Table of Contents

Introduction 1

About This Book 1

Conventions Used in This Book 2

What You're Not to Read 2

Foolish Assumptions 3

How This Book Is Organized 3

Part I: What Evolution Is 3

Part II: How Evolution Works 4

Part III: What Evolution Does 4

Part IV: Evolution and Your World 5

Part V: The Part of Tens 5

Icons Used in This Book 6

Where to Go from Here 6

Part 1: What Evolution 1s 7

Chapter 1: What Evolution Is and Why You Need to Know 9

Biological Evolution at a Glance 10

Gene defined 10

What's the (gene) frequency, Kenneth? 11

The timescales of evolution 12

Gene extremes: Mutation and extinction 12

Darwin and His Big Ideas 13

Natural selection 14

Speciation 16

How "fitness" fits in with natural selection 17

Understanding adaptive characters 17

The Study of Evolution, Post-Darwin 18

Applying Evolution Today 19

Conservation 19

Agriculture 20

Medicine 21

One Final Point: Just How Evolved Are You? 22

Chapter 2: The Science — Past and Present — of Evolution 23

Evolution: A Fact and a Theory 24

Evolution and gravity: Two peas in a scientific pod 24

How to think like a scientist 25

The Evidence of Evolution 27

Knowledge about DNA and genetics 28

Experimental evidence 28

Measurement of the rates of change 28

The Scientific Foundation of Evolution by Natural Selection 29

Gradualism: Changes over time 29

The age of the Earth 30

The fossil record 32

Biogeographic patterns, or location, location, location 35

Natural selection and speciation 36

Chapter 3: Getting into Your Genes: (Very) Basic Genetics 39

What Is Genetics? 39

DNA: A Molecule for Storing Genetic Information 40

Chromosomes: Where your DNA is 41

DNA's four-letter alphabet 41

Reading the Instructions: From DNA to RNA to Proteins 43

Transcription: Producing RNA 44

Protein-coding RNA and the genetic code 44

Non-protein-coding RNA 46

Getting Specific about Genes 47

Of alleles and loci 47

Dominant, recessive, or passive-aggressive? 48

Summing It All Up: Genomes 49

Size isn't everything: Sizing up the genome 49

Number of genes 50

Genome organization: Nuclear, mitochondrial, or free floating? ...51

How many copies? 52

Passing It On: Sexual Reproduction and the Genome 53

Dominating issues 53

Genotype and phenotype 54

What this has to do with natural selection 55

Part U: How Evolution Works 57

Chapter 4: Variation: A Key Requirement for Evolution 59

Understanding Variation 59

Key concepts in variation 60

Two kinds of variation: Phenotypic and genotypic 61

Variation that's important to evolution 62

Population structure and gene flow 63

Where Variation Comes From: Mutations 63

Important mutations 64

Which comes first — the mutant chicken or the selective agent? 64

Different kinds of mutations 65

Preventing bad mutations 67

Gene Frequency and the Hardy-Weinberg Equilibrium 68

What's the big idea? 69

Using the Hardy-Weinberg equilibrium 70

Chapter 5: Natural Selection and Adaptations in Action 73

Natural versus Artificial Selection 74

Directional selection 75

Stabilizing selection 75

Adaptation: Changes Resulting from Natural Selection 75

Exaptation: Selecting for one trait, ending up with another 77

Chromosomes in action: Linkage and hitchhikers 78

But wait — not all traits are adaptations 79

You can't get there from here: Constraints and trade-offs 80

Darwin's and Grants' Finches 82

Chapter 6: Random Evolution and Genetic Drift:

Sometimes It's All about Chance 85

Genetic Drift Defined 85

Wrapping Your Head Around Randomness 86

At the level of the individual 87

At the level of the gametes 88

Situations in Which Drift Is Important 89

When a population is small 89

When genetically different individuals have the same fitness 90

Drift or selection? When it's hard to tell 90

Genetic Drift in Action: When Big Populations Get Little 92

Population bottlenecks 92

Founder effects 94

The Shifting-Balance Hypothesis: It's What's Wright 95

The adaptive landscape: A 3-D fitness map 95

Being the best you can be — on your own peak 97

You just can't get there from here 97

Chapter 7: Quantitative Genetics: When Many Genes

Act at Once 99

Why Quantitative Genetics Is Important 100

Interacting genes 100

Multigenetic traits in medicine and agriculture 101

Understanding Quantitative Traits 102

Continuous and non-continuous traits 102

Crossing a threshold 102

QTL Mapping: Identifying What Genes Matter 103

Analyzing the Heritability of Quantitative Traits 104

Additive or non-additive? 105

Determining phenotypic variation 105

Broad- and narrow-sense heritability 106

Measuring the Strength of Selection 107

Chapter 8: Species and Speciation 111

Species and Speciation at a Glance 111

The biological-species concept 112

When one species becomes two 112

Going in Circles: Ring Species 113

The Components of Speciation 115

How little changes add up: Local adaptations 116

Reproductive isolation: The final step of speciation 117

Types of Speciation 118

Allopatric speciation: There IS a mountain high enough 118

Allopatric speciation by founder effect: Getting carried away 119

Parapatric speciation: I just can't live in your world 119

Sympatric speciation: Let's just be friends 121

Islands: Good Places to Vacation and Speciate 123

A Species Concept for Bacteria 123

Chapter 9: Phylogenetics: Reconstructing the Tree of Life 125

Understanding the Importance of Phylogenetic Classification 125

Drawing the Tree of Life: Branching Patterns and Speciation 128

A simple tree 128

A more complex tree 128

Reading Trees 129

Knowing your nodes 129

Getting oriented: Up, down, or round and round 130

Understanding groups 132

Reconstructing Trees: A How To Guide 134

Finding clues (aka characters) 135

Using outgroup analysis to determine derived and ancestral states 136

Grouping species 136

Testing phylogenetic trees 138

Reconstructing Trees: An Example 139

Identifying characters 139

Assigning polarity 140

Grouping species 140

A word about more complicated trees 142

Seeing Phylogenetic Trees in Action 142

Example 1: The Florida dentist 143

Example 2: General exposure to HIV 143

Example 3: Legal cases 144

Part HI: What Evolution Does 145

Chapter 10: The Evolution of Life History 147

Evolution and the Diversity of Life Histories 148

'Til Death Do Us Part: The Evolution of Life Span 149

Why die? Trade-offs and risks 149

Methuselah flies: The evolution of life span in the laboratory 150

The Trade-Off between Survival and Reproduction 153

It's good to reproduce often, except when it's not 154

Early vs. later reproduction: Why wait? 156

The trade-off between size and number of offspring 163

Why Age? 165

Chapter 11: Units of Selection and the Evolution of Social Behavior 167

Inclusive Fitness and Kin Selection 167

Your fitness + your relatives' fitness = inclusive fitness 168

Not reproducing to help your family: Kin selection 169

Levels of Selection 170

Group selection 170

Selection at the level of the gene 173

The Evolution of Altruistic Social Systems 175

Cooperative breeding 175

One good turn deserves another: Reciprocal altruism 177

Going to extremes: Eusociality 179

One is the loneliest number: Multicellularity 181

Chapter 12: Evolution and Sex 183

Sex Terms You Probably Thought You Knew 183

Sexual Selection: The Art of Picking a Mate 184

The Peacock's Tail: Sexual Selection and Female Choice 185

It's not how you feel, it's how you look:

Runaway-selection hypothesis 186

Or maybe it IS how you feel: The good-genes hypothesis 188

The handicap hypothesis 189

Sexual Selection and Male-Male Competition 189

Direct male-male contests 190

Indirect competition 191

Sperm competition 191

Being sneaky: Alternative male strategies 192

The Battle of the Sexes: Male-Female Conflict 192

Infanticide 193

Poison semen 194

Sex: It's Expensive, So Why Bother? 195

Idea 1: Sex produces parasite-resistant offspring 196

Idea 2: Sex speeds up adaptation by combining rare beneficial mutations 197

Idea 3: Sex is beneficial because it can eliminate bad mutations 199

Evolution of Separate Sexes and the 50-50 Sex Ratio 200

Sometimes, it's good to be discrete 201

One girl for every boy 202

'Sex' in Bacteria 203

Chapter 13: Co-evolution: The Evolution of Interacting Species . . .205

Co-evolution Defined 205

Co-evolution and species interactions 206

Outcomes of co-evolution 209

Interactions between Plants and Animals 210

Pollination wars 211

The evolution of pollination by animals 212

Seed dispersal 214

Trading food and shelter for defense 215

Disease Systems: Parasitic Co-evolution 215

Bunnies in the Outback 216

Disease-host interaction in the lab 217

Chapter 14: Evo-Devo: The Evolution of Development 219

Defining Development: From Embryo to Adult 220

Under construction: The development process in action 221

The effect of environment 221

Little changes mean a lot 223

Key Ideas about Evo-Devo 224

Developmental stages = Evolutionary stages 225

Earlier vs. later stages 226

It's all in the timing 226

Why any of this is important 228

Genes Responsible for Development: Hox Genes 229

Keeping it in the family 230

Chapter 15: Molecular Evolution 233

My Genome's Bigger than Your Genome! 234

Genome sizes at a glance 234

The C value and the C-value paradox 236

Distinguishing between genes and non-coding DNA 236

The Whys and Wherefores of Non-coding DNA 238

It performs a function 238

It serves no function but isn't harmful 239

It's parasitic! 239

Coding DNA: Changing the Number of Genes an Organism Has 240

Getting genes from other lines: Lateral gene transfer 240

Shuffling exons: Alternative gene splicing 241

Duplicating genes: A gene is born 242

The Neutral Theory of Molecular Evolution 243

Telling Time with Genes: The Molecular Clock 244

When you can't 244

When you can 244

Part 1V: Evolution and Your World 249

Chapter 16: Human Evolution 251

The Origin of Homo Sapiens: Where We Came From 251

Phylogenetic evidence: Hangin' round on the Tree of Life 252

Carved in stone: The fossils 254

Reconstructing the history of hominid evolution 257

Out of Africa: Hominid migration patterns 261

Evolution within Homo Sapiens 265

Natural selection: Still acting on humans 265

Relaxation of selection 267

Cultural evolution 267

Chapter 17: The Evolution of Antibiotic Resistance 269

Antibiotics and Antibiotic Resistance in a Nutshell 270

Splitting microbial hairs: Defining antibiotics 270

A brief history of antibiotic resistance 271

Becoming Resistant to Antibiotics: A How-to Guide 272

Evolution via mutation 273

Evolution via gene transfer 274

Resistance at the cellular and biochemical levels 275

Evolving a bit at a time: Partial resistance 276

The Battle against Antibiotic Resistance 277

New and improved! Making new drugs 277

Turning back the clock to bacterial sensitivity 278

Changing the way antibiotics are used 281

Chapter 18: HIV: The Origin and Evolution of a Virus 283

What Viruses Are 284

Are viruses alive? We say "Yes!" 284

Viral reproduction: DNA, RNA, or retro? 286

What Is HIV? 286

Sneaking around in your chromosome 287

Attacking T cells 287

Mutating like crazy 288

The History of the HIV Epidemic 288

Where it came from 289

A timeline 290

The Path and Evolution of HIV in the Patient 291

Increasing and growing more divergent 292

Reaching a plateau 293

Destroying T-cells in a different way 293

Other Interesting Facts about HIV 294

Some people may be resistant 294

HIV evolves in a new host 294

HIV has a high recombination rate 295

Using Evolution to Fight HIV 295

Chapter 19: Influenza: One Flu, Two Flu, Your Flu, Bird Flu 297

The Flu and Your Immune System 298

Act 1: The virus attacks and spreads 298

Act 2: The body fights back 298

Act 3: Building up the guard 299

Which leads to a sequel: The return of the flu 299

The Three Types of Influenza: A, B, C 299

The Evolution of Influenza A 300

Mechanisms of evolution: Mutation, recombination, or reassortment 300

Genes to know 301

Who gets the flu and from where 302

Learning from the Past: Flu Pandemics 305

Pandemics of 1889 and 1900 306

The Spanish flu (1918) 306

The Asian flu (1957) 306

The Hong Kong flu (1968) 307

The Russian flu (1977) 307

Fighting Back: The Art and Science of Making Flu Vaccines 308

Dead vaccines 308

Live vaccines 309

Predicting the future to make next year's vaccine 311

Making a more universal influenza A vaccine 313

Part V: The Part of Tens 315

Chapter 20: Ten Fascinating Fossil Finds 317

Dinosaurs 317

Archaeopteryx 319

Wrangle Island Mammoths 320

Pterosaurs (Pterodactyls) 320

Trilobites 321

Tiktaalik Rosea 322

Hallucigenia and the Burgess Shale 323

Stromatolites 324

Microfossils 325

Amber 326

Chapter 21: Ten Amazing Adaptations 327

Different Kinds of Teeth 327

Sight: The Evolution of the Eye 328

Cave Blindness 329

Back to the Sea 330

And Back to the Land Again 331

Photosynthesis 332

Deep-Sea Thermal-Vent Organisms 332

Endosymbiosis 333

Vertebrate Flight 333

Trap-jaw Ants 334

Chapter 22: Ten Arguments against Evolution and Why They're Wrong 335

It's Only a Theory 335

It Violates the Second Law of Thermodynamics 336

It's Been Proved Wrong (by Scientists!) 336

It's Completely Random 337

It Can't Result in Big Changes 338

No Missing Link Means No Proof 338

It Can't Account for Everything: Enter the Intelligent Designer 339

It Can't Create Complex Structures 340

It Should Be Taught with ID in Science Class 341

It's a Fringe Topic 342

It's at Odds with Biblical Creation 343

Index 345

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