Inferring Phylogenies

ISBN-10: 0878931775
ISBN-13: 9780878931774
Edition: 2002
List price: $99.95
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Description: Phylogenies, are the basic structures necessary to think about and analyse differences between species. This text covers the statistical, computational and algorithmic work that has taken place in the field over four decades.

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Book details

List price: $99.95
Copyright year: 2002
Publisher: Sinauer Associates, Incorporated
Publication date: 9/4/2003
Binding: Paperback
Pages: 580
Size: 7.00" wide x 8.75" long x 1.25" tall
Weight: 2.332
Language: English

Phylogenies, are the basic structures necessary to think about and analyse differences between species. This text covers the statistical, computational and algorithmic work that has taken place in the field over four decades.

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

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