Evolutionary Analysis

by Freeman, Scott

• ISBN13: 9780131063303
• ISBN10: 0131063308
• Additional ISBN(s): 9780130172914, 9780132275842
• Edition: 3rd
• Format: Hardcover
• Copyright: 2003-07-01
• Publisher: Pearson College Div
• More Book Details
• Purchase Benefits

Table of Contents

Preface	xi
PART 1 INTRODUCTION	1	(106)
A Case for Evolutionary Thinking: Understanding HIV	3	(32)
The Natural History of the HIV/AIDS Epidemic	4	(6)
Why Does AZT Work in the Short Run, But Fail in the Long Run?	10	(7)
Box 1.1 Can understanding how resistance evolves help researchers design better treatments?	14	(3)
Why is HIV Fatal?	17	(5)
Why Are Some People Resistant to Infection by HIV?	22	(2)
Where Did HIV Come From?	24	(11)
Box 1.2 When did HIV move from chimpanzees to humans?	28	(1)
Summary	29	(1)
Questions	30	(1)
Exploring the Literature	31	(1)
Citations	31	(4)
The Evidence for Evolution	35	(34)
Evidence of Change through Time	36	(11)
Box 2.1 A brief history of ideas on evolution	37	(10)
Evidence of Common Ancestry	47	(10)
Box 2.2 Homology and model organisms	56	(1)
The Age of Earth	57	(5)
Box 2.3 A closer look at radiometric dating	61	(1)
Is There Necessarily a Conflict between Evolutionary Biology and Religion?	62	(7)
Summary	64	(1)
Questions	65	(1)
Exploring the Literature	66	(1)
Citations	67	(2)
Darwinian Natural Selection	69	(38)
Artificial Selection: Domestic Animals and Plants	70	(2)
Evolution by Natural Selection	72	(2)
The Evolution of Flower Color in an Experimental Snapdragon Population	74	(2)
The Evolution of Beak Shape in Galapagos Finches	76	(11)
Box 3.1 Issues that complicate how heritabilities are estimated	82	(5)
The Nature of Natural Selection	87	(5)
The Evolution of Darwinism	92	(3)
The Debate over ``Scientific Creationism'' and Intelligent Design Theory	95	(12)
Summary	104	(1)
Questions	104	(1)
Exploring the Literature	105	(1)
Citations	105	(2)
PART 2 MECHANISMS OF EVOLUTIONARY CHANGE	107	(222)
Mutation and Genetic Variation	109	(32)
Where New Alleles Come From	109	(11)
Where New Genes Come From	120	(3)
Chromosome Alterations	123	(4)
Measuring Genetic Variation in Natural Populations	127	(14)
Box 4.1 Gel electrophoresis	132	(5)
Summary	137	(1)
Questions	137	(1)
Exploring the Literature	138	(1)
Citations	139	(2)
Mendelian Genetics in Populations I: Selection and Mutation as Mechanisms of Evolution	141	(54)
Mendelian Genetics in Populations: The Hardy--Weinberg Equilibrium Principle	142	(12)
Box 5.1 Combining probabilities	147	(5)
Box 5.2 The Hardy--Weinberg equilibrium principle with more than two alleles	152	(2)
Selection	154	(41)
Box 5.3 A general treatment of selection	159	(3)
Box 5.4 Hardy--Weinberg equilibrium among different mutant alleles that cause a recessive genetic disease	162	(2)
Box 5.5 Statistical analysis of allele and genotype frequencies using the X2 (chi-square) test	164	(2)
Box 5.6 Predicting the frequency of the CCR5-Δ32 allele in future generations	166	(1)
Patterns of Selection: Testing Predictions of Population Genetic Theory	166	(4)
Box 5.7 An algebraic treatment of selection on recessive and dominant alleles	170	(4)
Box 5.8 Stable equilibria with heterozygote superiority and unstable equilibria with heterozygote inferiority	174	(8)
Mutation	182	(2)
Box 5.9 A mathematical treatment of mutation as an evolutionary force	184	(3)
Box 5.10 Allele frequencies under mutation-selection balance	187	(1)
Box 5.11 Estimating mutation rates for recessive alleles	188	(2)
Summary	190	(1)
Questions	191	(1)
Exploring the Literature	192	(1)
Citations	193	(2)
Mendelian Genetics in Populations II: Migration, Genetic Drift, and Nonrandom Mating	195	(58)
Migration	197	(7)
Box 6.1 An algebraic treatment of migration as an evolutionary force	199	(2)
Box 6.2 Selection and migration in Lake Erie water snakes	201	(3)
Genetic Drift	204	(19)
Box 6.3 The probability that a given allele will be the one that drifts to fixation	213	(4)
Box 6.4 Effective population size	217	(5)
Box 6.5 The rate of evolutionary substitution under genetic drift	222	(1)
Genetic Drift and Molecular Evolution	223	(13)
Nonrandom Mating	236	(9)
Box 6.6 Genotype frequencies under genetic drift	241	(4)
Conservation Genetics of the Illinois Greater Prairie Chicken	245	(8)
Summary	248	(1)
Questions	248	(2)
Exploring the Literature	250	(1)
Citations	251	(2)
Evolution at Multiple Loci: Linkage and Sex	253	(36)
Evolution at Two Loci: Linkage Equilibrium and Linkage Disequilibrium	254	(13)
Box 7.1 The coefficient of linkage disequilibrium	257	(1)
Box 7.2 Hardy--Weinberg analysis for two loci	258	(4)
Box 7.3 Sexual reproduction reduces linkage disequilibrium	262	(5)
Practical Reasons for Measuring Linkage Disequilibrium	267	(7)
Box 7.4 Estimating the age of the CCR5-Δ32 mutation	269	(5)
The Adaptive Significance of Sex	274	(15)
Summary	285	(1)
Questions	286	(1)
Exploring the Literature	287	(1)
Citations	288	(1)
Evolution at Multiple Loci: Quantitative Genetics	289	(40)
The Nature of Quantitative Traits	289	(5)
Identifying Loci That Contribute to Quantitative Traits	294	(9)
Box 8.1 QTL mapping	300	(3)
Measuring Heritable Variation	303	(5)
Box 8.2 Additive genetic variation versus dominance genetic variation	306	(2)
Measuring Differences in Survival and Reproductive Success	308	(5)
Box 8.3 The selection gradient and the selection differential	310	(1)
Box 8.4 Selection on multiple traits and correlated characters	311	(2)
Predicting the Evolutionary Response to Selection	313	(4)
Modes of Selection and the Maintenance of Genetic Variation	317	(4)
The Bell-Curve Fallacy and Other Misinterpretations of Heritability	321	(8)
Summary	325	(1)
Questions	326	(1)
Exploring the Literature	327	(1)
Citations	328	(1)
PART 3 ADAPTATION	329	(218)
Studying Adaptation: Evolutionary Analysis of Form and Function	331	(42)
All Hypotheses Must Be Tested: The Giraffe's Neck Reconsidered	332	(3)
Experiments	335	(5)
Box 9.1 A primer on statistical testing	340	(1)
Observational Studies	340	(5)
The Comparative Method	345	(5)
Box 9.2 Calculating phylogenetically independent contrasts	348	(2)
Phenotypic Plasticity	350	(1)
Trade-Offs and Constraints	351	(7)
Selection Operates on Different Levels	358	(10)
Box 9.3 Categories of transposable elements	362	(6)
Strategies for Asking Interesting Questions	368	(5)
Summary	368	(1)
Questions	369	(1)
Exploring the Literature	370	(1)
Citations	371	(2)
Sexual Selection	373	(46)
Sexual Dimorphism and Sex	374	(7)
Male--Male Competition: Intrasexual Selection	381	(7)
Box 10.1 Alternative male mating strategies	385	(3)
Female Choice	388	(16)
Box 10.2 Extra-pair copulations and multiple mating	392	(9)
Box 10.3 Runaway sexual selection in stalk-eyed flies?	401	(3)
Diversity in Sex Roles	404	(2)
Sexual Selection in Plants	406	(4)
Sexual Dimorphism in Body Size in Humans	410	(9)
Summary	412	(1)
Questions	413	(2)
Exploring the Literature	415	(1)
Citations	416	(3)
Kin Selection and Social Behavior	419	(36)
Kin Selection and the Evolution of Altruism	420	(11)
Box 11.1 Calculating coefficients of relatedness	421	(5)
Box 11.2 Kin recognition	426	(5)
Evolution of Eusociality	431	(8)
Box 11.3 The evolution of the sex ratio	434	(5)
Parent--Offspring Conflict	439	(4)
Reciprocal Altruism	443	(12)
Box 11.4 Prisoner's dilemma: Analyzing cooperation and conflict using game theory	445	(4)
Summary	449	(1)
Questions	450	(1)
Exploring the Literature	451	(1)
Citations	452	(3)
Aging and Other Life History Characters	455	(46)
Basic Issues in Life History Analysis	457	(2)
Why Do Organisms Age and Die?	459	(15)
Box 12.1 A trade-off between cancer risk and aging	464	(11)
Box 12.2 Is there an evolutionary explanation for menopause?	475
How Many Offspring Should an Individual Produce in a Given Year?	474	(7)
How Big Should Each Offspring Be?	481	(6)
Conflicts of Interest between Life Histories	487	(3)
Life Histories in a Broader Evolutionary Context	490	(11)
Summary	496	(1)
Questions	496	(1)
Exploring the Literature	497	(1)
Citations	498	(3)
Evolution and Human Health	501	(46)
Evolving Pathogens: Evasion of the Host's Immune Response	503	(6)
Evolving Pathogens: Antibiotic Resistance	509	(4)
Evolving Pathogens: Virulence	513	(4)
Tissues as Evolving Populations of Cells	517	(4)
Box 13.1 Genetic sleuthing solves a medical mystery	518	(3)
The Adaptationist Program Applied to Humans	521	(7)
Adaptation and Medical Physiology: Fever	528	(5)
Adaptation and Human Behavior: Parenting	533	(14)
Box 13.2 Is cultural evolution Darwinian?	534	(8)
Summary	542	(1)
Questions	542	(1)
Exploring the Literature	543	(1)
Citations	544	(3)
PART 4 THE HISTORY OF LIFE	547	(224)
Reconstructing Evolutionary Trees	549	(34)
The Logic of Phylogeny Inference	550	(5)
The Phylogeny of Whales	555	(12)
Box 14.1 Alternatives to parsimony: Maximum liklihood and genetic distances	562	(5)
Using Phylogenies to Answer Questions	567	(16)
Summary	578	(1)
Questions	578	(3)
Exploring the Literature	581	(1)
Citations	581	(2)
Mechanisms of Speciation	583	(32)
Species Concept	583	(6)
Box 15.1 What about bacteria and archaea?	585	(4)
Mechanisms of Genetic Isolation	589	(7)
Mechanisms of Divergence	596	(7)
Secondary Contact	603	(5)
The Genetics of Speciation	608	(7)
Summary	611	(1)
Questions	612	(1)
Exploring the Literature	613	(1)
Citations	613	(2)
The Origins of Life and Precambrian Evolution	615	(48)
What Was the First Living Thing?	616	(10)
Where Did the First Living Thing Come From?	626	(10)
Box 16.1 The Panspermia Hypothesis	628	(8)
What Was the Last Common Ancestor of All Extant Organisms and What Is the Shape of the Tree of Life?	636	(15)
Box 16.2 Horizontal gene transfer in bacteria	647	(4)
How Did the Last Common Ancestor's Descendants Evolve into Today's Organisms?	651	(12)
Summary	656	(1)
Questions	657	(1)
Exploring the Literature	658	(1)
Citations	659	(4)
The Cambrian Explosion and Beyond	663	(38)
The Nature of the Fossil Record	664	(3)
The Cambrian Explosion	667	(10)
Macroevolutionary Patterns	677	(7)
Mass Extinctions	684	(17)
Summary	697	(1)
Questions	697	(1)
Exploring the Literature	698	(1)
Citations	699	(2)
Development and Evolution	701	(26)
Homeotic Genes, Pattern Formation, and Diversification	702	(7)
The Genetics of Homology: Limbs	709	(7)
Flowers	716	(5)
Lessons from Evo-Devo Research	721	(6)
Summary	723	(1)
Questions	724	(1)
Exploring the Literature	724	(1)
Citations	725	(2)
Human Evolution	727	(44)
Relationships among Humans and the Extant Apes	728	(7)
Box 19.1 Genetic differences between humans, chimpanzees, and gorillas	736
The Recent Ancestry of Humans	735	(11)
The Origin of the Species Homo sapiens	746	(13)
Box 19.2 Genetic diversity among living humans	749	(9)
Box 19.3 Using linkage disequilibrium to date the divergence between African and non-African populations	758	(1)
The Evolution of Uniquely Human Traits	759	(12)
Summary	765	(1)
Questions	766	(1)
Exploring the Literature	767	(1)
Citations	767	(4)
Glossary	771	(7)
Illustration Credits	778	(6)
Index	784