Evolution

Cover
Front Endpapers
Front Matter
	Copyright Page
	Dedication
	Brief Contents
	Contents
	Preface
		Acknowledgments
	How to Learn Evolutionary Biology
	Media and Supplements
UNIT I An Idea that Changed the World
Chapter 1 Evolutionary Biology
	Nothing in Biology Makes Sense except in the Light of Evolution”
	What Is Evolution? Is It Fact or Theory?
	The Evolution of Evolutionary Biology
		Before Darwin
		Charles Darwin
		Darwin’s evolutionary theory
		Evolutionary biology after Darwin
		The evolutionary synthesis
		Evolutionary biology since the synthesis
	How Evolution Is Studied
	Philosophical Issues
		Ethics, religion, and evolution
	Summary
Chapter 2 The Tree of Life
	The Tree of Life, from Darwin to Today
	Phylogenetic Trees
		Inferring phylogenies: An introduction
	Variations on the Phylogenetic Theme
		Branches of a phylogenetic tree sometimes rejoin
		Not only organisms have “phylogenies”
	Phylogenetic Insights into Evolutionary History
		Inferring the history of character evolution
		Estimating time of divergence
		Patterns of evolution
	Summary
Chapter 3 Natural Selection and Adaptation
	Adaptive Evolution Observed
	Natural Selection
		The meaning of natural selection
		Natural selection and chance
		The effective environment depends on the organism
	Levels of Selection
		Selfish genes and unselfish behaviors
		Selection of organisms and groups
		Species selection
	The Nature of Adaptations
		Selection of and selection for
		Recognizing adaptations
	Imperfections and Constraints
	Natural Selection and the Evolution of Diversity
	What Not To Expect of Natural Selection
	Summary
UNIT II How Evolution Works
Chapter 4 Mutation and Variation
	The Machinery of Inheritance
	The Inheritance of Variation
		Gene mixing by segregation
		Gene mixing by recombination
		Gene mixing with asexual inheritance
	Mutation: The Ultimate Source of Variation
		Point mutations
		Structural mutations
	Rates and Effects of Mutations
		Mutation rates
		Effects of mutations
		Germ line mutations and somatic mutations
	Is Mutation Random?
	Nongenetic Inheritance
	Summary
Chapter 5 The Genetical Theory of Natural Selection
	Natural Selection and Evolution in Real Time
	Evolution by Selection and Inheritance
	Fitness: The Currency of Selection
	Positive Selection: The Spread of Beneficial Mutations
		The rate of adaptation
		Chance and adaptation: The probability that a beneficial mutation spreads
	Evolutionary Side Effects
		Hitchhiking: When one allele goes for a ride with another
	When Selection Preserves Variation
		Overdominance
		Other forms of balancing selection
	Selection That Favors the Most Common
		Underdominance: When heterozygotes suffer
		Positive frequency-dependent selection
	The Evolution of a Population’s Mean Fitness
		The fundamental theorem of natural selection and the adaptive landscape
	Deleterious Mutations
		A mutation-selection balance
		The mutation load
	Summary
Chapter 6 Phenotypic Evolution
	Genotypes and Phenotypes
	Fitness Functions Describe Selection on Quantitative Traits
	Measuring the Strength of Directional Selection
	Evolution by Directional Selection
		When genes interact: Dominance and epistasis
		Adaptation from standing genetic variation versus new mutations
		Can adaptation rescue species from extinction?
	Artificial Selection
	Correlated Traits
		Constraints and trade-offs
		The causes of genetic correlations
	Phenotypic Plasticity
	The Genetic Architecture of Quantitative Traits
		Quantitative trait loci
		The genetics of quantitative traits
	Summary
Chapter 7 Genetic Drift: Evolution at Random
	What Is Random Genetic Drift?
	The Genealogy of Genes
	How Strong Is Genetic Drift?
		Populations that change in size
	Drift and Genetic Variation within Species
		Estimating population size
	Genetic Drift and Natural Selection
		Crossing an adaptive valley by drift
		The fate of beneficial mutations in large populations
	The Evolution of Differences among Species
		The neutral theory of molecular evolution
	Searching the Genes for Signatures of Adaptation
		Synonymous versus nonsynonymous differences
		The MK test
		Divergence among populations
	Summary
Chapter 8 Evolution in Space
	Patterns in Space
	Gene Flow
		How is gene flow measured?
	Genetic Divergence between Populations
	Gene Flow and Selection
		Tension zones
	Gene Flow and Drift
		Gene flow, local adaptation, and drift
	The Evolution of Dispersal
	The Evolution of Species’ Ranges
	Summary
Chapter 9 Species and Speciation
	What Are Species?
	Reproductive Isolation
		Prezygotic barriers
		Postzygotic barriers
		How fast does reproductive isolation evolve?
	The Causes of Speciation
	The Geography of Speciation
		Allopatric speciation
		Sympatric speciation
		Parapatric speciation
	The Genomics of Speciation
	Summary
UNIT III Products of  Evolution: What Natural Selection Has Wrought
Chapter 10 All About Sex
	What Are Females and Males?
	Sexual Selection
		Why are males sexually selected?
		Sexual selection by male-male competition
		Sexual selection by female choice
		Sexual selection in flowering plants
	Sex Ratios
	Why Sex?
		Advantages to sex in changing environments
		Selective interference favors sex and recombination
	Selfing and Outcrossing
	Summary
Chapter 11 How to Be Fit
	Life History Traits as Components of Fitness
		Costs of reproduction
		Fitness in age-structured populations
		Senescence
	Evolution of the Population Growth Rate and Density
		Diverse life histories
		Number of offspring
		Life histories and mating strategies
	Specialists and Generalists
		Advantages of specialization
		Specialization without trade-offs
		Experiments on niche evolution
	Summary
Chapter 12 Cooperation and Conflict
	The Costs and Benefits of Interacting
	Social Interactions and Cooperation
	Cooperation among Unrelated Individuals
		Reciprocity
	Shared Genes and the Evolution of Altruism
		Spite
	Conflict and Cooperation in Close Quarters: The Family
		Conflict between mates
		Murder in the family
		Parent-offspring conflict
		Eusocial animals: The ultimate families
	Levels of Selection
		Selfish DNA
		Selfish mitochondria
		Group selection
	Cooperation and Major Evolutionary Transitions
	Summary
Chapter 13 Interactions among Species
	Coevolution and Interactions among Species
	The Evolution of Enemies and Victims
		Aposematism and mimicry
		Plants and herbivores
		Parasite-host interactions and infectious disease
	Mutualisms
	The Evolution of Competitive Interactions
	Evolution and Community Structure
	Summary
Chapter 14 The Evolution of Genes and Genomes
	The Birth of a Gene
		Gene families
	The Death of a Gene
	Evolution of Protein-Coding Genes
		Evolution of coding regions by genetic drift
		Evolution of coding regions by positive selection
	Evolution of Gene Expression
	Gene Structure
	Chromosome Evolution
		Fissions, fusions, and the evolution of chromosome number
		Inversions and the evolution of chromosome structure
	Evolution of Genome Size and Content
		Genomes large and small
		Genetic parasites and transposable elements
		Routes to the evolution of the smallest and largest genomes
	Summary
Chapter 15 Evolution and Development
	Comparative Development and Evolution
	Gene Regulation
		Hox genes and the genetic toolkit
	Developmental-Genetic Bases of Phenotypic Evolution
		regulatory mutations
		Evolution by
		regulatory mutations
		Evolution by
		Overview: The genetics and development of phenotypic evolution
	Evolvability and Developmental Pathways
	Constraints on Adaptive Evolution
	Phenotypic Plasticity and Canalization
		Does phenotypic plasticity contribute to evolution?
	Summary
UNIT IV Macroevolution and the History of Life
Chapter 16 Phylogeny: The Unity and Diversity of Life
	Inferring Phylogenies
		Why estimating phylogenies can be hard
		Methods for estimating phylogenies
	How Do We Use Phylogenies?
		Dating evolutionary events
		Discovering the history of genes and cultures
		Reconstructing ancestors
		Studying adaptations: The comparative method
		Classification
	Summary
Chapter 17 The History of Life
	Some Geological Fundamentals
		The fossil record
	Before Life Began2
	The Emergence of Life
	Precambrian Life
	The Cambrian Explosion and the Origins of Animal Diversity
	Paleozoic Life
		The colonization of land
		Paleozoic life on land
		The end-Permian mass extinction
	Mesozoic Life
	The Cenozoic Era
		The modern world takes shape
		The adaptive radiation of mammals
		Pleistocene events
	Summary
Chapter 18 The Geography of Evolution
	Biogeographic Evidence for Evolution
	Major Patterns of Distribution
		Historical factors affecting geographic distributions
	Historical Explanations of Geographic Distributions
		Vicariance
		Dispersal
		Phylogeography
	Geographic Range Limits: Ecology and Evolution
	Geographic Patterns of Diversity
	Summary
Chapter 19 The Evolution of Biological Diversity
	Estimating and Modeling Changes in Biological Diversity
		Studying diversity in the fossil record
	Diversity through the Phanerozoic
		Rates of origination and extinction
		Mass extinctions
	Phylogenetic Studies of Diversity
		The shapes of phylogenies
	Does Species Diversity Reach Equilibrium?
	Summary
Chapter 20 Macroevolution: Evolution above the Species Level
	The Origin of Major New Forms of Life
		The origin of mammals
	Gradualism and Saltation
	The Evolution of Novelty
		Incipient and novel features: Permissive conditions and natural selection
		Complex characteristics
		Homology and the emergence of novel characters
	From Microevolution to Macroevolution
		Rates of evolution
		Gradualism and punctuated equilibria
		Speciation and phenotypic evolution
	Trends, Predictability, and Progress
		Trends: Kinds and causes
		Are there major trends in the history of life?
		Predictability and contingency in evolution
		The question of progress
	Summary
UNIT V Evolution and Homo sapiens
Chapter 21 The Evolutionary Story of
	Where Did We Come From?
		Our closest living relatives
		How humans differ from other apes
		Our ancestry: Hominins through time
	The Arrival of
		The human history of hybridization
		The diversity of human populations
	Brain and Language
	Diet and Agriculture: A Revolution in Our World
	Natural Selection, Past and Present
		Our genetic loads
		Natural selection and evolution in real time
		Evolutionary mismatches
	The Evolution of Culture
	Summary
Chapter 22 Evolution and Society
	Creationism and Science
		Creationism
		The nature of science
	The Evidence for Evolution
		The fossil record
		Phylogenetic and comparative studies
		Genes and genomes
		Biogeography
		Failures of the argument from design
		Evolution, and its mechanisms, observed
	The Uses and Implications of Evolutionary Science
		Evolution by natural selection: A broad and flexible concept
		Practical applications of evolutionary science
		Using organisms’ adaptations
		Agriculture and natural resources
		Conservation
		Health and medicine
	Evolution and Human Behavior
		Variation in cognitive and behavioral traits
		Human behavior: Evolution and culture
		Understanding nature and humanity
	Summary
Appendix: A Statistics Primer
	Probability Distributions
	Descriptive Statistics
	Estimation
	Testing Hypotheses
	Likelihood
	Bayesian Inference
	Summary
Glossary
Literature Cited
Illustration and Photo Credits
Index
Back Endpapers