- Author: Joseph Felsenstein
- Sinauer Associates, 2004
- Box link
Chapter 1: Parsimony methods
- One of the earliest methods of inferring phylogenies are parsimony methods. Edwards and Cavalli-Sforza (1963) declared that the preferred evolutionary tree is the one that involves ‘the minimum net amount of evolution’.
- In other words, we seek the phylogeny within which the fewest events occur while reconstructing the series of evolutionary events.
A simple example
- Assume we have 5 species, each of which ahs been scored for 6 characters. Each character can only have 2 states: 0 or 1.
- An event only allows a change in a character state from 0 –> 1 or 1 –>0.
- The initial state at the root node can be either state 0 or state 1.
- To find the most parsimonious tree, we must have a way of calculating how many changes of state are needed on a given tree. Suppose that someone proposes the phylogeny shown in Figure 1.1 (p. 2). The dataset is small enough in this example such that one can just “eyeball” the best reconstruction of evolution.
Chapter 2: Counting evolutionary changes
Chapter 3: How many trees are there?
Chapter 4: Finding the best tree by heuristic search
Chapter 5: Finding the best tree by branch and bound
Chapter 6: Ancestral states and branch lengths
Chapter 7: Variants of parsimony
Chapter 8: Compatibility
Chapter 9: Statistical properties of parsimony
Chapter 10: A digression on history and philosophy
Chapter 11: Distance matrix methods
Chapter 12: Quartets of species
Chapter 13: Models of DNA evolution
Chapter 14: Models of protein evolution
Chapter 15: Restriction sites, RAPDs, AFLPs, and microsatellites
Chapter 16: Likelihood methods
Chapter 17: Hadamard methods
Chapter 18: Bayesian inference of phylogenies
Chapter 19: Testing models, trees, and clocks
Chapter 20: Bootstrap, jackknife, and permutation tests
Chapter 21: Paired-sites tests
Chapter 22: Invariants
Chapter 23: Brownian motion and gene frequencies
Chapter 24: Quantitative characters
Chapter 25: Comparative methods
Chapter 26: Coalescent trees
Chapter 27: Likelihood calculations on coalescents
Chapter 28: Coalescents and species trees
Chapter 29: Alignment, gene families, and genomics
Chapter 30: Consensus trees and distances between trees
Chapter 31: Biogeography, hosts, and parasites
Chapter 32: Phylogenies and paleontology
Chapter 33: Tests based on tree shape
Chapter 34: Drawing trees
Chapter 35: Phylogeny software