The Comparative Method in Evolutionary Biology

From Darwin onward, it has been second nature for evolutionary biologists to think comparatively, because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. It examines how the comparative method complements other approaches, identifies the biological causes of similarity among species, and discusses methods for reconstructing phylogenetic trees, along with many other topics. The book will interest all students, professionals, and researchers in evolutionary biology, ecology, genetics and related fields.

The Comparative Method for Studying Adaptation

Introduction

1

(6)

The organization of this book

7

(2)

Two traditions in comparative biology: descent and guilds

9

(2)

The comparative approach for studying diversity

11

(11)

The comparative method and other ways of studying evolution

22

(5)

Testing adaptationist ideas using experiment, observation, and comparison

27

(4)

Defining characters and environments

31

(2)

Summary

33

(2)

Why Worry about Phylogeny?

Introduction

35

(1)

Correlation, causation, phylogeny, and confounding variables

36

(2)

Three reasons why phylogenetically related species are similar

38

(10)

Afterwords

48

(1)

Summary

49

(1)

Reconstructing Phylogenetic Trees and Ancestral Character States

Introduction

50

(1)

Reconstruction of phylogenetic trees

51

(20)

Finding ancestral character states

71

(6)

Summary

77

(1)

Comparative Analysis of Discrete Data

Introduction

78

(1)

The problem

79

(3)

Character transitions and discrete variables

82

(1)

Counting evolutionary events

83

(5)

Tests of directional hypotheses with discrete characters

88

(6)

A statistical model of evolutionary change

94

(7)

Estimating transition probabilities by maximum likelihood

101

(2)

Applying the statistical model to a real data set

103

(1)

Relationship of the statistical model to previous methods

104

(6)

Discussion

110

(3)

Summary

113

(1)

Comparative Analysis of Continuous Variables

Introduction

114

(2)

Testing hypotheses on continuous variables

116

(5)

Species analyses

121

(2)

Analysis of higher nodes

123

(6)

Stearns' phylogenetic-subtraction method

129

(5)

Phylogenetic autocorrelation method

134

(3)

A maximum likelihood approach

137

(1)

Independent comparisons methods

138

(21)

Testing hypotheses with independent comparisons

159

(3)

Directional methods

162

(5)

Selected computer simulation results

167

(2)

Conclusions

169

(1)

Summary

170

(1)

Determining the Forms of Comparative Relationships

Introduction

171

(1)

The fundamental allometric relation

172

(2)

Types of allometric relationship

174

(1)

Interpreting allometric lines

175

(4)

Techniques for fitting allometric equations

179

(7)

Applying the models for continuous variables to allometric relationships

186

(10)

Explaining allometry

196

(2)

Allometric models with more than one independent variable

198

(4)

Summary

202

(1)

Conclusion

203

(3)

References

206

(25)

Author Index

231

(5)

Subject Index

236

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The Comparative Method in Evolutionary Biology

Summary

Table of Contents

Supplemental Materials