Divergence With Genetic Exchange

by Michael L. Arnold

Overview

The study of genetic exchange resulting from natural hybridization, horizontal gene transfer, and viral recombination has long been marked by controversy between researchers holding different conceptual frameworks. Those subscribing to a doctrine of 'species purity' have traditionally been reluctant to recognise inferences suggesting anything other than a marginal role for non-allopatric divergence leading to gene transfer between different lineages. However, an increasing number of evolutionary biologists now accept that there is a growing body of evidence indicating the existence of non-allopatric diversification across many lineages and all domains of biological diversity.

Divergence with Genetic Exchange investigates the mechanisms associated with evolutionary divergence and diversification, focussing on the role played by the exchange of genes between divergent lineages, a process recently termed 'divergence-with-gene-flow'. Although the mechanisms by which such divergent forms of life exchange genomic material may differ widely, the outcomes of interest - adaptive evolution and the formation of new hybrid lineages - do not. Successive chapters cover the history of the field, detection methodologies, outcomes, implications for conservation programs, and the effects on the human lineage associated with the process of genetic transfer between divergent lineages.

This research level text is suitable for senior undergraduate and graduate level students taking related courses in departments of genetics, ecology and evolution. It will also be of relevance and use to professional evolutionary biologists and systematists seeking a comprehensive and authoritative overview of this rapidly expanding field.

Product Details

ISBN-13:	9780198755111
Publisher:	Oxford University Press
Publication date:	12/22/2015
Edition description:	New Edition
Pages:	272
Product dimensions:	7.40(w) x 9.60(h) x 0.70(d)

About the Author

Michael L. Arnold, Distinguished Research Professor, Department of Genetics, University of Georgia

Mike Arnold, Distinguished Research Professor of Genetics at the University of Georgia, has concentrated his research work in the area of evolutionary genetics, particularly the study of genetic exchange. Mike has championed the view of such exchange as a critical evolutionary process. For example, through breeding experiments and genomic analyses, Mike's research group has demonstrated that natural hybridization often leads to significant gene exchange between closely related species. Mike is particularly well known for studies involving the plants known as Louisiana Irises, which have become a classic example of the role of hybridization in adaptive evolution and speciation. Mike is the author of four books and more than 130 academic articles.

Table of Contents

1 Genetic exchange: An historical consideration 1

1.1 The evolutionary role of genetic exchange: Divergent viewpoints 1

1.2 Divergence-with-gene-flow: A process by any other name is still introgressive hybridization and sympatric divergence 4

1.3 Hybrid zone studies: Theoretical foundations 6

1.4 Hybrid zone studies: Testing the models 7

1.4.1 Hybrid zones and the form of selection: Voles and spruce trees 7

1.4.2 Hybrid zones and the form of selection: Next-generation sequencing and genome scans in salamanders and butterflies 9

1.4.3 Hybrid zones and the form of selection; A genomic outlook 9

1.5 Adaptive genetic exchange in animals and plants 11

1.5.1 Adaptive trait transfer: Dogs, wolves, and coat color genes 12

1.5.2 Adaptive trait transfer: Louisiana irises 13

1.5.3 Adaptive trait transfer: Darwin's finches 15

1.5.4 Adaptive trait transfer: Senecio and the origin of floral traits 15

1.6 The origin of hybrid taxa in animals and plants 16

1.6.1 The origin of hybrid animal taxa: Swallowtail butterflies 16

1.6.2 The origin of hybrid animal taxa: Sparrows 17

1.6.3 The origin of hybrid animal taxa: Cichlids 18

1.6.4 The origin of hybrid plant taxa: Pinus densata 19

1.6.5 The origin of hybrid plant taxa: Cotton 20

1.7 Genetic exchange between divergent lineages 20

1.7.1 Exchange between divergent lineages: Recombination between viruses and mammals 21

1.7.2 Exchange between divergent lineages: Horizontal gene transfer between bacteria and animals 21

1.7.3 Exchange between divergent lineages: Plant genomes receive foreign genes and genomes 22

1.8 Conclusions 22

2 Genetic exchange and species concepts 24

2.1 Species concepts and genetic exchange: Resolution and conflict avoidance 24

2.2 Genetic exchange and the biological species concept 27

2.3 Genetic exchange and the phylogenetic species concept 28

2.4 Genetic exchange and the cohesion species concept 31

2.5 Genetic exchange and the prokaryotic species concept 32

2.6 Genetic exchange and the genie species concept 33

2.7 Conclusions 34

3 Testing for genetic exchange 35

3.1 Genetic exchange: A testable hypothesis 35

3.2 Testing the hypothesis: Genetic exchange and incomplete lineage sorting 36

3.2.1 Genetic exchange and incomplete lineage sorting: Some analytical approaches 36

3.2.2 Genetic exchange and incomplete lineage sorting: Flycatchers 37

3.2.3 Genetic exchange and incomplete lineage sorting: Alpine lake whitefish 38

3.2.4 Genetic exchange and incomplete lineage sorting: Yeast 38

3.2.5 Genetic exchange and incomplete lineage sorting: Pampas grasses 40

3.2.6 Genetic exchange and incomplete lineage sorting: Orchids 41

3.3 Testing the hypothesis: The fossil record and genetic exchange 41

3.3.1 Genetic exchange detected in the fossil record: Paleopolyploidy in plants 42

3.3.2 Genetic exchange detected in the fossil record: Corals 42

3.3.3 Genetic exchange detected in the fossil record: Land snails 43

3.3.4 Genetic exchange detected in the fossil record: Mammoths 44

3.4 Testing the hypothesis: Contemporary hybrid zones 45

3.4.1 Genetic exchange and hybrid zones: Louisiana irises 45

3.4.2 Genetic exchange and hybrid zones: Eucalyptus 47

3.4.3 Genetic exchange and hybrid zones: Oaks 48

3.4.4 Genetic exchange and hybrid zones: Australian grasshoppers 49

3.4.5 Genetic exchange and hybrid zones: Chickadees 53

3.4.6 Genetic exchange and hybrid zones: House mice 54

3.5 Testing the hypothesis: hrtragenomic divergence 55

3.6 Conclusions 57

4 Genetic exchange, reproductive barriers, and the mosaic genome 58

4.1 Genetic exchange and reproductive isolation: Two sides of the same coin 58

4.2 Genetic exchange and reproductive isolation in Louisiana irises: Prezygotic processes 60

4.2.1 Niche differentiation and reproductive isolation 60

4.2.2 Phenology, pollen competition, and reproductive isolation 63

4.2.3 Pollen competition and reproductive isolation 64

4.3 Genetic exchange and reproductive isolation in Louisiana irises: Postzygotic processes 67

4.3.1 Hybrid viability and reproductive isolation 68

4.3.2 Hybrid fertility and reproductive isolation 69

4.4 Genetic exchange and reproductive isolation in viral clades 70

4.4.1 Pre-exchange isolating barriers and viral reassortment: HIV 70

4.4.2 Pre-exchange isolating barriers and viral reassortment: Influenza 71

4.5 Genetic exchange and reproductive isolation in bacterial clades 72

4.5.1 Pre-exchange isolating barriers and HGT: Yersinia 73

4.6 Generic exchange and postzygotic reproductive isolation in eukaryotes: Hybrid viability and fertility 74

4.6.1 Hybrid inviability and introgressive hybridization: Anopheles 75

4.6.2 Hybrid sterility and introgressive hybridization: Helianthus 77

4.7 Conclusions 78

5 Genetic exchange and fitness 79

5.1 Genetic exchange and fitness: Recombinant genotypes are just like everybody else 79

5.2 Genetic exchange and fitness: Environment-independent and -dependent selection on animal hybrids 80

5.2.1 Genetic exchange and hybrid fitness in animals: Drosophila 80

5.2.2 Genetic exchange and hybrid fitness in animals; Tigriopus 84

5.2.3 Genetic exchange and hybrid fitness in animals: Rana 86

5.3 Generic exchange and fitness: Environment-independent and -dependent selection on plant hybrids 88

5.3.1 Genetic exchange and hybrid fitness in plants: Ipomopsis 89

5.3.2 Genetic exchange and hybrid fitness in plants: Mimulus 91

5.4 Genetic exchange and fitness: Horizontal gene transfer and selection in prokaryotes 92

5.4.1 Horizontal gene transfer and the fitness of bacteria: Theory 93

5.4.2 Horizontal gene transfer and the fitness of bacteria: Experiments 94

5.4.3 Horizontal gene transfer and the fitness of bacteria: Shigella 95

5.4.4 Horizontal gene transfer and the fitness of bacteria: Legionella 96

5.5 Genetic exchange and fitness: Reassortment and selection in viruses 97

5.5.1 Genetic exchange and viral fitness: Polioviruses 98

5.5.2 Genetic exchange and viral fitness: Herpesviruses 100

5.5.3 Genetic exchange and viral fitness: Bacteriophages 100

5.6 Conclusions 102

6 Evolutionary outcomes of genetic exchange 103

6.1 Genetic exchange: Its role in genomic and organismic evolution 103

6.2 Genetic exchange and organismic evolution: Intiogression, hybrid speciation, and adaptive radiations in animals 104

6.2.1 Genetic exchange and animal evolution: Divergence-with-introgression 104

6.2.2 Genetic exchange and animal evolution: Homoploid hybrid speciation 109

6.2.3 Genetic exchange and animal evolution: Allopolyploid speciation 114

6.2.4 Genetic exchange and animal evolution: Adaptive radiations 119

6.3 Genetic exchange and organismic evolution: lntrogression, hybrid speciation, and adaptive radiations in plants 123

6.3.1 Genetic exchange and plant evolution: Divergence-with-introgression 123

6.3.2 Genetic exchange and plant evolution: Homoploid hybrid speciation 125

6.3.3 Genetic exchange and plant evolution: Allopolyploid speciation 126

6.3.4 Genetic exchange and plant evolution: Adaptive radiations 127

6.4 Conclusions 129

7 Genetic exchange and conservation 130

7.1 Genetic exchange and the conservation and restoration of endangered organisms 130

7.2 Introgressive hybridization and the conservation of endangered animals 132

7.2.1 Introgressive hybridization and the conservation of endangered animals: North American and Asian bears 133

7.2.2 Introgressive hybridization and the conservation of endangered animals: Sharks 134

7.2.3 Introgressive hybridization and the conservation of endangered animals: Felids 135

7.2.4 Introgressive hybridization and the conservation of endangered animals: Trout 137

7.3 Introgressive hybridization and the conservation of endangered plants 138

7.3.1 Introgressive hybridization and the conservation of endangered plants: Poplar 139

7.3.2 Introgressive hybridization and the conservation of endangered plants: Cordgrass 140

7.4 Conclusions 142

8 Genetic exchange and humans 145

8.1 Genetic exchange and the evolution of Homo sapiens 145

8.2 Genetic exchange and the evolution of New World primates: Howler monkeys and marmosets 146

8.2.1 Howler monkeys 146

8.2.2 Marmosets 147

8.3 Genetic exchange and the evolution of Old World primates: Langurs and leaf monkeys 148

8.4 Genetic exchange and the evolution of Old World primates: Baboons 149

8.5 Genetic exchange and the evolution of Old World primates: Gorillas, chimpanzees, and humans 151

8.5.1 Genetic exchange and the evolution of Old World primates: Gorilla x Homo x Pan 152

8.5.2 Genetic exchange and the evolution of Old World primates: Gorilla 154

8.5.3 Genetic exchange and the evolution of Old World primates: Pan 155

8.5.4 Genetic exchange and the evolution of Old World primates: Homo 156

8.6 Genetic exchange and the ecological setting of Homo sapiens 163

8.7 Genetic exchange and the evolution of human food sources 163

8.7.1 Genetic exchange and the evolution of human food sources: Apples 164

8.7.2 Genetic exchange and the evolution of human food sources; Maize 165

8.7.3 Genetic exchange and the evolution of human food sources: Pigs 166

8.7.4 Genetic exchange and the evolution of human food sources: Chickens 167

8.8 Genetic exchange and the evolution of human companions 168

8.8.1 Genetic exchange and the evolution of human companions: Dogs 169

8.8.2 Genetic exchange and the evolution of human companions: Horses 170

8.9 Genetic exchange and the evolution of human drugs 171

8.10 Conclusions 172

9 Epilogue 173

9.1 Genetic exchange is [still] pervasive 173

Glossary 177

References 181

Index 243

Editorial Reviews

"Overall, Divergence with Genetic Exchange is clearly written, rigorous in scholarship, and logical in its organization. The book will be very useful to academics, especially graduate students looking for a detailed treatment of this subject." BioScience

"Arnold's Divergence with Genetic Exchange, with its comprehensive treatment of different evolutionary topics and wealth of references, is a must for everyone who wants to extend their view beyond Mayr's species dogma and its consequence that 'hybridization is unimportant in animal taxa.' ... This book will also be most valuable in the further development of the recent discussion on using networks (webs-of-life) to expand our evolutionary thinking..." —Systematic Biology

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