Relaxed Phylogenetics and Dating with Confidence

1962, Molecular disease, evolution and genic heterogeneity., Horizons in biochemistry, 189

1965, Evolutionary divergence and convergence in proteins., Evolving genes and proteins, 97, 10.1016/B978-1-4832-2734-4.50017-6

1986, Rates of DNA sequence evolution differ between taxonomic groups., Science, 231, 1393, 10.1126/science.3082006

1997, Vagaries of the molecular clock., Proc Nat Acad Sci U S A, 94, 7776, 10.1073/pnas.94.15.7776

1989, Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders., Jpn J Genet, 64, 243, 10.1266/jjg.64.243

2000, Estimation of primate speciation dates using local molecular clocks., Mol Biol Evol, 17, 1081, 10.1093/oxfordjournals.molbev.a026389

1978, Cases in which parsimony or compatibility methods will be positively misleading., Syst Zool, 27, 401, 10.2307/2412923

2004, Tracing the decay of the historical signal in biological sequence data., Syst Biol, 53, 628

2001, MRBAYES: Bayesian inference of phylogenetic trees., Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754

1981, Evolutionary trees from DNA sequences: A maximum likelihood approach., J Mol Evol, 17, 368, 10.1007/BF01734359

2004, PHYLIP (Phylogeny Inference Package) version 3.6 [computer program]

2003, PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4 [computer program]

1998, Estimating divergence dates from molecular sequences., Mol Biol Evol, 15, 442, 10.1093/oxfordjournals.molbev.a025940

1997, A nonparametric approach to estimating divergence times in the absence of rate constancy., Mol Biol Evol, 14, 1218, 10.1093/oxfordjournals.molbev.a025731

1998, Estimating the rate of evolution of the rate of molecular evolution., Mol Biol Evol, 15, 1647, 10.1093/oxfordjournals.molbev.a025892

1989, Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea., J Hum Evol, 18, 461, 10.1016/0047-2484(89)90075-4

2002, Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny., Syst Biol, 51, 703, 10.1080/10635150290102375

2005, Closing the gap between rocks and clocks., Heredity, 94, 461, 10.1038/sj.hdy.6800644

1970, Monte Carlo sampling methods using Markov chains and their applications., Biometrika, 57, 97, 10.1093/biomet/57.1.97

1953, Equations of state calculations by fast computing machines., J Chem Phys, 21, 1087, 10.1063/1.1699114

2003, BEAST version 1.3 [computer program]

2005, Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation., Mol Biol Evol, 22, 1355, 10.1093/molbev/msi125

2003, Tracer version 1.2 [computer program]

2003, Selection-driven evolution of emergent dengue virus., Mol Biol Evol, 20, 1650, 10.1093/molbev/msg182

1997, Long term trends in the evolution of H(3) HA1 human influenza type A., Proc Natl Acad Sci U S A, 94, 7712, 10.1073/pnas.94.15.7712

2003, Ecological and immunological determinants of influenza evolution., Nature, 422, 428, 10.1038/nature01509

1985, Dating of the human–ape splitting by a molecular clock of mitochondrial DNA., J Mol Evol, 22, 160, 10.1007/BF02101694

1994, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods., J Mol Evol, 39, 306, 10.1007/BF00160154

2000, Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies., Bioinformatics, 16, 395, 10.1093/bioinformatics/16.4.395

2002, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data., Genetics, 161, 1307, 10.1093/genetics/161.3.1307

2003, Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials., Mol Phylogenet Evol, 28, 186, 10.1016/S1055-7903(03)00122-2

1993, Body size, metabolic rate, generation time, and the molecular clock., Proc Natl Acad Sci U S A, 90, 4087, 10.1073/pnas.90.9.4087

1996, Determinants of rate variation in mammalian DNA sequence evolution., J Mol Evol, 43, 610, 10.1007/BF02202109

1999, A new marsupial from the Early Eocene Tingamarra local fauna of Murgon, southeastern Queensland: A prototypical Australian marsupial?, J Mammal Evol, 6, 289, 10.1023/A:1020517808869

2004, Precision of molecular time estimates., Trends Genet, 20, 242, 10.1016/j.tig.2004.03.004

1990, The general stochastic model of nucleotide substitution., J Theor Biol, 142, 485, 10.1016/S0022-5193(05)80104-3

2003, Genome-scale approaches to resolving incongruence in molecular phylogenies., Nature, 425, 798, 10.1038/nature02053

2002, A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history., Genome Res, 12, 1080, 10.1101/gr.187002

2004, Dating the monocot–dicot divergence and the origin of core eudicots using whole chloroplast genomes., J Mol Evol, 58, 424, 10.1007/s00239-003-2564-9

2004, Phylogenomics of eukaryotes: impact of missing data on large alignments., Mol Biol Evol, 21, 1740, 10.1093/molbev/msh182

2004, Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution., Proc Natl Acad Sci U S A, 101, 13994, 10.1073/pnas.0404142101

2003, Comparative analyses of multi-species sequences from targeted genomic regions., Nature, 424, 788, 10.1038/nature01858

2004, Genome-scale phylogeny and the detection of systematic biases., Mol Biol Evol, 21, 1455, 10.1093/molbev/msh137

2005, Rooting a phylogenetic tree with nonreversible substitution models., BMC Evol Biol, 5, 2, 10.1186/1471-2148-5-2

2002, Inferring the root of a phylogenetic tree., Syst Biol, 51, 32, 10.1080/106351502753475862

2004, The importance of proper model assumption in bayesian phylogenetics., Syst Biol, 53, 265, 10.1080/10635150490423520

2005, Branch-length prior influences Bayesian posterior probability of phylogeny., Syst Biol, 54, 455, 10.1080/10635150590945313

2002, Model misspecification and probabilistic tests of topology: evidence from empirical data sets., Syst Biol, 51, 509, 10.1080/10635150290069922

1997, Mass survival of birds across the Cretaceous–Tertiary boundary: Molecular evidence., Science, 275, 1109, 10.1126/science.275.5303.1109

2002, Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach., Mol Biol Evol, 19, 101, 10.1093/oxfordjournals.molbev.a003974

2000, Estimating divergence times in the presence of an overdispersed molecular clock., Mol Biol Evol, 17, 1647, 10.1093/oxfordjournals.molbev.a026264

1995, Phylogenetic test of the molecular clock and linearized trees., Mol Biol Evol, 12, 823

2001, Performance of a divergence time estimation method under a probabilistic model of rate evolution., Mol Biol Evol, 18, 352, 10.1093/oxfordjournals.molbev.a003811

2002, Divergence time and evolutionary rate estimation with multilocus data., Syst Biol, 51, 689, 10.1080/10635150290102456

2003, Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa., Mol Biol Evol, 20, 1947, 10.1093/molbev/msg226

1982, The coalescent., Stoch Proc Appl, 13, 235, 10.1016/0304-4149(82)90011-4

1982, On the genealogy of large populations., J Appl Probab, 19, 27, 10.2307/3213548

2005, Bayesian coalescent inference of past population dynamics from molecular sequences., Mol Biol Evol, 22, 1185, 10.1093/molbev/msi103

2000, An integrated framework for the inference of viral population history from reconstructed genealogies., Genetics, 155, 1429, 10.1093/genetics/155.3.1429

2004, Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations., Genetics, 168, 2407, 10.1534/genetics.104.030411

1924, A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S., Philos Trans R Soc Lond B, 213, 21

1994, The reconstructed evolutionary process., Philos Trans R Soc Lond B Biol Sci, 344, 305, 10.1098/rstb.1994.0068

1997, Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo Method., Mol Biol Evol, 14, 717, 10.1093/oxfordjournals.molbev.a025811

2005, Molecular dates for the “cambrian explosion”: The influence of prior assumptions., Syst Biol, 54, 672, 10.1080/10635150590947212

1998, Genealogical inference from microsatellite data., Genetics, 150, 499, 10.1093/genetics/150.1.499

2003, Measurably evolving populations., Trends Ecol Evol, 18, 481, 10.1016/S0169-5347(03)00216-7

2000, Timing the ancestor of the HIV-1 pandemic strains., Science, 288, 1789, 10.1126/science.288.5472.1789

2004, The molecular population genetics of HIV-1 group O., Genetics, 167, 1059, 10.1534/genetics.104.026666

2003, The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: A Bayesian coalescent approach., Mol Biol Evol, 20, 381, 10.1093/molbev/msg043