메뉴 건너뛰기




Volumn 109, Issue 47, 2012, Pages 19333-19338

Estimating divergence times in large molecular phylogenies

Author keywords

Bioinformatics; Relaxed clocks; Timescales

Indexed keywords

NUCLEOTIDE;

EID: 84869752137     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1213199109     Document Type: Article
Times cited : (494)

References (43)
  • 1
    • 84859206090 scopus 로고    scopus 로고
    • Many neglected tropical diseases may have originated in the Paleolithic or before: New insights from genetics
    • Trueba G, Dunthorn M (2012) Many neglected tropical diseases may have originated in the Paleolithic or before: New insights from genetics. PLoS Negl Trop Dis 6(3):e1393.
    • (2012) PLoS Negl Trop Dis , vol.6 , Issue.3
    • Trueba, G.1    Dunthorn, M.2
  • 2
    • 79960130696 scopus 로고    scopus 로고
    • TimeTree2: Species divergence times on the iPhone
    • Kumar S, Hedges SB (2011) TimeTree2: Species divergence times on the iPhone. Bioinformatics 27(14):2023-2024.
    • (2011) Bioinformatics , vol.27 , Issue.14 , pp. 2023-2024
    • Kumar, S.1    Hedges, S.B.2
  • 3
    • 82255195530 scopus 로고    scopus 로고
    • The Cambrian conundrum: Early divergence and later ecological success in the early history of animals
    • Erwin DH, et al. (2011) The Cambrian conundrum: Early divergence and later ecological success in the early history of animals. Science 334(6059):1091-1097.
    • (2011) Science , vol.334 , Issue.6059 , pp. 1091-1097
    • Erwin, D.H.1
  • 4
    • 80055070300 scopus 로고    scopus 로고
    • Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
    • Meredith RW, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334(6055):521-524.
    • (2011) Science , vol.334 , Issue.6055 , pp. 521-524
    • Meredith, R.W.1
  • 5
    • 70349298549 scopus 로고    scopus 로고
    • eds Hedges SB, Kumar S (Oxford Univ Press, New York)
    • Hedges SB, Kumar S (2009) The Timetree of Life, eds Hedges SB, Kumar S (Oxford Univ Press, New York).
    • (2009) The Timetree of Life
    • Hedges, S.B.1    Kumar, S.2
  • 6
    • 80052179542 scopus 로고    scopus 로고
    • Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times
    • Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S (2011) Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol 28(9):2439-2442.
    • (2011) Mol Biol Evol , vol.28 , Issue.9 , pp. 2439-2442
    • Battistuzzi, F.U.1    Billing-Ross, P.2    Paliwal, A.3    Kumar, S.4
  • 7
    • 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. Mol Biol Evol 28(7):2161-2172.
    • (2011) Mol Biol Evol , vol.28 , Issue.7 , pp. 2161-2172
    • Dos Reis, M.1    Yang, Z.2
  • 8
    • 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(12):1647-1657.
    • (1998) Mol Biol Evol , vol.15 , Issue.12 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 9
    • 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. Syst Biol 51(5):689-702.
    • (2002) Syst Biol , vol.51 , Issue.5 , pp. 689-702
    • Thorne, J.L.1    Kishino, H.2
  • 11
    • 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
  • 12
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang ZH (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586-1591.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.H.1
  • 13
    • 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(12):2669-2680.
    • (2007) Mol Biol Evol , vol.24 , Issue.12 , pp. 2669-2680
    • Lepage, T.1    Bryant, D.2    Philippe, H.3    Lartillot, N.4
  • 14
    • 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(3):421-424.
    • (2009) Biol Lett , vol.5 , Issue.3 , pp. 421-424
    • Ho, S.Y.W.1
  • 15
    • 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. Mol Biol Evol 27(6):1289-1300.
    • (2010) Mol Biol Evol , vol.27 , Issue.6 , pp. 1289-1300
    • Battistuzzi, F.U.1    Filipski, A.2    Hedges, S.B.3    Kumar, S.4
  • 16
    • 79960629871 scopus 로고    scopus 로고
    • Time-dependent rates of molecular evolution
    • Ho SYW, et al. (2011) Time-dependent rates of molecular evolution. Mol Ecol 20(15):3087-3101.
    • (2011) Mol Ecol , vol.20 , Issue.15 , pp. 3087-3101
    • Ho, S.Y.W.1
  • 17
    • 1942422549 scopus 로고    scopus 로고
    • Precision of molecular time estimates
    • Hedges SB, Kumar S (2004) Precision of molecular time estimates. Trends Genet 20(5):242-247.
    • (2004) Trends Genet , vol.20 , Issue.5 , pp. 242-247
    • Hedges, S.B.1    Kumar, S.2
  • 18
    • 70350116756 scopus 로고    scopus 로고
    • Calibrating and constraining molecular clocks
    • eds Hedges SB, Kumar S (Oxford Univ Press, New York)
    • Benton MJ, Donoghue PCJ, Asher RJ (2009) Calibrating and constraining molecular clocks. The Timetree of Life, eds Hedges SB, Kumar S (Oxford Univ Press, New York), pp 35-86.
    • (2009) The Timetree of Life , pp. 35-86
    • Benton, M.J.1    Donoghue, P.C.J.2    Asher, R.J.3
  • 19
    • 84863116561 scopus 로고    scopus 로고
    • Best practices for justifying fossil calibrations
    • Parham JF, et al. (2012) Best practices for justifying fossil calibrations. Syst Biol 61(2):346-359.
    • (2012) Syst Biol , vol.61 , Issue.2 , pp. 346-359
    • Parham, J.F.1
  • 20
    • 33747798028 scopus 로고    scopus 로고
    • The origin and diversification of eukaryotes: Problems with molecular phylogenetics and molecular clock estimation
    • Roger AJ, Hug LA (2006) The origin and diversification of eukaryotes: Problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci 361(1470):1039-1054.
    • (2006) Philos Trans R Soc Lond B Biol Sci , vol.361 , Issue.1470 , pp. 1039-1054
    • Roger, A.J.1    Hug, L.A.2
  • 21
    • 34547762740 scopus 로고    scopus 로고
    • The impact of fossils and taxon sampling on ancient molecular dating analyses
    • Hug LA, Roger AJ (2007) The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol Biol Evol 24(8):1889-1897.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1889-1897
    • Hug, L.A.1    Roger, A.J.2
  • 22
    • 8144221423 scopus 로고    scopus 로고
    • Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
    • Near TJ, Sanderson MJ (2004) Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Philos Trans R Soc Lond B Biol Sci 359(1450):1477-1483.
    • (2004) Philos Trans R Soc Lond B Biol Sci , vol.359 , Issue.1450 , pp. 1477-1483
    • Near, T.J.1    Sanderson, M.J.2
  • 23
    • 13944259078 scopus 로고    scopus 로고
    • Assessing concordance of fossil calibration points in molecular clock studies: An example using turtles
    • Near TJ, Meylan PA, Shaffer HB (2005) Assessing concordance of fossil calibration points in molecular clock studies: An example using turtles. Am Nat 165(2):137-146.
    • (2005) Am Nat , vol.165 , Issue.2 , pp. 137-146
    • Near, T.J.1    Meylan, P.A.2    Shaffer, H.B.3
  • 24
    • 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(3):367-380.
    • (2009) Syst Biol , vol.58 , Issue.3 , pp. 367-380
    • Ho, S.Y.W.1    Phillips, M.J.2
  • 25
    • 72049121650 scopus 로고    scopus 로고
    • The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
    • Inoue J, Donoghue PCJ, Yang Z (2010) The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol 59(1):74-89.
    • (2010) Syst Biol , vol.59 , Issue.1 , pp. 74-89
    • Inoue, J.1    Donoghue, P.C.J.2    Yang, Z.3
  • 26
    • 80052346740 scopus 로고    scopus 로고
    • Establishing a time-scale for plant evolution
    • Clarke JT, Warnock RCM, Donoghue PCJ (2011) Establishing a time-scale for plant evolution. New Phytol 192(1):266-301.
    • (2011) New Phytol , vol.192 , Issue.1 , pp. 266-301
    • Clarke, J.T.1    Warnock, R.C.M.2    Donoghue, P.C.J.3
  • 27
    • 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. Syst Biol 60(4):519-527.
    • (2011) Syst Biol , vol.60 , Issue.4 , pp. 519-527
    • Dornburg, A.1    Beaulieu, J.M.2    Oliver, J.C.3    Near, T.J.4
  • 28
    • 0004128472 scopus 로고
    • Cambridge Univ Press, Cambridge, UK
    • Edwards AWF (1972) Likelihood (Cambridge Univ Press, Cambridge, UK).
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 30
    • 0028151465 scopus 로고
    • Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes
    • Shimmin LC, Chang BH, Li WH (1994) Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes. J Mol Evol 39(6):569-578.
    • (1994) J Mol Evol , vol.39 , Issue.6 , pp. 569-578
    • Shimmin, L.C.1    Chang, B.H.2    Li, W.H.3
  • 31
    • 0037572240 scopus 로고    scopus 로고
    • Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx, and Zfa in the mouse genus Mus
    • Tucker PK, Adkins RM, Rest JS (2003) Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx, and Zfa in the mouse genus Mus. Mol Biol Evol 20 (6):999-1005.
    • (2003) Mol Biol Evol , vol.20 , Issue.6 , pp. 999-1005
    • Tucker, P.K.1    Adkins, R.M.2    Rest, J.S.3
  • 32
    • 38349150505 scopus 로고    scopus 로고
    • Fast genes and slow clades: Comparative rates of molecular evolution in mammals
    • Bininda-Emonds ORP (2007) Fast genes and slow clades: Comparative rates of molecular evolution in mammals. Evol Bioinform Online 3:59-85.
    • (2007) Evol Bioinform Online , vol.3 , pp. 59-85
    • Bininda-Emonds, O.R.P.1
  • 33
    • 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. Mol Biol Evol 19(1):101-109.
    • (2002) Mol Biol Evol , vol.19 , Issue.1 , pp. 101-109
    • Sanderson, M.J.1
  • 34
    • 0032580152 scopus 로고    scopus 로고
    • A molecular timescale for vertebrate evolution
    • Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392(6679):917-920.
    • (1998) Nature , vol.392 , Issue.6679 , pp. 917-920
    • Kumar, S.1    Hedges, S.B.2
  • 35
    • 0037227485 scopus 로고    scopus 로고
    • The temporal distribution of gene duplication events in a set of highly conserved human gene families
    • Friedman R, Hughes AL (2003) The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 20(1):154-161.
    • (2003) Mol Biol Evol , vol.20 , Issue.1 , pp. 154-161
    • Friedman, R.1    Hughes, A.L.2
  • 36
    • 23744452485 scopus 로고    scopus 로고
    • Estimating the tempo and mode of gene family evolution from comparative genomic data
    • Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15 (8):1153-1160.
    • (2005) Genome Res , vol.15 , Issue.8 , pp. 1153-1160
    • Hahn, M.W.1    De Bie, T.2    Stajich, J.E.3    Nguyen, C.4    Cristianini, N.5
  • 37
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: How duplicated genes find new functions
    • Conant GC, Wolfe KH (2008) Turning a hobby into a job: How duplicated genes find new functions. Nat Rev Genet 9(12):938-950.
    • (2008) Nat Rev Genet , vol.9 , Issue.12 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 38
    • 0037387372 scopus 로고    scopus 로고
    • Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference
    • Rosenberg MS, Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol 20(4):610-621.
    • (2003) Mol Biol Evol , vol.20 , Issue.4 , pp. 610-621
    • Rosenberg, M.S.1    Kumar, S.2
  • 39
    • 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(3):352-361.
    • (2001) Mol Biol Evol , vol.18 , Issue.3 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 40
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A, Grassly NC (1997) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 13(3):235-238.
    • (1997) Comput Appl Biosci , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 41
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano TA (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22(2):160-174.
    • (1985) J Mol Evol , vol.22 , Issue.2 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.A.3
  • 42
    • 72649094717 scopus 로고    scopus 로고
    • Discovering the timetree of life
    • Oxford Univ Press, New York
    • Hedges SB, Kumar S (2009) Discovering the timetree of life. The Timetree of Life (Oxford Univ Press, New York), pp 3-18.
    • (2009) The Timetree of Life , pp. 3-18
    • Hedges, S.B.1    Kumar, S.2
  • 43
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739.
    • (2011) Mol Biol Evol , vol.28 , Issue.10 , pp. 2731-2739
    • Tamura, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.