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Preface | |
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Parsimony methods | |
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A simple example | |
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Methods of rooting the tree | |
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Branch lengths | |
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Unresolved questions | |
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Counting evolutionary changes | |
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The Fitch algorithm | |
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The Sankoff algorithm | |
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Using the algorithms when modifying trees | |
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Further economies | |
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How many trees are there? | |
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Rooted bifurcating trees | |
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Unrooted bifurcating trees | |
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Multifurcating trees | |
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Tree shapes | |
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Labeled histories | |
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Perspective | |
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Finding the best tree by heuristic search | |
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Nearest-neighbor interchanges | |
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Subtree pruning and regrafting | |
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Tree bisection and reconnection | |
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Other tree rearrangement methods | |
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Speeding up rearrangements | |
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Sequential addition | |
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Star decomposition | |
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Tree space | |
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Search by reweighting of characters | |
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Simulated annealing | |
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History | |
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Finding the best tree by branch and bound | |
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A nonbiological example | |
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Finding the optimal solution | |
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NP-hardness | |
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Branch and bound methods | |
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Phylogenies: Despair and hope | |
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Branch and bound for parsimony | |
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Improving the bound | |
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Rules limiting the search | |
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Ancestral states and branch lengths | |
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Reconstructing ancestral states | |
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Accelerated and delayed transformation | |
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Branch lengths | |
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Variants of parsimony | |
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Camin-Sokal parsimony | |
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Parsimony on an ordinal scale | |
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Dollo parsimony | |
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Polymorphism parsimony | |
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Unknown ancestral states | |
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Multiple states and binary coding | |
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Dollo parsimony and multiple states | |
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Polymorphism parsimony and multiple states | |
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Transformation series analysis | |
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Weighting characters | |
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Successive weighting and nonlinear weighting | |
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Compatibility | |
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Testing compatibility | |
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The Pairwise Compatibility Theorem | |
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Cliques of compatible characters | |
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Finding the tree from the clique | |
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Other cases where cliques can be used | |
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Where cliques cannot be used | |
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Statistical properties of parsimony | |
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Likelihood and parsimony | |
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Consistency and parsimony | |
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Some perspective | |
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A digression on history and philosophy | |
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How phylogeny algorithms developed | |
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Different philosophical frameworks | |
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Distance matrix methods | |
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Branch lengths and times | |
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The least squares methods | |
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The statistical rationale | |
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Generalized least squares | |
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Distances | |
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The Jukes-Cantor model--an example | |
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Why correct for multiple changes? | |
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Minimum evolution | |
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Clustering algorithms | |
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UPGMA and least squares | |
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Neighbor-joining | |
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Other approximate distance methods | |
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A puzzling formula | |
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Consistency and distance methods | |
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A limitation of distance methods | |
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Quartets of species | |
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The four point metric | |
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The split decomposition | |
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Short quartets methods | |
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The disk-covering method | |
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Challenges for the short quartets and DCM methods | |
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Three-taxon statement methods | |
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Other uses of quartets with parsimony | |
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Consensus supertrees | |
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Neighborliness | |
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De Soete's search method | |
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Quartet puzzling and searching tree space | |
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Perspective | |
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Models of DNA evolution | |
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Kimura's two-parameter model | |
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Calculation of the distance | |
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The Tamura-Nei model, F84, and HKY | |
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The general time-reversible model | |
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The general 12-parameter model | |
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LogDet distances | |
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Other distances | |
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Variance of distance | |
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Rate variation between sites or loci | |
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Models with nonindependence of sites | |
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Models of protein evolution | |
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Amino acid models | |
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The Dayhoff model | |
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Other empirically-based models | |
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Codon-based models | |
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Protein structure and correlated change | |
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Restriction sites, RAPDs, AFLPs, and microsatellites | |
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Restriction sites | |
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Modeling restriction fragments | |
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RAPDs and AFLPs | |
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Microsatellite models | |
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Likelihood methods | |
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Maximum likelihood | |
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Computing the likelihood of a tree | |
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Unrootedness | |
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Finding the maximum likelihood tree | |
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Inferring ancestral sequences | |
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Rates varying among sites | |
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Models with clocks | |
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Are ML estimates consistent? | |
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Hadamard methods | |
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The edge length spectrum and conjugate spectrum | |
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The closest tree criterion | |
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DNA models | |
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Computational effort | |
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Extensions of Hadamard methods | |
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Bayesian inference of phylogenies | |
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Bayes' theorem | |
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Bayesian methods for phylogenies | |
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Markov chain Monte Carlo methods | |
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The Metropolis algorithm | |
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Bayesian MCMC for phylogenies | |
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Proposal distributions | |
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Computing the likelihoods | |
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Summarizing the posterior | |
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Priors on trees | |
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Controversies over Bayesian inference | |
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Applications of Bayesian methods | |
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Testing models, trees, and clocks | |
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Likelihood and tests | |
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Likelihood ratios near asymptopia | |
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Multiple parameters | |
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Interval estimates | |
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Testing assertions about parameters | |
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Choosing among nonnested hypotheses: AIC and BIC | |
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The problem of multiple topologies | |
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Interior branch tests | |
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Testing the molecular clock | |
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Simulation tests based on likelihood | |
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More exact tests and confidence intervals | |
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Bootstrap, jackknife, and permutation tests | |
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The bootstrap and the jackknife | |
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Bootstrapping and phylogenies | |
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The delete-half jackknife | |
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The bootstrap and jackknife for phylogenies | |
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The multiple-tests problem | |
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Independence of characters | |
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Identical distribution--a problem? | |
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Invariant characters and resampling methods | |
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Biases in bootstrap and jackknife probabilities | |
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Alternatives to P values | |
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Parametric bootstrapping | |
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Permutation tests | |
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Paired-sites tests | |
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Multiple trees | |
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Testing other parameters | |
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Perspective | |
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Invariants | |
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Symmetry invariants | |
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Three-species invariants | |
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Lake's linear invariants | |
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Cavender's quadratic invariants | |
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Drolet and Sankoff's k-state quadratic invariants | |
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Clock invariants | |
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General methods for finding invariants | |
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Invariants and evolutionary rates | |
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Testing invariants | |
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What use are invariants? | |
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Brownian motion and gene frequencies | |
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Brownian motion | |
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Likelihood for a phylogeny | |
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What likelihood to compute? | |
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Multiple characters and Kronecker products | |
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Pruning the likelihood | |
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Maximizing the likelihood | |
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Inferring ancestral states | |
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Gene frequencies and Brownian motion | |
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Quantitative characters | |
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Neutral models of quantitative characters | |
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Changes due to natural selection | |
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Correcting for correlations | |
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Punctuational models | |
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Inferring phylogenies and correlations | |
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Chasing a common optimum | |
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The character-coding "problem" | |
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Continuous-character parsimony methods | |
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Threshold models | |
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Comparative methods | |
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An example with discrete states | |
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An example with continuous characters | |
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The contrasts method | |
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Correlations between characters | |
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When the tree is not completely known | |
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Inferring change in a branch | |
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Sampling error | |
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The standard regression and other variations | |
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Paired-lineage tests | |
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Discrete characters | |
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Molecular applications | |
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Coalescent trees | |
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Kingman's coalescent | |
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Bugs in a box--an analogy | |
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Effect of varying population size | |
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Migration | |
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Effect of recombination | |
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Coalescents and natural selection | |
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Likelihood calculations on coalescents | |
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The basic equation | |
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Using accurate genealogies--a reverie | |
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Two random sampling methods | |
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Bayesian methods | |
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Single-tree methods | |
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Summary-statistic methods | |
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Coalescents and species trees | |
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Methods of inferring the species phylogeny | |
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Alignment, gene families, and genomics | |
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Alignment | |
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Parsimony method | |
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Probabilistic models | |
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Gene families | |
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Comparative genomics | |
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Genome signature methods | |
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Consensus trees and distances between trees | |
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Consensus trees | |
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A dismaying result | |
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Distances between trees | |
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What do consensus trees and tree distances tell us? | |
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Biogeography, hosts, and parasites | |
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Component compatibility | |
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Brooks parsimony | |
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Event-based parsimony methods | |
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Randomization tests | |
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Statistical inference | |
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Phylogenies and paleontology | |
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Stratigraphic indices | |
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Stratophenetics | |
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Stratocladistics | |
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Controversies | |
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A not-quite-likelihood method | |
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Stratolikelihood | |
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Fossils within species: Sequential sampling | |
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Between species | |
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Tests based on tree shape | |
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Using the topology only | |
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Harding's probabilities of tree shapes | |
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Tests from shapes | |
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Tests using times | |
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Characters and key innovations | |
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Work remaining | |
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Drawing trees | |
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Issues in drawing rooted trees | |
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Unrooted trees | |
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Challenges | |
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Phylogeny software | |
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Trees, records, and pointers | |
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Declaring records | |
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Traversing the tree | |
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Unrooted tree data structures | |
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Tree file formats | |
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Widely used phylogeny programs and packages | |
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References | |
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Index | |