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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 | |