terms of the licence agreement, an individual user may print out a PDF of a single chapter of a m... more terms of the licence agreement, an individual user may print out a PDF of a single chapter of a monograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: Tasmania University; date: This book summarizes the statistical models and computational algorithms for comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, and statistical phylogeography. The book presents and explains the models of nucleotide, amino acid, and codon substitution, and their use in calculating pairwise sequence distances and in reconstruction of phylogenetic trees. All major methods for phylogeny reconstruction are covered in detail, including neighbour joining, maximum parsimony, maximum likelihood, and Bayesian methods. Using motivating examples, the book includes a comprehensive introduction to Bayesian computation using Markov chain Monte Carlo (MCMC). Advanced topics include estimation of species divergence times using the molecular clock, detection of molecular adaptation, simulation of molecular evolution, as well as species tree estimation and species delimitation using genomic sequence data. This chapter discusses the hypothesis of the molecular clock and its use to date species divergences. It introduces various tests of the molecular clock as well as strategies to relax the clock in divergence time estimation. Bayesian methods of divergence time estimation are discussed in detail, including different prior models of rate drift such as the correlated-rate model based on the geometric Brownian motion
terms of the licence agreement, an individual user may print out a PDF of a single chapter of a m... more terms of the licence agreement, an individual user may print out a PDF of a single chapter of a monograph in OSO for personal use (for details see http://www.oxfordscholarship.com/page/privacy-policy). Subscriber: Tasmania University; date: This book summarizes the statistical models and computational algorithms for comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, and statistical phylogeography. The book presents and explains the models of nucleotide, amino acid, and codon substitution, and their use in calculating pairwise sequence distances and in reconstruction of phylogenetic trees. All major methods for phylogeny reconstruction are covered in detail, including neighbour joining, maximum parsimony, maximum likelihood, and Bayesian methods. Using motivating examples, the book includes a comprehensive introduction to Bayesian computation using Markov chain Monte Carlo (MCMC). Advanced topics include estimation of species divergence times using the molecular clock, detection of molecular adaptation, simulation of molecular evolution, as well as species tree estimation and species delimitation using genomic sequence data. This chapter discusses the hypothesis of the molecular clock and its use to date species divergences. It introduces various tests of the molecular clock as well as strategies to relax the clock in divergence time estimation. Bayesian methods of divergence time estimation are discussed in detail, including different prior models of rate drift such as the correlated-rate model based on the geometric Brownian motion
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