【書名】

【著者】Joseph Felsenstein

【刊行】August 2003（本には「2004年」と記されている）

【出版】Sinauer Associates, Sunderland

【URL 】<http://www.sinauer.com/detail.php?id=1775>

【頁数】xx+664 pp.

【定価】US$ 59.95 (paperback)

【ISBN】0-87893-177-5

【備考】Companion Webpages

Errata <http://evolution.gs.washington.edu/book/typos.html>

Datasets <http://evolution.gs.washington.edu/book/datasets.html>

【目次】

PREFACE

1. Parsimony methods

A simple example

Branch lengths

Unresolved questions

2. Counting evolutionary changes

The Fitch algorithm

Sankoff's algorithm

3. How many trees are there?

Rooted bifurcating trees

Unrooted bifurcating trees

Multifurcating trees

Tree shapes

Labelled histories

Perspective

4. 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

History

5. 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 rules

6. Ancestral states and branch lengths

Reconstructing ancestral states

Branch lengths

7. 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 weighting

8. 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 anyway

9. Statistical properties of parsimony

Likelihood and parsimony

Consistency and parsimony

Some perspective

10. A digression on history and philosophy

How phylogeny algorithms developed

Different philosophical frameworks

11. 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 methods

12. 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 method

13. 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 loci

14. Models of protein evolution

Protein models

15. Restriction sites, RAPDs, and microsatellites

Restriction sites

Modelling restriction fragments

RAPDs and AFLPs

Microsatellite models

16. 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 methods

18. 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 inference

19. 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 likelihood

20. 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 bootstrapping

21. 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 frequencies

24. 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 models

25. 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 characters

26. Coalescent trees

Kingman's coalescent

Bugs in a box-an analogy

Effect of varying population size

Migration

Effect of recombination

27. Likelihood calculations on coalescents

The basic equation

Using accurate genealogies-a reverie

Two random sampling methods

Fu's method

Watterson's method

28. Alignment, gene families, and genomics

Alignment

Parsimony method

Probabilistic models

Gene families

Comparative genomics

29. Coalescents and species trees

Methods of inferring the species phylogeny

30. Consensus trees and distances between trees

Consensus trees

A dismaying result

Distances between trees

31. Biogeography, hosts, and parasites

Component compatibility

Brooks parsimony

Event-based parsimony methods

Statistical inference

32. Phylogenies and paleontology

Stratophenetics

Stratocladistics

Controversies

Stratolikelihood

Fossils within species: sequential sampling

Between species

33. Tests based on tree shape

Using the topology only

Harding's probabilities of tree shapes

Tests from shapes

Tests using branch lengths

Work remaining

34. Drawing trees

35. Phylogeny software

REFERENCES