Phylogenetic systematics turns over a new leaf.

Long restricted to the domain of molecular systematics and studies of molecular evolution, likelihood methods are now being used in analyses of discrete morphological data, specifically to estimate ancestral character states and for tests of character correlation. Biologists are beginning to apply likelihood models within a Bayesian statistical framework, which promises not only to provide answers that evolutionary biologists desire, but also to make practical the application of more realistic evolutionary models.

[1]  S. Muse Evolutionary analyses of DNA sequences subject to constraints of secondary structure. , 1995, Genetics.

[2]  B. Larget,et al.  Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees , 2000 .

[3]  M. Pagel Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[4]  J. Huelsenbeck,et al.  A compound poisson process for relaxing the molecular clock. , 2000, Genetics.

[5]  M. Newton,et al.  Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo , 1997 .

[6]  D. Schluter,et al.  RECONSTRUCTING ANCESTOR STATES WITH MAXIMUM LIKELIHOOD : SUPPORT FOR ONE- AND TWO-RATE MODELS , 1999 .

[7]  H. Munro,et al.  Mammalian protein metabolism , 1964 .

[8]  Z. Yang,et al.  Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.

[9]  B. Rannala,et al.  Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. , 1997, Molecular biology and evolution.

[10]  M. Norell,et al.  Two feathered dinosaurs from northeastern China , 1998, Nature.

[11]  M. Pagel The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies , 1999 .

[12]  S. Muse,et al.  A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. , 1994, Molecular biology and evolution.

[13]  H. Kishino,et al.  Estimating the rate of evolution of the rate of molecular evolution. , 1998, Molecular biology and evolution.

[14]  Todd H. Oakley,et al.  Reconstructing ancestral character states: a critical reappraisal. , 1998, Trends in ecology & evolution.

[15]  M A Newton,et al.  Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods , 1999, Biometrics.

[16]  M. Pagel,et al.  Accelerated evolution as a consequence of transitions to mutualism. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Douglas E. Soltis,et al.  Molecular Systematics of Plants , 1992, Springer US.

[18]  J. Oliver,et al.  The general stochastic model of nucleotide substitution. , 1990, Journal of theoretical biology.

[19]  olph,et al.  Reconstructing Ancestor States with Maximum Likelihood : Support for One-and Two-Rate Models , 2002 .

[20]  K. Crandall,et al.  Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood , 1997 .

[21]  M. Pagel Inferring evolutionary processes from phylogenies , 1997 .

[22]  J. Felsenstein CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[23]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[24]  E. Tillier,et al.  Neighbor Joining and Maximum Likelihood with RNA Sequences: Addressing the Interdependence of Sites , 1995 .

[25]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[26]  Bob Mau,et al.  Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences , 1999 .

[27]  G A Churchill,et al.  Sample size for a phylogenetic inference. , 1992, Molecular biology and evolution.

[28]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[29]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[30]  D. Schluter,et al.  LIKELIHOOD OF ANCESTOR STATES IN ADAPTIVE RADIATION , 1997, Evolution; international journal of organic evolution.

[31]  Ramakant Sharma,et al.  Phylogeny Estimation and Hypothesis Testing using Maximum Likelihood , 2003 .

[32]  S. Jeffery Evolution of Protein Molecules , 1979 .

[33]  P. Lewis Maximum Likelihood as an Alternative to Parsimony for Inferring Phylogeny Using Nucleotide Sequence Data , 1998 .

[34]  T. Jukes CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[35]  Z. Yang,et al.  Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. , 1993, Molecular biology and evolution.