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Volumn 371, Issue 1699, 2016, Pages

Bayesian phylogenetic estimation of fossil ages

Author keywords

Bayesian phylogenetics; Divergence time dating; Fossil dating; Morphological clock; Morphological evolution; Phylogenetic inference

Indexed keywords

BAYESIAN ANALYSIS; DATING METHOD; DIVERGENCE; FOSSIL RECORD; MOLECULAR ANALYSIS; MORPHOLOGY; PHYLOGENETICS; PROBABILITY;

EID: 84975230911     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2015.0129     Document Type: Article
Times cited : (22)

References (44)
  • 1
    • 34447333669 scopus 로고    scopus 로고
    • Rocks and clocks: Calibrating the Tree of Life using fossils and molecules
    • Donoghue PCJ, Benton MJ. 2007 Rocks and clocks: calibrating the Tree of Life using fossils and molecules. Trends Ecol. Evol. 22, 424-431. (doi:10. 1016/j.tree.2007.05.005)
    • (2007) Trends Ecol. Evol , vol.22 , pp. 424-431
    • Donoghue, P.C.J.1    Benton, M.J.2
  • 2
    • 0037373563 scopus 로고    scopus 로고
    • The modern molecular clock
    • Bromham L, Penny D. 2003 The modern molecular clock. Nat. Rev. Genet. 4, 216-224. (doi:10.1038/ nrg1020)
    • (2003) Nat. Rev. Genet , vol.4 , pp. 216-224
    • Bromham, L.1    Penny, D.2
  • 3
    • 0038518200 scopus 로고    scopus 로고
    • Dating the tree of life
    • Benton MJ, Ayala FJ. 2003 Dating the tree of life. Science 300, 1698-1700. (doi:10.1126/science. 1077795)
    • (2003) Science , vol.300 , pp. 1698-1700
    • Benton, M.J.1    Ayala, F.J.2
  • 6
    • 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. (doi:10.1093/sysbio/syp035)
    • (2009) Syst. Biol , vol.58 , pp. 367-380
    • Ho, S.1    Phillips, M.J.2
  • 7
    • 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. Syst. Biol. 61, 138-149. (doi:10.1093/ sysbio/syr087)
    • (2012) Syst. Biol , vol.61 , pp. 138-149
    • Heled, J.1    Drummond, A.J.2
  • 8
    • 84929584290 scopus 로고    scopus 로고
    • Calibrated birth-death phylogenetic time-tree priors for Bayesian inference
    • Heled J, Drummond AJ. 2015 Calibrated birth-death phylogenetic time-tree priors for Bayesian inference. Syst. Biol. 64, 369-383. (doi:10.1093/sysbio/syu089)
    • (2015) Syst. Biol , vol.64 , pp. 369-383
    • Heled, J.1    Drummond, A.J.2
  • 9
    • 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. (doi:10. 1093/oxfordjournals.molbev.a025892)
    • (1998) Mol. Biol. Evol , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 10
    • 30144435978 scopus 로고    scopus 로고
    • Estimation of divergence times from molecular sequence data
    • (ed. R Nielsen, Berlin, Germany: Springer
    • Thorne JL, Kishino H. 2005 Estimation of divergence times from molecular sequence data. In Statistical methods in molecular evolution (ed. R Nielsen), pp. 233-256. Berlin, Germany: Springer.
    • (2005) Statistical Methods in Molecular Evolution , pp. 233-256
    • Thorne, J.L.1    Kishino, H.2
  • 11
    • 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. Mol. Biol. Evol. 23, 212-226. (doi:10.1093/ molbev/msj024)
    • (2006) Mol. Biol. Evol , vol.23 , pp. 212-226
    • Yang, Z.1    Rannala, B.2
  • 12
    • 33344465800 scopus 로고    scopus 로고
    • Relaxed phylogenetics and dating with confidence
    • Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi:10.1371/ journal.pbio.0040088)
    • (2006) Plos Biol , pp. 4
    • Drummond, A.J.1    Ho, S.2    Phillips, M.J.3    Rambaut, A.4
  • 13
    • 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 Biol. 8, 114. (doi:10.1186/1741-7007-8-114)
    • (2010) BMC Biol , vol.8 , pp. 114
    • Drummond, A.J.1    Suchard, M.A.2
  • 14
    • 0030456553 scopus 로고    scopus 로고
    • On the probability of ancestors in the fossil record
    • Foote M. 1996 On the probability of ancestors in the fossil record. Paleobiology 22, 141-151.
    • (1996) Paleobiology , vol.22 , pp. 141-151
    • Foote, M.1
  • 15
    • 0030776127 scopus 로고    scopus 로고
    • Maximum likelihood estimation of phylogeny using stratigraphic data
    • Huelsenbeck JP, Rannala B. 1997 Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 23, 174-180.
    • (1997) Paleobiology , vol.23 , pp. 174-180
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 16
    • 0037129204 scopus 로고    scopus 로고
    • Using the fossil record to estimate the age of the last common ancestor of extant primates
    • Tavaré S, Marshall CR, Will O, Soligo C, Martin RD. 2002 Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416, 726-729. (doi:10.1038/416726a)
    • (2002) Nature , vol.416 , pp. 726-729
    • Tavaré, S.1    Marshall, C.R.2    Will, O.3    Soligo, C.4    Martin, R.D.5
  • 17
    • 84881583545 scopus 로고    scopus 로고
    • Modelling distributions of fossil sampling rates over time, space and taxa: Assessment and implications for macroevolutionary studies
    • Wagner PJ, Marcot JD. 2013 Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies. Methods Ecol. Evol. 4, 703-713. (doi:10. 1111/2041-210X.12088)
    • (2013) Methods Ecol. Evol , vol.4 , pp. 703-713
    • Wagner, P.J.1    Marcot, J.D.2
  • 20
    • 84892572735 scopus 로고    scopus 로고
    • A mitochondrial genome sequence of a hominin from Sima de los Huesos
    • Meyer M et al. 2014 A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403-406. (doi:10.1038/nature12788)
    • (2014) Nature , vol.505 , pp. 403-406
    • Meyer, M.1
  • 22
    • 84919628839 scopus 로고    scopus 로고
    • Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration
    • Gavryushkina A, Welch D, Stadler T, Drummond AJ. 2014 Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput. Biol. 10, e1003919. (doi:10.1371/journal.pcbi. 1003919)
    • (2014) Plos Comput. Biol , pp. 10
    • Gavryushkina, A.1    Welch, D.2    Stadler, T.3    Drummond, A.J.4
  • 24
    • 84966603244 scopus 로고    scopus 로고
    • Total-Evidence dating under the fossilized birth–death process
    • Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F. 2016 Total-Evidence dating under the fossilized birth–death process. Syst. Biol. 2, 228-249. (doi:10.1093/sysbio/syv080)
    • (2016) Syst. Biol , vol.2 , pp. 228-249
    • Zhang, C.1    Stadler, T.2    Klopfstein, S.3    Heath, T.A.4    Ronquist, F.5
  • 25
  • 26
    • 78651014126 scopus 로고
    • Suggestions as to quantitative measurement of rates of evolution
    • Haldane JBS. 1949 Suggestions as to quantitative measurement of rates of evolution. Evolution 3, 51-56. (doi:10.2307/2405451)
    • (1949) Evolution , vol.3 , pp. 51-56
    • Haldane, J.B.S.1
  • 28
    • 0020572129 scopus 로고
    • Rates of evolution: Effects of time and temporal scaling
    • Gingerich PD. 1983 Rates of evolution: effects of time and temporal scaling. Science 222, 159-161. (doi:10.1126/science.222.4620.159)
    • (1983) Science , vol.222 , pp. 159-161
    • Gingerich, P.D.1
  • 29
    • 0027385729 scopus 로고
    • Quantification and comparison of evolutionary rates
    • Gingerich PD. 1993 Quantification and comparison of evolutionary rates. Am. J. Sci. 293A, 453-478. (doi:10.2475/ajs.293.A.453)
    • (1993) Am. J. Sci , vol.293A , pp. 453-478
    • Gingerich, P.D.1
  • 32
    • 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, Schulmeister S, Murray DL, Rasnitsyn AP. 2012 A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. 61, 973-999. (doi:10.1093/sysbio/sys058)
    • (2012) Syst. Biol , vol.61 , pp. 973-999
    • Ronquist, F.1    Klopfstein, S.2    Vilhelmsen, L.3    Schulmeister, S.4    Murray, D.L.5    Rasnitsyn, A.P.6
  • 33
    • 77953503093 scopus 로고    scopus 로고
    • The basal penguin (Aves: Sphenisciformes) Perudyptes devriesi and a phylogenetic evaluation of the penguin fossil record
    • Ksepka DT, Clarke JA. 2010 The basal penguin (Aves: Sphenisciformes) Perudyptes devriesi and a phylogenetic evaluation of the penguin fossil record. Bull. Am. Museum Nat. Hist. 337, 1-77. (doi:10.1206/653.1)
    • (2010) Bull. Am. Museum Nat. Hist , vol.337 , pp. 1-77
    • Ksepka, D.T.1    Clarke, J.A.2
  • 34
    • 84858194408 scopus 로고    scopus 로고
    • New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguins
    • Ksepka DT, Fordyce RE, Ando T, Jones CM. 2012 New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguins. J. Vertebr. Paleontol. 32, 235-254. (doi:10.1080/02724634.2012.652051)
    • (2012) J. Vertebr. Paleontol , vol.32 , pp. 235-254
    • Ksepka, D.T.1    Fordyce, R.E.2    Ando, T.3    Jones, C.M.4
  • 35
    • 84928253935 scopus 로고    scopus 로고
    • Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution
    • Slater GJ. 2015 Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution. Proc. Natl Acad. Sci. USA 112, 4897-4902. (doi:10.1073/pnas.1403666111)
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. 4897-4902
    • Slater, G.J.1
  • 37
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F et al. 2012 MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539-542. (doi:10.1093/sysbio/sys029)
    • (2012) Syst. Biol , vol.61 , pp. 539-542
    • Ronquist, F.1
  • 38
    • 84904626200 scopus 로고    scopus 로고
    • The fossilized birth–death process for coherent calibration of divergence-time estimates
    • Heath TA, Huelsenbeck JP, Stadler T. 2014 The fossilized birth–death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957–E2966. (doi:10.1073/pnas.1319091111)
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. E2957-E2966
    • Heath, T.A.1    Huelsenbeck, J.P.2    Stadler, T.3
  • 39
    • 84886120543 scopus 로고    scopus 로고
    • Recursive algorithms for phylogenetic tree counting. Algorithms Mol
    • Gavryushkina A, Welch D, Drummond AJ. 2013 Recursive algorithms for phylogenetic tree counting. Algorithms Mol. Biol. 8, 26. (doi:10.1186/1748-7188-8-26)
    • (2013) Biol , vol.8 , pp. 26
    • Gavryushkina, A.1    Welch, D.2    Drummond, A.J.3
  • 40
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to estimating phylogeny from discrete morphological character data
    • Lewis PO. 2001 A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913-925. (doi:10.1080/ 106351501753462876)
    • (2001) Syst. Biol , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 41
    • 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. (doi:10.1007/BF00160154)
    • (1994) J. Mol. Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 42
    • 0002024701 scopus 로고
    • On the generalized ‘birth-anddeath’ process
    • Kendall DG. 1948 On the generalized ‘birth-anddeath’ process. Ann. Math. Stat. 19, 1-15. (doi:10. 1214/aoms/1177730285)
    • (1948) Ann. Math. Stat , vol.19 , pp. 1-15
    • Kendall, D.G.1
  • 43
    • 79951566251 scopus 로고    scopus 로고
    • Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie W, Lewis P, Fan Y, Kuo L, Chen M. 2011 Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60, 150-160. (doi:10.1093/sysbio/syq085)
    • (2011) Syst. Biol , vol.60 , pp. 150-160
    • Xie, W.1    Lewis, P.2    Fan, Y.3    Kuo, L.4    Chen, M.5
  • 44
    • 84942027491 scopus 로고    scopus 로고
    • Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa
    • Berger LR et al. 2015 Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. Elife 4, e09560. (doi:10.7554/eLife.09560)
    • (2015) Elife , vol.4
    • Berger, L.R.1


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