-
2
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
Baele G., Lemey P., Bedford T., Rambaut A., Suchard M.A., Alekseyenko A.V. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 2012, 29:2157-2167.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
Lemey, P.2
Bedford, T.3
Rambaut, A.4
Suchard, M.A.5
Alekseyenko, A.V.6
-
3
-
-
84877663836
-
Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics
-
Baele G., Li W.L.S., Drummond A.J., Suchard M.A., Lemey P. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 2013, 30:239-243.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 239-243
-
-
Baele, G.1
Li, W.L.S.2
Drummond, A.J.3
Suchard, M.A.4
Lemey, P.5
-
4
-
-
33845883023
-
Paleontological evidence to date the tree of life
-
Benton M.J., Donoghue P.C.J. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 2007, 24:26-53.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 26-53
-
-
Benton, M.J.1
Donoghue, P.C.J.2
-
5
-
-
84904598169
-
-
An experimentally determined evolutionary model dramatically improves phylogenetic fit. bioRxiv. doi:.
-
Bloom, J.D., 2014. An experimentally determined evolutionary model dramatically improves phylogenetic fit. bioRxiv. doi:. doi:10.1101/002899.
-
(2014)
-
-
Bloom, J.D.1
-
6
-
-
79952128500
-
Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards
-
Brandley M.C., Wang Y., Guo X., de Oca A.N.M., Fería-Ortíz M., Hikida T., Ota H. Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards. Syst. Biol. 2011, 60:3-15.
-
(2011)
Syst. Biol.
, vol.60
, pp. 3-15
-
-
Brandley, M.C.1
Wang, Y.2
Guo, X.3
de Oca, A.N.M.4
Fería-Ortíz, M.5
Hikida, T.6
Ota, H.7
-
7
-
-
77649255616
-
Bayesian dating of shallow phylogenies with a relaxed clock
-
Brown R.P., Yang Z. Bayesian dating of shallow phylogenies with a relaxed clock. Syst. Biol. 2010, 59:119-131.
-
(2010)
Syst. Biol.
, vol.59
, pp. 119-131
-
-
Brown, R.P.1
Yang, Z.2
-
8
-
-
80053362389
-
Rate variation and estimation of divergence times using strict and relaxed clocks
-
Brown R., Yang Z. Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol. Biol. 2011, 11:271.
-
(2011)
BMC Evol. Biol.
, vol.11
, pp. 271
-
-
Brown, R.1
Yang, Z.2
-
9
-
-
41049092682
-
Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages
-
Brown J.W., Rest J.S., García-Moreno J., Sorenson M.D., Mindell D.P. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biol. 2008, 6:6.
-
(2008)
BMC Biol.
, vol.6
, pp. 6
-
-
Brown, J.W.1
Rest, J.S.2
García-Moreno, J.3
Sorenson, M.D.4
Mindell, D.P.5
-
10
-
-
0037565011
-
Extracting time from phylogenies: positive interplay between fossil and genetic data
-
Conroy C.J., Van Tuinen M. Extracting time from phylogenies: positive interplay between fossil and genetic data. J. Mammal. 2003, 84:444-455.
-
(2003)
J. Mammal.
, vol.84
, pp. 444-455
-
-
Conroy, C.J.1
Van Tuinen, M.2
-
11
-
-
79959462209
-
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
-
Dos Reis M., Yang Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 2011, 28:2161-2172.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 2161-2172
-
-
Dos Reis, M.1
Yang, Z.2
-
12
-
-
84873505893
-
The unbearable uncertainty of Bayesian divergence time estimation
-
Dos Reis M., Yang Z. The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 2013, 51:30-43.
-
(2013)
J. Syst. Evol.
, vol.51
, pp. 30-43
-
-
Dos Reis, M.1
Yang, Z.2
-
13
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
-
(2007)
BMC Evol. Biol.
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
14
-
-
0042512083
-
Measurably evolving populations
-
Drummond A.J., Pybus O.G., Rambaut A., Forsberg R., Rodrigo A.G. Measurably evolving populations. Trends Ecol. Evol. 2003, 18:481-488.
-
(2003)
Trends Ecol. Evol.
, vol.18
, pp. 481-488
-
-
Drummond, A.J.1
Pybus, O.G.2
Rambaut, A.3
Forsberg, R.4
Rodrigo, A.G.5
-
16
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969-1973.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
17
-
-
68949086557
-
Evaluating the mitochondrial timescale of human evolution
-
Endicott P., Ho S.Y.W., Metspalu M., Stringer C. Evaluating the mitochondrial timescale of human evolution. Trends Ecol. Evol. 2009, 24:515-521.
-
(2009)
Trends Ecol. Evol.
, vol.24
, pp. 515-521
-
-
Endicott, P.1
Ho, S.Y.W.2
Metspalu, M.3
Stringer, C.4
-
18
-
-
42449137071
-
Selection of fossils for calibration of molecular dating models 1
-
Gandolfo M.A., Nixon K.C., Crepet W.L. Selection of fossils for calibration of molecular dating models 1. Ann. Missouri Bot. Gard. 2008, 95:34-42.
-
(2008)
Ann. Missouri Bot. Gard.
, vol.95
, pp. 34-42
-
-
Gandolfo, M.A.1
Nixon, K.C.2
Crepet, W.L.3
-
19
-
-
37549027209
-
GEIGER: investigating evolutionary radiations
-
Harmon L.J., Weir J.T., Brock C.D., Glor R.E., Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics 2008, 24:129-131.
-
(2008)
Bioinformatics
, vol.24
, pp. 129-131
-
-
Harmon, L.J.1
Weir, J.T.2
Brock, C.D.3
Glor, R.E.4
Challenger, W.5
-
20
-
-
84865256173
-
A hierarchical Bayesian model for calibrating estimates of species divergence times
-
Heath T.A. A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst. Biol. 2012, 61:793-809.
-
(2012)
Syst. Biol.
, vol.61
, pp. 793-809
-
-
Heath, T.A.1
-
21
-
-
84857198898
-
A dirichlet process prior for estimating lineage-specific substitution rates
-
Heath T.A., Holder M.T., Huelsenbeck J.P. A dirichlet process prior for estimating lineage-specific substitution rates. Mol. Biol. Evol. 2012, 29:939-955.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 939-955
-
-
Heath, T.A.1
Holder, M.T.2
Huelsenbeck, J.P.3
-
22
-
-
84555188625
-
Calibrated tree priors for relaxed phylogenetics and divergence time estimation
-
Heled J., Drummond A.J. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Syst. Biol. 2012, 61:138-149.
-
(2012)
Syst. Biol.
, vol.61
, pp. 138-149
-
-
Heled, J.1
Drummond, A.J.2
-
23
-
-
84904616644
-
-
Calibrated birth-death phylogenetic time-tree priors for Bayesian inference. arXiv Prepr. arXiv1311.4921.
-
Heled, J., Drummond, A.J., 2013. Calibrated birth-death phylogenetic time-tree priors for Bayesian inference. arXiv Prepr. arXiv1311.4921.
-
(2013)
-
-
Heled, J.1
Drummond, A.J.2
-
24
-
-
34347329101
-
Calibrating molecular estimates of substitution rates and divergence times in birds
-
Ho S.Y.M. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 2007, 38:409-414.
-
(2007)
J. Avian Biol.
, vol.38
, pp. 409-414
-
-
Ho, S.Y.M.1
-
25
-
-
67649133122
-
An examination of phylogenetic models of substitution rate variation among lineages
-
Ho S.Y.W. An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 2009, 5:421-424.
-
(2009)
Biol. Lett.
, vol.5
, pp. 421-424
-
-
Ho, S.Y.W.1
-
26
-
-
31444442779
-
Molecular clocks: when times are a-changin'
-
Ho S.Y.W., Larson G. Molecular clocks: when times are a-changin'. Trends Genet. 2006, 22:79-83.
-
(2006)
Trends Genet.
, vol.22
, pp. 79-83
-
-
Ho, S.Y.W.1
Larson, G.2
-
27
-
-
70350103638
-
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
-
Ho S.Y.W., Phillips M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 2009, 58:367-380.
-
(2009)
Syst. Biol.
, vol.58
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
28
-
-
20444427160
-
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
-
Ho S.Y.W., Phillips M.J., Cooper A., Drummond A.J. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 2005, 22:1561-1568.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1561-1568
-
-
Ho, S.Y.W.1
Phillips, M.J.2
Cooper, A.3
Drummond, A.J.4
-
29
-
-
17744387938
-
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
-
Ho S.Y.W., Phillips M.J., Drummond A.J., Cooper A. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol. Biol. Evol. 2005, 22:1355-1363.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1355-1363
-
-
Ho, S.Y.W.1
Phillips, M.J.2
Drummond, A.J.3
Cooper, A.4
-
30
-
-
0037377762
-
Molecular clocks and the puzzle of RNA virus origins
-
Holmes E.C. Molecular clocks and the puzzle of RNA virus origins. J. Virol. 2003, 77:3893-3897.
-
(2003)
J. Virol.
, vol.77
, pp. 3893-3897
-
-
Holmes, E.C.1
-
31
-
-
34547762740
-
The impact of fossils and taxon sampling on ancient molecular dating analyses
-
Hug L.A., Roger A.J. The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol. Biol. Evol. 2007, 24:1889-1897.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1889-1897
-
-
Hug, L.A.1
Roger, A.J.2
-
32
-
-
72049121650
-
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
-
Inoue J., Donoghue P.C.J., Yang Z. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 2010, 59:74-89.
-
(2010)
Syst. Biol.
, vol.59
, pp. 74-89
-
-
Inoue, J.1
Donoghue, P.C.J.2
Yang, Z.3
-
33
-
-
0035103260
-
Performance of a divergence time estimation method under a probabilistic model of rate evolution
-
Kishino H., Thorne J.L., Bruno W.J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 2001, 18:352-361.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 352-361
-
-
Kishino, H.1
Thorne, J.L.2
Bruno, W.J.3
-
34
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
35
-
-
33644826560
-
Computing Bayes factors using thermodynamic integration
-
Lartillot N., Philippe H. Computing Bayes factors using thermodynamic integration. Syst. Biol. 2006, 55:195-207.
-
(2006)
Syst. Biol.
, vol.55
, pp. 195-207
-
-
Lartillot, N.1
Philippe, H.2
-
36
-
-
0032855033
-
Molecular clock calibrations and metazoan divergence dates
-
Lee M.S.Y. Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 1999, 49:385-391.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 385-391
-
-
Lee, M.S.Y.1
-
37
-
-
37549001784
-
A general comparison of relaxed molecular clock models
-
Lepage T., Bryant D., Philippe H., Lartillot N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 2007, 24:2669-2680.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 2669-2680
-
-
Lepage, T.1
Bryant, D.2
Philippe, H.3
Lartillot, N.4
-
38
-
-
84862908923
-
Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics
-
Li W.L.S., Drummond A.J. Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol. 2012, 29:751-761.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 751-761
-
-
Li, W.L.S.1
Drummond, A.J.2
-
39
-
-
18144364012
-
Taxon sampling effects in molecular clock dating: an example from the African Restionaceae
-
Linder H.P., Hardy C.R., Rutschmann F. Taxon sampling effects in molecular clock dating: an example from the African Restionaceae. Mol. Phylogenet. Evol. 2005, 35:569-582.
-
(2005)
Mol. Phylogenet. Evol.
, vol.35
, pp. 569-582
-
-
Linder, H.P.1
Hardy, C.R.2
Rutschmann, F.3
-
40
-
-
79955364420
-
Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence
-
Linder M., Britton T., Sennblad B. Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence. Syst. Biol. 2011, 60:329-342.
-
(2011)
Syst. Biol.
, vol.60
, pp. 329-342
-
-
Linder, M.1
Britton, T.2
Sennblad, B.3
-
41
-
-
48249095547
-
Molecular ecology and natural history of Simian foamy virus infection in wild-living chimpanzees
-
Liu W., Worobey M., Li Y., Keele B.F., Bibollet-Ruche F., Guo Y., Goepfert P.A., Santiago M.L., Ndjango J.-B.N., Neel C. Molecular ecology and natural history of Simian foamy virus infection in wild-living chimpanzees. PLoS Pathog. 2008, 4:e1000097.
-
(2008)
PLoS Pathog.
, vol.4
-
-
Liu, W.1
Worobey, M.2
Li, Y.3
Keele, B.F.4
Bibollet-Ruche, F.5
Guo, Y.6
Goepfert, P.A.7
Santiago, M.L.8
Ndjango, J.-B.N.9
Neel, C.10
-
42
-
-
84555194967
-
Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches
-
Lukoschek V., Keogh J.S., Avise J.C. Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches. Syst. Biol. 2012, 61:22-43.
-
(2012)
Syst. Biol.
, vol.61
, pp. 22-43
-
-
Lukoschek, V.1
Keogh, J.S.2
Avise, J.C.3
-
43
-
-
4944255292
-
Dating lineages: molecular and paleontological approaches to the temporal framework of clades
-
Magallón S.A. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. Int. J. Plant Sci. 2004, 165:S7-S21.
-
(2004)
Int. J. Plant Sci.
, vol.165
-
-
Magallón, S.A.1
-
44
-
-
43949092742
-
A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points
-
Marshall C.R. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 2008, 171:726-742.
-
(2008)
Am. Nat.
, vol.171
, pp. 726-742
-
-
Marshall, C.R.1
-
45
-
-
0035134159
-
Historical perspective of foamy virus epidemiology and infection
-
Meiering C.D., Linial M.L. Historical perspective of foamy virus epidemiology and infection. Clin. Microbiol. Rev. 2001, 14:165-176.
-
(2001)
Clin. Microbiol. Rev.
, vol.14
, pp. 165-176
-
-
Meiering, C.D.1
Linial, M.L.2
-
46
-
-
84876022648
-
Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages
-
Molak M., Lorenzen E.D., Shapiro B., Ho S.Y.W. Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages. Mol. Biol. Evol. 2013, 30:253-262.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 253-262
-
-
Molak, M.1
Lorenzen, E.D.2
Shapiro, B.3
Ho, S.Y.W.4
-
47
-
-
8144221423
-
Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection
-
Near T.J., Sanderson M.J. Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection. Philos. Trans. R. Soc. London. Ser. B: Biol. Sci. 2004, 359:1477-1483.
-
(2004)
Philos. Trans. R. Soc. London. Ser. B: Biol. Sci.
, vol.359
, pp. 1477-1483
-
-
Near, T.J.1
Sanderson, M.J.2
-
48
-
-
13944259078
-
Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles
-
Near T.J., Meylan P.A., Shaffer H.B. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 2005, 165:137-146.
-
(2005)
Am. Nat.
, vol.165
, pp. 137-146
-
-
Near, T.J.1
Meylan, P.A.2
Shaffer, H.B.3
-
49
-
-
84877929456
-
Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion
-
Paradis E. Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Mol. Phylogenet. Evol. 2013.
-
(2013)
Mol. Phylogenet. Evol.
-
-
Paradis, E.1
-
50
-
-
1042304216
-
APE: analyses of phylogenetics and evolution in R language
-
Paradis E., Claude J., Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20:289-290.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
51
-
-
84863116561
-
Best practices for justifying fossil calibrations
-
Parham J.F., Donoghue P.C.J., Bell C.J., Calway T.D., Head J.J., Holroyd P.A., Inoue J.G., Irmis R.B., Joyce W.G., Ksepka D.T. Best practices for justifying fossil calibrations. Syst. Biol. 2012, 61:346-359.
-
(2012)
Syst. Biol.
, vol.61
, pp. 346-359
-
-
Parham, J.F.1
Donoghue, P.C.J.2
Bell, C.J.3
Calway, T.D.4
Head, J.J.5
Holroyd, P.A.6
Inoue, J.G.7
Irmis, R.B.8
Joyce, W.G.9
Ksepka, D.T.10
-
52
-
-
67349118917
-
Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny
-
Phillips M.J. Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 2009, 441:132-140.
-
(2009)
Gene
, vol.441
, pp. 132-140
-
-
Phillips, M.J.1
-
53
-
-
84904645818
-
-
R Core Team R: A Language and Environment for Statistical Computing. R Found. Stat. Comput.
-
R Core Team, 2008. R: A Language and Environment for Statistical Computing. R Found. Stat. Comput.
-
(2008)
-
-
-
54
-
-
0034044313
-
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
-
Rambaut A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 2000, 16:395-399.
-
(2000)
Bioinformatics
, vol.16
, pp. 395-399
-
-
Rambaut, A.1
-
55
-
-
34548556039
-
Inferring speciation times under an episodic molecular clock
-
Rannala B., Yang Z. Inferring speciation times under an episodic molecular clock. Syst. Biol. 2007, 56:453-466.
-
(2007)
Syst. Biol.
, vol.56
, pp. 453-466
-
-
Rannala, B.1
Yang, Z.2
-
56
-
-
33645030825
-
Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times
-
Rutschmann F. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers. Distrib. 2006, 12:35-48.
-
(2006)
Divers. Distrib.
, vol.12
, pp. 35-48
-
-
Rutschmann, F.1
-
57
-
-
34547468349
-
Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points
-
Rutschmann F., Eriksson T., Salim K.A., Conti E. Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points. Syst. Biol. 2007, 56:591-608.
-
(2007)
Syst. Biol.
, vol.56
, pp. 591-608
-
-
Rutschmann, F.1
Eriksson, T.2
Salim, K.A.3
Conti, E.4
-
58
-
-
34547481471
-
Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds
-
Sanders K.L., Lee M.S.Y. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biol. Lett. 2007, 3:275-279.
-
(2007)
Biol. Lett.
, vol.3
, pp. 275-279
-
-
Sanders, K.L.1
Lee, M.S.Y.2
-
59
-
-
0030773749
-
A nonparametric approach to estimating divergence times in the absence of rate constancy
-
Sanderson M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 1997, 14:1218-1231.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 1218-1231
-
-
Sanderson, M.J.1
-
60
-
-
0036135468
-
Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach
-
Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19:101-109.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 101-109
-
-
Sanderson, M.J.1
-
61
-
-
0034639688
-
Simian foamy virus infection among zoo keepers
-
Sandstrom P.A., Phan K.O., Switzer W.M., Fredeking T., Chapman L., Heneine W., Folks T.M. Simian foamy virus infection among zoo keepers. Lancet 2000, 355:551-552.
-
(2000)
Lancet
, vol.355
, pp. 551-552
-
-
Sandstrom, P.A.1
Phan, K.O.2
Switzer, W.M.3
Fredeking, T.4
Chapman, L.5
Heneine, W.6
Folks, T.M.7
-
62
-
-
84863116093
-
Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
-
Sauquet H., Ho S.Y.W., Gandolfo M.A., Jordan G.J., Wilf P., Cantrill D.J., Bayly M.J., Bromham L., Brown G.K., Carpenter R.J. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst. Biol. 2012, 61:289-313.
-
(2012)
Syst. Biol.
, vol.61
, pp. 289-313
-
-
Sauquet, H.1
Ho, S.Y.W.2
Gandolfo, M.A.3
Jordan, G.J.4
Wilf, P.5
Cantrill, D.J.6
Bayly, M.J.7
Bromham, L.8
Brown, G.K.9
Carpenter, R.J.10
-
63
-
-
79951548848
-
Phangorn: phylogenetic analysis in R
-
Schliep K.P. Phangorn: phylogenetic analysis in R. Bioinformatics 2011, 27:592-593.
-
(2011)
Bioinformatics
, vol.27
, pp. 592-593
-
-
Schliep, K.P.1
-
64
-
-
0036433299
-
Dating the time of origin of major clades: molecular clocks and the fossil record
-
Smith A.B., Peterson K.J. Dating the time of origin of major clades: molecular clocks and the fossil record. Annu. Rev. Earth Planet. Sci. 2002, 30:65-88.
-
(2002)
Annu. Rev. Earth Planet. Sci.
, vol.30
, pp. 65-88
-
-
Smith, A.B.1
Peterson, K.J.2
-
65
-
-
0037007019
-
Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils
-
Soltis P.S., Soltis D.E., Savolainen V., Crane P.R., Barraclough T.G. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl. Acad. Sci. USA 2002, 99:4430-4435.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4430-4435
-
-
Soltis, P.S.1
Soltis, D.E.2
Savolainen, V.3
Crane, P.R.4
Barraclough, T.G.5
-
67
-
-
20144388927
-
Ancient co-speciation of simian foamy viruses and primates
-
Switzer W.M., Salemi M., Shanmugam V., Gao F., Cong M., Kuiken C., Bhullar V., Beer B.E., Vallet D., Gautier-Hion A. Ancient co-speciation of simian foamy viruses and primates. Nature 2005, 434:376-380.
-
(2005)
Nature
, vol.434
, pp. 376-380
-
-
Switzer, W.M.1
Salemi, M.2
Shanmugam, V.3
Gao, F.4
Cong, M.5
Kuiken, C.6
Bhullar, V.7
Beer, B.E.8
Vallet, D.9
Gautier-Hion, A.10
-
68
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne J.L., Kishino H., Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 1998, 15:1647-1657.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
69
-
-
0345832031
-
The effect of external and internal fossil calibrations on the avian evolutionary timescale
-
Van Tuinen M., Hedges S.B. The effect of external and internal fossil calibrations on the avian evolutionary timescale. J. Paleontol. 2004, 78.
-
(2004)
J. Paleontol.
, vol.78
-
-
Van Tuinen, M.1
Hedges, S.B.2
-
70
-
-
33749602096
-
Detecting the node-density artifact in phylogeny reconstruction
-
Venditti C., Meade A., Pagel M. Detecting the node-density artifact in phylogeny reconstruction. Syst. Biol. 2006, 55:637-643.
-
(2006)
Syst. Biol.
, vol.55
, pp. 637-643
-
-
Venditti, C.1
Meade, A.2
Pagel, M.3
-
71
-
-
84863012163
-
Exploring uncertainty in the calibration of the molecular clock
-
Warnock R.C.M., Yang Z., Donoghue P.C.J. Exploring uncertainty in the calibration of the molecular clock. Biol. Lett. 2012, 8:156-159.
-
(2012)
Biol. Lett.
, vol.8
, pp. 156-159
-
-
Warnock, R.C.M.1
Yang, Z.2
Donoghue, P.C.J.3
-
72
-
-
20144362109
-
Molecular dating when rates vary
-
Welch J.J., Bromham L. Molecular dating when rates vary. Trends Ecol. Evol. 2005, 20:320-327.
-
(2005)
Trends Ecol. Evol.
, vol.20
, pp. 320-327
-
-
Welch, J.J.1
Bromham, L.2
-
73
-
-
79951566251
-
Improving marginal likelihood estimation for Bayesian phylogenetic model selection
-
Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.-H. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 2011, 60:150-160.
-
(2011)
Syst. Biol.
, vol.60
, pp. 150-160
-
-
Xie, W.1
Lewis, P.O.2
Fan, Y.3
Kuo, L.4
Chen, M.-H.5
-
74
-
-
28944451210
-
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
-
Yang Z., Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 2006, 23:212-226.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 212-226
-
-
Yang, Z.1
Rannala, B.2
-
75
-
-
0033933640
-
Estimation of primate speciation dates using local molecular clocks
-
Yoder A.D., Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 2000, 17:1081-1090.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 1081-1090
-
-
Yoder, A.D.1
Yang, Z.2
-
76
-
-
84904688361
-
-
Molecular disease, evolution and genetic heterogeneity. In: Kasha, M., Pullman, B. (Eds.), New York.
-
Zuckerkandl, E., Pauling, L., 1962. Molecular disease, evolution and genetic heterogeneity. In: Kasha, M., Pullman, B. (Eds.), New York.
-
(1962)
-
-
Zuckerkandl, E.1
Pauling, L.2
|