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20. Evolutionary Developmental Biology: (Tutorial) Sample Chapter

• • Changes In Development, And The Genes Controlling Development, Underlie Morphological Evolution

  • The Theory Of Recapitulation Is A Classic Idea (Largely Discredited) About The Relation Between Development And Evolution

  • Humans May Have Evolved From Ancestral Apes By Changes In Regulatory Genes

  • Many Genes That Regulate Development Have Been Identified Recently

  • Modern Developmental Genetic Discoveries Have Challenged And Clarified The Meaning On Homology

  • The Hox Gene Complex Has Expanded At Two Points In The Evolution Of Animals

  • Changes In The Embryonic Expression Of Genes Are Associated With Evolutionary Changes In Morphology

  • Evolution Of Genetic Switches Enables Evolutionary Innovation, Making The System More "Evolvable"

  • Conclusion

Summary

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21. Rates Of Evolution: (Tutorial)

• • Rates Of Evolution Can Be Expressed In "Darwins," As Illustrated By A Study Of Horse Evolution

  • Why Do Evolutionary Rates Vary?

  • The Theory Of Punctuated Equilibrium Applies The Theory Of Allopatric Speciation To Predict The Pattern Of Change In The Fossil Record

  • What Is The Evidence For Punctuated Equilibrium And For Phyletic Gradualism?

  • Evolutionary Rates Can Be Measured For Non-Continuous Character Changes, As Illustrated By A Study Of "Living Fossil" Lungfish

  • Taxonomic Data Can Be Used To Describe The Rate Of Evolution Of Higher Taxonomic Groups

  • Conclusion

Summary

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22. Coevolution: (Tutorial)

• • Coevolution Can Give Rise To Coadaptations Between Species

  • Coadaptation Suggests, But Is Not Conclusive Evidence Of, Coevolution

  • Insect-Plant Coevolution

  • Coevolutionary Relations Will Often Be Diffuse

  • Parasite-Host Coevolution

  • Coevolution Can Proceed In An "Arms Race"

  • The Probability That A Species Will Go Extinct Is Approximately Independent Of How Long It Has Existed

  • Antagonistic Coevolution Can Have Various Forms, Including The Red Queen Mode

  • Both Biological And Physical Hypotheses Should Be Tested On Macroevolutionary Observations

Summary

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23. Extinction And Radiation: (Tutorial)

• • The Number Of Species In A Taxon Increases Durings Phases Of Adaptive Radiation

  • Causes And Consequences Of Extinctions Can Be Studied In The Fossil Record

  • Mass Extinctions

  • Distributions Of Extinction Rates May Fit A Power Law

  • Changes In The Quality Of The Sedimentary Record Through Time Are Associated With Changes In The Observed Extinction Rate

  • Species Selection

  • One Higher Taxon May Replace Another, Because Of Chance, Environmental Change, Or Competitive Replacement

  • Species Diversity May Have Increased Logistically Or Exponentially Since The Cambrian, Or It May Have Increased Little At All

  • Conclusion: Biologists And Paleontologists Have Held A Range Of Views About The Importance Of Mass Extinctions In The History Of Life

Summary

Further Reading

Study And Review Questions

Glossary

Answers To Study And Review Questions

References

Index

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4. Natural Selection And Variation: (Tutorial) Sample Chapter

• • In Nature, There Is A Struggle For Existence

  • Natural Selection Operates If Some Conditions Are Met

  • Natural Selection Explains Both Evolution And Adaptation

  • Natural Selection Can Be Directional, Stabilizing, Or Disruptive

  • Variation In Natural Populations Is Widespread

  • Organisms In A Population Vary In Reproductive Success

  • New Variation Is Generated By Mutation And Recombination

  • New Variation Created By Recombination And Mutation Is Random With Respect To The Direction Of Adaptation

Summary

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Part II: Evolutionary Genetics:

5. The Theory Of Natural Selection: (Tutorial 1|Tutorial 2)

• • Population Genetics Is Concerned With Genotype And Gene Frequencies

  • An Elementary Population Genetic Model Has Four Main Steps

  • Genotype Frequencies In The Absence Of Selection Go To The Hardy-Weinberg Equilibrium

  • We Can Test, By Simple Observation, Whether Genotypes In A Population Are At The Hardy-Weinberg Equilibrium

  • The Hardy-Weinberg Theorem Is Important Conceptually, Historically, In Practical >Research, And In The Workings Of Theoretical Models

  • The Simplest Model Of Selection Is For One Favored Allele At One Locus

  • The Model Of Selection Can Be Applied To The Peppered Moth

  • Pesticide Resistance In Insects Is An Example Of Natural Selection

  • Fitnesses Are Important Numbers In Evolutionary Theory And Can Be Estimated By Three Main Methods

  • Natural Selection Operating On A Favored Allele At A Single Locus Is Not Meant To Be A General Model Of Evolution

  • A Recurrent Disadvantageous Mutation Will Evolve To A Calculable Equilibrial Frequency

  • Heterozygous Advantage

  • The Fitness Of A Genotype May Depend On Its Frequency

  • Subdivided Populations Require Special Population Genetic Principles

Summary

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6. Random Events In Population Genetics: (Tutorial)

• • The Frequency Of Alleles Can Change At Random Through Time In A Process Called Genetic Drift

  • A Small Founder Population May Have A Non-Representative Sample Of The Ancestral Population's Genes

  • One Gene Can Be Substituted For Another By Random Drift

  • Hardy-Weinberg "Equilibrium" Assumes The Absence Of Genetic Drift

  • Neutral Drift Over Time Produces A March To Homozygosity

  • A Calculable Amount Of Polymorphism Will Exist In A Population Because Of Neutral Mutation

  • Population Size And Effective Population Size

Summary

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7. Natural Selection And Random Drift In Molecular Evolution: (Tutorial)

• • Random Drift And Natural Selection Can Both Hypothetically Explain Molecular Evolution

  • Rates Of Molecular Evolution And Amounts Of Genetic Variation Can Be Measured

  • Rates Of Molecular Evolution Are Arguably Too Constant For A Process Controlled By Natural Selection

  • The Molecular Clock Shows A Generation Time Effect

  • The Nearly Neutral Theory

  • Evolutionary Rate And Functional Constraint

  • Conclusion And Comment: The Neutralist Paradigm Shift

  • Genomic Sequences Have Led To New Ways Of Studying Molecular Evolution

  • Conclusion: 35 Years Of Research On Molecular Evolution

Summary

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8. Two-Locus And Multilocus Population Genetics: (Tutorial)

• • Mimicry In Papilio Is Controlled By More Than One Genetic Locus

  • Genotypes At Different Loci In Papilio Memnon Are Coadapted

  • Mimicry In Heliconius Is Controlled By More Than One Gene, But They Are Not Tightly Linked

  • Two-Locus Genetics Is Concerned With Haplotype Frequencies

  • Frequencies Of Haplotypes May Or May Not Be In Linkage Equilibrium

  • Human HLA Genes Are A Multilocus Gene System

  • Linkage Disequilibrium Can Exist For Several Reasons

  • Two-Locus Models Of Natural Selection Can Be Built

  • Hitch-Hiking Occurs In Two-Locus Selection Models

  • Selective Sweeps Can Provide Evidence Of Selection In DNA Sequences

  • Linkage Disequilibrium Can Be Advantageous, Neutral, Or Disadvantageous

  • Wright Invented The Influential Concept Of An Adaptive Topography

  • The Shifting Balance Theory Of Evolution

Summary

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9. Quantitative Genetics: (Tutorial)

• • Climatic Changes Have Driven The Evolution Of Beak Size In One Of Darwin's Finches

  • Quantitative Genetics Is Concerned With Characters Controlled By Large Numbers Of Genes

  • Variation Is First Divided Into Genetic And Environmental Effects

  • Variance Of A Character Is Divided Into Genetic And Environmental Effects

  • Relatives Have Similar Genotypes, Producing The Correlation Between Relatives

  • Heritability Is The Proportion Of Phenotypic Variance That Is Additive

  • A Character's Heritability Determines Its Response To Artificial Selection

  • Strength Of Selection Has Been Estimated In Many Studies Of Natural Populations

  • Relations Between Genotype And Phenotype May Be Non-Linear, Producing Remarkable Responses To Selection

  • Stabilizing Selection Reduces The Genetic Variability Of A Character

  • Characters In Natural Populations Subject To Stabilizing Selection Show Genetic Variation

  • Levels Of Genetic Variation In Natural Populations Are Imperfectly Understood

  • Conclusion

Summary

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Part III: Adaptation And Natural Selection:

10. Adaptive Explanation: (Tutorial)

• • Natural Selection Is The Only Known Explanation For Adaptation

  • Pluralism Is Appropriate In The Study Of Evolution, Not Of Adaptation

  • Natural Selection Can In Principle Explain All Known Adaptations

  • New Adaptations Evolve In Continuous Stages From Pre Existing Adaptations, But The Continuity Takes Various Forms

  • Genetics Of Adaptation

  • Three Main Methods Are Used To Study Adaptation

  • Adaptations In Nature Are Not Perfect

  • How Can We Recognize Adaptations?

Summary

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11. The Units Of Selection: (Tutorial)

• • What Entities Benefit From The Adaptations Produced By Selection?

  • Natural Selection Has Produced Adaptations That Benefit Various Levels Of Organization

  • Another Sense Of "Unit Of Selection" Is The Entity Whose Frequency Is Adjusted Directly By Natural Selection

  • The Two Senses Of "Unit Of Selection" Are Compatible; One Specifies The Entity That Generally Shows Phenotypic Adaptations, The Other The Entity Whose Frequency Is Generally Adjusted By Natural Selection

Summary

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12. Adaptations In Sexual Reproduction: (Tutorial)

• • The Existence Of Sex Is An Outstanding, Unsolved Problem In Evolutionary Biology

  • There Are Two Main Theories In Which Sex May Have A Short-Term Advantage

  • Conclusion: It Is Uncertain How Sex Is Adaptive

  • The Theory Of Sexual Selection Explains Many Differences Between Males And Females

  • The Sex Ratio Is A Well Understood Adaptation

  • Different Adaptations Are Understood In Different Levels Of Detail

Summary

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Part IV: Evolution And Diversity:

13. Species Concepts And Intraspecific Variation: (Tutorial) Sample Chapter

• • In Practice Species Are Recognized And Defined By Phenetic Characters

  • Several Closely Related Species Concepts Exist

  • Isolating Barriers

  • Geographic Variation Within A Species Can Be Understood In Terms Of Population Genetic And Ecological Processes

  • "Population Thinking" And "Typological Thinking" Are Two Ways Of Thinking About Biological Diversity

  • Ecological Influences On The Form Of A Species Are Shown By The Phenomenon Of >Character Displacement

  • Some Controversial Issues Exist Between The Phenetic, Biological, And Ecological >Species Concepts

  • Taxonomic Concepts May Be Nominalist Or Realist

  • Conclusion

Summary

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14. Speciation: (Tutorial)

• • How Can One Species Split Into Two Reproductively Isolated Groups Of Organisms?

  • A Newly Evolving Species Could Theoretically Have An Allopatric, Parapatric, Or Sympatric Geographic Relation With Its Ancestor

  • Reproductive Isolation Can Evolve As A By-Product Of Divergence In Allopatric Populations

  • The Dobzhansky-Muller Theory Of Postzygotic Isolation

  • An Interim Conclusion: Two Solid Generalizations About Speciation

  • Reinforcement

  • Some Plant Species Have Originated By Hybridization

  • Speciation May Occur In Non-Allopatric Populations, Either Parapatrically Or Sympatrically

  • Parapatric Speciation

  • Sympatric Speciation

  • The Influence Of Sexual Selection In Speciation Is One Current Trend In Research

  • Identification Of Genes That Cause Reproductive Isolation Is Another Current Trend In Research

  • Conclusion

Summary

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15. The Reconstruction Of Phylogeny: (Tutorial)

• • Phylogenies Express The Ancestral Relations Between Species

  • Phyogenies Are Inferred From Morphological Characters Using Cladistic Techniques

  • Homologies Provide Reliable Evidence For Phylogenetic Inference, And Homoplasies Provide Unreliable Evidence

  • Homologies Can Be Distinguished From Homoplasies By Several Criteria

  • Derived Homologies Are More Reliable Indicators Of Phylogenetic Relations Than Are Ancestral Homologies

  • The Polarity Of Character States Can Be Inferred By Several Techniques

  • Some Character Conflict May Remain After Cladistic Character Analysis Is Complete

  • Molecular Sequences Are Becoming Increasingly Important In Phylogenetic Inference, And They Have Distinct Properties

  • Several Statistical Techniques Exist To Infer Phylogenies From Molecular Sequences

  • Molecular Phylogenetics In Action

  • Several Problems Have Been Encountered In Molecular Phylogenetics

  • Paralogous Genes Can Be Used To Root Unrooted Trees

  • Molecular Evidence Successfully Challenged Paleontological Evidence In The Analysis Of Human Phylogenetic Relations

  • Unrooted Trees Can Be Inferred From Other Kinds Of Evidence, Such As Chromosomal Inversions In Hawaiian Fruitflies

  • Conclusion

Summary

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16. Classification And Evolution: (Tutorial)

• • Biologists Classify Species Into A Hierarchy Of Groups

  • There Are Phenetic And Phylogenetic Principles Of Classification

  • There Are Phenetic, Cladistic, And Evolutionary Schools Of Classification

  • A Method Is Needed To Judge The Merit Of A School Of Classification

  • Phenetic Classification Uses Distance Measures And Cluster Statistics

  • Phylogenetic Classification Uses Inferred Phylogenetic Relations

  • Evolutionary Classification Is A Synthesis Of Phenetic And Phylogenetic Principles

  • The Principle Of Divergence Explains Why Phylogeny Is Hierarchical

  • Conclusion

Summary

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17. Evolutionary Biogeography: (Tutorial)

• • Species Have Defined Geographic Distributions

  • Ecological Characteristics Of A Species Limit Its Geographic Distribution

  • Geographic Distributions Are Influenced By Dispersal

  • Geographic Distributions Are Influenced By Climate, Such As In The Ice Ages

  • Local Adaptive Radiations Occur On Island Archipelagos

  • Species Of Large Geographic Areas Tend To Be More Closely Related To Other Local Species Than To Ecologically Similar Species Elsewhere In The Globe

  • Geographic Distributions Are Influenced By Vicariance Events, Some Of Which Are Caused By Plate Tectonic Movement

  • The Great American Interchange

  • Conclusion

Summary

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Part V: Macroevolution:

18. The History Of Life: (Tutorial)

• • Fossils Are Remains Of Organisms From The Past And Are Preserved In Sedimentary >Rocks

  • Geological Time Is Divided Into A Series Of Eras, Periods, And Epochs

  • The Cambrian Explosion

  • Evolution Of Land Plants

  • Vertebrate Evolution

  • Human Evolution

  • Macroevolution May Or May Not Be An Extrapolated Form Of Microevolution

Summary

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19. Evolutionary Genomics: (Tutorial)

• • Our Expanding Knowledge Of Genome Sequences Is Making It Possible To Ask, And Answer, Questions About The Evolution Of Genomes

  • The Human Genome Documents The History Of The Human Gene Set Since Early Life

  • The History Of Duplications Can Be Inferred In A Genomic Sequence

  • Genome Size Can Shrink By Gene Loss

  • Symbiotic Mergers, And Horizontal Gene Transfer, Between Species Influence Genome Evolution

  • The X/Y Sex Chromosomes Provide An Example Of Evolutionary Genomic Research At The Chromosomal Level

  • Genome Sequences Can Be Used To Study The History Of Non-Coding DNA

  • Conclusion

Summary

Further Reading

Study And Review Questions