ISBN : 9780878931774
Phylogenies (evolutionary trees) are basic to thinking about and analyzing differences between species. Statistical, computational, and algorithmic work on them has been ongoing for four decades, with great advances in understanding. Yet no book has summarized this work until now. Inferring Phylogenies explains clearly the assumptions and logic of making inferences about phylogenies, and using them to make inferences about evolutionary processes. It is an essential text and reference for anyone who wants to understand how phylogenies are reconstructed and how they are used.As phylogenies are inferred with various kinds of data, this book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.Inferring Phylogenies is intended for graduate-level courses, assuming some knowledge of statistics, mathematics (calculus and fundamental matrix algebra), molecular sequences, and quantitative genetics.
1 Parsimony methods
2 Counting evolutionary changes
3 How many trees are there?
4 Finding the best tree by heuristic search
5 Finding the best tree by branch and bound
6 Ancestral states and branch lengths
7 Variants of parsimony
8 Compatibility
9 Statistical properties of parsimony
10 A digression on history and philosophy
11 Distance matrix methods
12 Quartets of species
13 Models of DNA evolution
14 Models of protein evolution
15 Restriction sites, RAPDs, AFLPs, and microsatellites
16 Likelihood methods
17 Hadamard methods
18 Bayesian inference of phylogenies
19 Testing models, trees, and clocks
20 Bootstrap, jackknife, and permutation tests
21 Paired-sites tests
22 Invariants
23 Brownian motion and gene frequencies
24 Quantitative characters
25 Comparative methods
26 Coalescent trees
27 Likelihood calculations on coalescents
28 Coalescents and species trees
29 Alignment, gene families, and genomics
30 Consensus trees and distances between trees
31 Biogeography, hosts, and parasites
32 Phylogenies and paleontology
33 Tests based on tree shape
34 Drawing trees
35 Phylogeny software
