Joseph Felsenstein
（2004年，Sinauer Associates，ISBN:0878931775）
統計学的系統学（statistical phylogenetics）の［早くも定番となりつつある］教科書．700ページ近くある分量を，典型的な日本的ペースに則って輪読やセミナーでやるとしたら，いったい何年かかるのか．書評や正誤表が載っているコンパニオン・サイトは必見（山ほど書評が出ていて，逐一 Felsenstein が“逆書評”している），そして文中に載っているデータセットのダウンロード・サイトも役に立つだろう．
【目次】
PREFACE1. Parsimony methods
A simple example
Branch lengths
Unresolved questions2. Counting evolutionary changes
The Fitch algorithm
Sankoff's algorithm3. How many trees are there?
Rooted bifurcating trees
Unrooted bifurcating trees
Multifurcating trees
Tree shapes
Labelled histories
Perspective4. Finding the best tree by heuristic search
Nearest-neighbor interchanges
Subtree pruning and regrafting
Tree bisection and reconnection
Sequential addition
Star decomposition
Tree space
Search by reweighting of characters
History5. Finding the best tree-branch and bound
A non-biological example
NP-hardness
Branch and bound
Phylogenies: despair and hope
Branch and bound for parsimony
Improving the bound
Zharkikh's rules6. Ancestral states and branch lengths
Reconstructing ancestral states
Branch lengths7. Variants of parsimony
Camin-Sokal parsimony
Dollo parsimony
Polymorphism parsimony
Unknown ancestral states
Multiple states and binary coding
Dollo parsimony and multiple states
Polymorphism parsimony and multiple states
Weighting characters
Successive weighting and nonlinear weighting8. Compatibility
Testing compatibility
The pairwise compatibility theorem
Cliques of compatible characters
Finding the tree from the clique
Other cases where cliques can be used
Where cliques cannot be used
Using compatibility on molecules anyway9. Statistical properties of parsimony
Likelihood and parsimony
Consistency and parsimony
Some perspective10. A digression on history and philosophy
How phylogeny algorithms developed
Different philosophical frameworks11. Distance matrix methods
The least squares methods
The statistical rationale
Generalized least squares
Distances
The Jukes-Cantor model-an example
Why correct for multiple changes?
Minimum evolution
Clustering algorithms
UPGMA and least squares
Neighbor-joining
Other approximate distance methods12. Quartets of species
The four-point metric
The split decomposition
Short quartets methods
The Disk Covering Method
Challenges for the short quartets and DCM methods
Quartet puzzling and searching tree space
Consensus supertrees
Neighborliness
De Soete's search method13. Models of DNA evolution
Kimura's 2-parameter model
Calculation of the distance
The Tamura-Nei model, F84, and HKY
The general time-reversible model
The general 12-parameter model
LogDet distances
Rate variation between sites or loci14. Models of protein evolution
Protein models
15. Restriction sites, RAPDs, and microsatellites
Restriction sites
Modelling restriction fragments
RAPDs and AFLPs
Microsatellite models16. Likelihood methods
Maximum likelihood
An example
Computing the likelihood of a tree
Economizing on the computation
Handling ambiguity and error
Unrootedness
Finding the maximum likelihood tree
Rates varying among sites
Models with clocks
Are ML estimates consistent?17. Hadamard methods
The edge length spectrum and conjugate spectrum
The closest tree criterion
DNA models
Computational effort
Extensions of Hadamard methods18. Bayesian inference of phylogenies
Bayes' theorem
Bayesian methods for phylogenies
Markov Chain Monte Carlo methods
Bayesian MCMC for phylogenies
Proposal distributions
Computing the likelihoods
Summarizing the posterior
Priors on trees
Controversies over Bayesian inference19. Testing trees by likelihood
Likelihood ratios near asymptopia
Multiple parameters
Interval estimates
Testing assertions about parameters
The problem of multiple topologies
Testing the molecular clock
Simulation tests based on likelihood20. Bootstrap and randomization tests
The bootstrap and the jackknife
Bootstrapping estimates of phylogenies
The delete-half jackknife
The bootstrap and jackknife for phylogenies
The multiple tests problem
Independence of characters
Identical distribution-a problem?
Invariant characters and resampling methods
Biases in bootstrap and jackknife probabilities
Parametric bootstrapping21. Paired sites tests
Multiple trees
22. Invariants
Symmetry invariants
Three-species invariants
Lake's linear invariants
Cavender's quadratic invariants
Drolet and Sankoff's quadratic invariant
Clock invariants
General methods for finding invariants
Invariants and evolutionary rates
What use are invariants?23. Continuous characters and gene frequencies
Brownian motion
Likelihood for a phylogeny
What likelihood to compute?
Multiple characters and Kronecker products
Pruning the likelihood
Maximizing the likelihood
Brownian motion and gene frequencies24. Quantitative characters
Neutral models of quantitative characters
Changes due to natural selection
Correcting for correlations
Punctuational models
Inferring phylogenies and correlations
Chasing a common optimum
The character-coding "problem"
Continuous character parsimony methods
Threshold models25. Comparative methods
An example with discrete states
An example with continuous characters
The contrasts method
Correlations between characters
Sampling error
The standard regression
Polyfurcations
Paired lineage tests
Discrete characters26. Coalescent trees
Kingman's coalescent
Bugs in a box-an analogy
Effect of varying population size
Migration
Effect of recombination27. Likelihood calculations on coalescents
The basic equation
Using accurate genealogies-a reverie
Two random sampling methods
Fu's method
Watterson's method28. Alignment, gene families, and genomics
Alignment
Parsimony method
Probabilistic models
Gene families
Comparative genomics29. Coalescents and species trees
Methods of inferring the species phylogeny
30. Consensus trees and distances between trees
Consensus trees
A dismaying result
Distances between trees31. Biogeography, hosts, and parasites
Component compatibility
Brooks parsimony
Event-based parsimony methods
Statistical inference32. Phylogenies and paleontology
Stratophenetics
Stratocladistics
Controversies
Stratolikelihood
Fossils within species: sequential sampling
Between species33. Tests based on tree shape
Using the topology only
Harding's probabilities of tree shapes
Tests from shapes
Tests using branch lengths
Work remaining34. Drawing trees
35. Phylogeny software
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