Phylogenetic reconstruction methods: an overview.

Initially designed to infer evolutionary relationships based on morphological and physiological characters, phylogenetic reconstruction methods have greatly benefited from recent developments in molecular biology and sequencing technologies with a number of powerful methods having been developed specifically to infer phylogenies from macromolecular data. This chapter, while presenting an overview of basic concepts and methods used in phylogenetic reconstruction, is primarily intended as a simplified step-by-step guide to the construction of phylogenetic trees from nucleotide sequences using fairly up-to-date maximum likelihood methods implemented in freely available computer programs. While the analysis of chloroplast sequences from various Vanilla species is used as an illustrative example, the techniques covered here are relevant to the comparative analysis of homologous sequences datasets sampled from any group of organisms.

[1]  S. Tavaré.  Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .

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

[3]  O. Gascuel,et al.  Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. , 2006, Systematic biology.

[4]  M. A. STEEL,et al.  Loss of information in genetic distances , 1988, Nature.

[5]  Rodrigo Lopez,et al.  Petabyte-scale innovations at the European Nucleotide Archive , 2008, Nucleic Acids Res..

[6]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[7]  M. Nei,et al.  Molecular Evolution and Phylogenetics , 2000 .

[8]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[9]  A. Haeseler,et al.  The Phylogenetic Handbook: Phylogenetic inference using maximum likelihood methods , 2009 .

[10]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[11]  D. Posada.  jModelTest: phylogenetic model averaging. , 2008, Molecular biology and evolution.

[12]  B. Rannala,et al.  Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference , 1996, Journal of Molecular Evolution.

[13]  P. Besse,et al.  Evidence of transoceanic dispersion of the genus Vanilla based on plastid DNA phylogenetic analysis. , 2010, Molecular phylogenetics and evolution.

[14]  Peter Godfrey-Smith,et al.  Reconstructing the Past: Parsimony, Evolution, and Inference , 1989 .

[15]  J. Farris,et al.  Quantitative Phyletics and the Evolution of Anurans , 1969 .

[16]  Jack Sullivan,et al.  Does choice in model selection affect maximum likelihood analysis? , 2008, Systematic biology.

[17]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[18]  I. Poole,et al.  The Evolution of plant physiology : from whole plants to ecosystems , 2004 .

[19]  R. Sokal,et al.  A QUANTITATIVE APPROACH TO A PROBLEM IN CLASSIFICATION† , 1957, Evolution; International Journal of Organic Evolution.

[20]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) for genome scale research in life science , 2002, Nucleic Acids Res..

[21]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[22]  O. Gascuel,et al.  Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes , 2011, Systematic biology.

[23]  L. Cavalli-Sforza,et al.  PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES , 1967, Evolution; international journal of organic evolution.

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

[25]  John P. Huelsenbeck,et al.  The Phylogenetic Handbook: Bayesian phylogenetic analysis using MRBAYES , 2009 .

[26]  H. Akaike.  A new look at the statistical model identification , 1974 .

[27]  S. Ho,et al.  Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets , 2010, BMC Evolutionary Biology.

[28]  J. Farris.  Methods for Computing Wagner Trees , 1970 .

[29]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[30]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[31]  Wayne P. Maddison,et al.  Outgroup Analysis and Parsimony , 1984 .

[32]  L. Pauling,et al.  Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.

[33]  G. Schwarz.  Estimating the Dimension of a Model , 1978 .

[34]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[35]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[36]  J. Felsenstein.  Maximum-likelihood estimation of evolutionary trees from continuous characters. , 1973, American journal of human genetics.

[37]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

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

[39]  Larry S. Davis,et al.  Automatic online tuning for fast Gaussian summation , 2008, NIPS.

[40]  J. Aldrich.  R.A. Fisher and the making of maximum likelihood 1912-1922 , 1997 .

[41]  K. Crandall,et al.  The Effect of Recombination on the Accuracy of Phylogeny Estimation , 2002, Journal of Molecular Evolution.

[42]  Luay Nakhleh,et al.  Recombination and phylogeny: effects and detection , 2005, Int. J. Bioinform. Res. Appl..

[43]  Zaid Abdo,et al.  Performance-based selection of likelihood models for phylogeny estimation. , 2003, Systematic biology.

[44]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[45]  Ramón Doallo,et al.  ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..

[46]  O Gascuel,et al.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.

[47]  D. Penny,et al.  Branch and bound algorithms to determine minimal evolutionary trees , 1982 .

[48]  J. Langdale,et al.  A step by step guide to phylogeny reconstruction. , 2006, The Plant journal : for cell and molecular biology.

[49]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[50]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.