobey M, Han GZ, Rambaut A, (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature, 508, 254-257.
    • (2014) Nature , vol.508 , pp. 254-257
    • Worobey, M.1    Han, G.Z.2    Rambaut, A.3
  • 153
    • 79955119965 scopus 로고    scopus 로고
    • A distance-based least-square method for dating speciation events
    • Xia X, Yang Q, (2011) A distance-based least-square method for dating speciation events. Molecular Phlyogenetics and Evolution, 59, 342-353.
    • (2011) Molecular Phlyogenetics and Evolution , vol.59 , pp. 342-353
    • Xia, X.1    Yang, Q.2
  • 154
    • 79951566251 scopus 로고    scopus 로고
    • Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie W, Lewis PO, Fan Y, Kuo L, Chen MH, (2011) Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology, 60, 150-160.
    • (2011) Systematic Biology , vol.60 , pp. 150-160
    • Xie, W.1    Lewis, P.O.2    Fan, Y.3    Kuo, L.4    Chen, M.H.5
  • 155
    • 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. Journal of Molecular Evolution, 39, 306-314.
    • (1994) Journal of Molecular Evolution , vol.39 , pp. 306-314
    • Yang, Z.1
  • 156
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang Z, (1996) Maximum-likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution, 42, 587-596.
    • (1996) Journal of Molecular Evolution , vol.42 , pp. 587-596
    • Yang, Z.1
  • 157
    • 20144385989 scopus 로고    scopus 로고
    • A heuristic rate smoothing procedure for maximum likelihood estimtion of species divergence times
    • Yang Z, (2004) A heuristic rate smoothing procedure for maximum likelihood estimtion of species divergence times. Acta Zoologica Sinica, 50, 645-656.
    • (2004) Acta Zoologica Sinica , vol.50 , pp. 645-656
    • Yang, Z.1
  • 158
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z, (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586-1591.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 160
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • Yang Z, Rannala B, (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molecular Biology and Evolution, 17, 717-724.
    • (1997) Molecular Biology and Evolution , vol.17 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 161
    • 28944451210 scopus 로고    scopus 로고
    • Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
    • Yang Z, Rannala B, (2006) Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution, 23, 212-226.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 212-226
    • Yang, Z.1    Rannala, B.2
  • 162
    • 0033933640 scopus 로고    scopus 로고
    • Estimation of primate speciation dates using local molecular clocks
    • Yoder AD, Yang Z, (2000) Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution, 17, 1081-1090.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 1081-1090
    • Yoder, A.D.1    Yang, Z.2
  • 163
    • 0001778604 scopus 로고
    • A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S
    • Yule GU, (1924) A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S. Philosophical Transactions of the Royal Society of London B, 213, 21-87.
    • (1924) Philosophical Transactions of the Royal Society of London B , vol.213 , pp. 21-87
    • Yule, G.U.1
  • 164
    • 0017227120 scopus 로고
    • Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins
    • Zuckerkandl E, (1976) Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. Journal of Molecular Evolution, 7, 167-183.
    • (1976) Journal of Molecular Evolution , vol.7 , pp. 167-183
    • Zuckerkandl, E.1
  • 165
    • 0002331493 scopus 로고
    • Molecular disease, evolution, and genic heterogeneity
    • (eds Kasha M. Pullman B.), Academic Press, New York, USA
    • Zuckerkandl E, Pauling L, (1962) Molecular disease, evolution, and genic heterogeneity. In: Horizons in Biochemistry (eds, Kasha M, Pullman B,), pp. 189-225. Academic Press, New York, USA.
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2
  • 166
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • (eds Bryson V. Vogek H.J.), Academic Press, New York
    • Zuckerkandl E, Pauling L, (1965) Evolutionary divergence and convergence in proteins. In: Evolving Genes and Proteins (eds, Bryson V, Vogek HJ,), pp. 97-166. Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2


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