Inferring phylogenies
Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. This title explains the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes
Print Book, English, ©2004
Sinauer Associates, Sunderland, Mass., ©2004
xx, 664 pages : illustrations, 1 map ; 23 cm
9780878931774, 0878931775
52127769
Parsimony methods
Counting evolutionary changes
How many trees are there?
Finding the best tree by heuristic search
Finding the best tree : branch and bound
Ancestral states and branch lengths
Variants of parsimony
Compatibility
Statistical properties of parsimony
A digression on history and philosophy
Distance matrix methods
Quartets of species
Models of DNA evolution
Models of protein evolution
Restriction sites, RAPDS, and microsatellites
Likelihood methods
Hadamard methods
Bayesian inference of phylogenies
Testing models, trees and clocks
Bootstrap, jackknife, and permutation tests
Paired sites tests
Invariants
Brownian motion and gene frequencies
Quantitative characters
Comparative methods
Coalescent trees
Likelihood calculations on coalescents
Coalescents and species trees
Alignment, gene families, and genomics
Consensus trees and distances between trees
Biogeography, hosts, and parasites
Phylogenies and paleontology
Tests based on tree shape
Drawing trees
Phylogeny software