Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

Berger JO (1985) Statistical decision theory and Bayesian analysis. Springer-Verlag, New York

Bishop MJ, Friday AE (1985) Evolutionary trees from nucleic acid and protein sequences. Proc R Soc Lond [Biol] 226:271–302

Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570

Edwards AWF (1970) Estimation of the branch points of a branching diffusion process (with discussion). J R Stat Soc B 32:155–174

Feller W (1939) Die grundlagen der volterraschen theorie des kampfer ums dasein in wahrsheinlichkeits theoretischen behandlung. Acta Biotheor 5:1–40

Felsenstein J (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22:240–249

Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

Felsenstein J, Kishino H (1993) Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst Biol 42:193–200

Fukami-Kobayashi K, Tateno Y (1991) Robustness of maximum likelihood tree estimation against different patterns of base substitution. J Mol Evol 32:79–91

Gaut BS, Lewis PO (1995) Success of maximum likelihood phylogeny inference in the four-taxon case. Mol Biol Evol 12:152–162

Goldman N (1990) Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Syst Zool 39:345–361

Grimmett GR, Stirzaker DR (1992) Probability and Random Processes. 2nd ed. Clarendon Press, Oxford

Hasegawa M, Yano T (1984) Maximum likelihood method of phylogenetic inference from DNA sequence data. Bull Biomet Soc Jpn 5:1–7

Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160–174

Hasegawa M, Kishino H, Saitou N (1991) On the maximum likelihood method in molecular phylogenetics. J Mol Evol 32:443–445

Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing the confidence in phylogenetic analysis. Syst Biol 42:182–192

Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S, Takahata N (1992) Man's place in Hominoidea revealed by mitochondrial DNA genealogy. J Mol Evol 35:32–43

Huelsenbeck JP (1995a) The performance of phylogenetic methods in simulation. Syst Biol 44:17–48

Huelsenbeck JP (1995b) The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 12:843–849

Kendall DG (1949) Stochastic processes and population growth. J R Star Soc B 11:230–264

Kishino H, Hasegawa M (1989) Evaluation of maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170–179

Kuhner MK, Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11:459–468

Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140:1421–1430

Miyamoto MM, Slighton JL, Goodman M (1987) Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region. Science 238:369–373

Nee S, May RM, Harvey PH (1994) The reconstructed evolutionary process. Philos Trans R Soc Lond Biol 344:305–311

Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1992) Numerical recipes in C: the art of scientific computing. 2nd ed. Cambridge University Press, Cambridge

Raup DM (1985) Mathematical models of cladogenesis. Paleobiology 11:42–52

Robert CP (1994) The Bayesian choice: a decision-theoretic motivation. Springer-Verlag, New York

Takezaki N, Rzhetsky A, Nei M (1995) Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 12:823–833

Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11:261–277

Thompson EA (1975) Human evolutionary trees. Cambridge University Press, Cambridge, England

Thorne JL, Kishino H, Felsenstein J (1992) Inching toward reliability: an improved likelihood model of sequence evolution. J Mol Evol 34:3–16

Yang Z (1993) Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10:1396–1401

Yang Z (1994a) Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst Biol 43:329–342

Yang Z (1994b) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39:306–314

Yang Z (1995) Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J Mol Evol 40:689–697

Yang Z (1996) Phylogenetic analysis by parsimony and likelihood methods. J Mol Evol 42:294–307

Yang Z, Goldman N, Friday AE (1995) Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst Biol 44:384–399

Yule GU (1925) A mathematical theory of evolution, based on the conclusions of Dr. J.C. Willis, F.R.S. Philos Trans R Soc Lond Biol 213:21–87

Zharkikh A, Li W-H (1992) Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: 1. four taxa with a molecular clock. Mol Biol Evol 9:1119–1147