Barbara A. Ambrose is the Cullman Assistant Curator of Plant Genomics at The New York Botanical Garden, Bronx, New York, USA.Michael Purugganan is the Dorothy Schiff Professor of Genomics at the Department of Biology, Center for Genomics and Systems Biology, New York University, New York, USA, and at the Center for Genomics and Systems Biology, NYU Abu Dhabi Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.

“In summary, the very good introductory parts make the book more easily accessible for beginners, undergraduates, and teachers, while the up-to-date and in-depth discussions are highly useful for every scientist who is interested in the evolution of plant forms. Overall, I will finish with my congratulations to the authors for this extremely interesting, excellent, state-of-the-art, and well-prepared book.”  (Journal of Plant Physiology, 14 September 2013)“Overall I felt that this book will be a great first port of call for those interested in morphological evolution and it will be useful at all levels from undergraduate onwards. It will be particularly useful for molecular and developmental biologists wishing to move into a comparative approach.”  (Annals of Botany, 1 July 2013)

• List of Contributors xiii Preface xvAcknowledgments xvii1 Phylogenetic Analyses and Morphological Innovations in Land Plants 1James A. Doyle1.1 Introduction 21.2 Basic innovations in cell structure and life cycle: aquatic streptophytes 41.3 Invasion of the land: “bryophytes” 91.4 Origin of vascular plants: the importance of fossils 111.5 Early innovations within vascular plants: leaves, roots, and heterospory 131.6 Innovations on the line to seed plants: “progymnosperms” and “seed ferns” 181.7 Innovations within seed plants, especially conifers 221.8 Origin of angiosperms and their innovations 261.9 Innovations within angiosperms: monocots and eudicots 33Acknowledgments 36References 362 The Evolution of Body Form in Bryophytes 51Bernard Goffinet and William R. Buck2.1 Fundamental Bauplan of bryophytes 532.1.1 The apical meristem is unicellular and growth is modular 532.1.2 The architecture of the gametophyte varies within bryophytes 542.1.3 Bryophytes differ consistently in their sporophytes 542.2 Phylogenetic relationships of bryophytes 552.3 Evolution of plant form in liverworts 612.3.1 The gametophyte 612.3.2 The sporophyte 642.3.3 Evolutionary trends 652.4 Evolution of plant form in mosses 672.4.1 The gametophyte 672.4.2 The sporophyte 732.4.3 Evolutionary trends 762.5 Evolution of plant form in hornworts 782.5.1 The gametophyte 782.5.2 The sporophyte 802.5.3 Evolutionary trends 802.6 The ancestral developmental toolbox of land plants 80Acknowledgments 84References 843 The Morphology and Development of Lycophytes 91Barbara A. Ambrose3.1 Introduction 913.2 Vasculature 963.3 Shoot apical meristems 963.4 Sporophyte architecture 993.5 Microphylls 1013.6 Sporangia 1033.7 Roots 1053.8 Structural enigmas 1063.8.1 Ligules 1063.8.2 Rhizophores 1083.9 Conclusions 109Acknowledgments 110References 1104 Evolutionary Morphology of Ferns (Monilophytes) 115Harald Schneider4.1 Introduction 1154.2 Context of evolutionary plant morphology 1174.2.1 Perspective 1: rapid radiation versus stasis in the evolution of fern body plans 1204.2.2 Perspective 2: key structures and organs of fern body plans 1234.2.3 Perspective 3: genomics and evo-devo of ferns 132Acknowledgments 134References 1345 Gymnosperms 141Dennis Wm. Stevenson5.1 Introduction 1415.2 Architecture 1425.3 Shoots 1445.4 Leaves 1475.5 Roots 1505.6 Seeds 1525.7 Seedlings 1535.8 Embryology 154References 1596 Identifying Key Features in the Origin and Early Diversification of Angiosperms 163Paula J. Rudall6.1 Introduction: key features of flowering plants 1636.2 Patterning of flowers and inflorescences 1646.3 Eight extant lineages of flowering plants 1676.4 Origin of the angiosperms: the phylogenetic framework 1696.5 Resolving conflicting hypotheses of flower origin 1706.6 Evolution of the perianth 1746.7 Carpels, gynoecia, and organ fusion 1746.8 Origins of floral diversity: deep-node characters and genome duplications 1766.9 Contrasting floral ground plans 1786.10 Iterative origins of floral symmetry patterns and floral novelties 1796.11 Constraints and canalization in floral evolution 180Acknowledgments 181References 1817 Genomics, Adaptation, and the Evolution of Plant Form 189Kristen Shepard7.1 Overview 1897.2 The types of genetic variation present within species 1917.3 From phenotype to genotype: map-based approaches to identifying adaptive genes 1937.3.1 The genetic architecture of quantitative traits 1937.3.2 Family-based mapping 1937.3.3 Advantages and disadvantages of family-based QTL mapping 1947.3.4 Population-based mapping 1957.3.5 Advantages and disadvantages of populationbased QTL mapping 1967.3.6 Additional considerations in QTL mapping 1967.3.7 Emerging approaches for detecting QTL 1977.4 From genotype to phenotype: molecular population genetics and adaptive evolution 1977.4.1 Overview of molecular population genetics 1977.4.2 Signatures of selection on DNA sequences 1987.4.3 Demographic factors can complicate inferences of selection 1997.4.4 Gathering nucleotide sequence data 1997.4.5 Interpreting the sequence data: summary statistics and tests of neutrality 2007.4.6 Nucleotide diversity and divergence 2017.4.7 Analysis of the site frequency spectrum: Tajima’s D and similar tests 2017.4.8 Analyses of linkage disequilibrium: haplotype-based tests 2027.4.9 Comparing diversity to divergence: McDonald-Kreitman and HKA tests 2027.4.10 Detecting local adaptation: population differentiation and reduced variability 2037.5 Bringing it all together—the need for thorough testing of adaptive hypotheses 2047.5.1 Techniques for testing the functional consequences of polymorphisms 2047.5.2 Testing adaptive hypotheses 2067.6 Case studies in molecular population genomic approaches to the evolution of plant form 2077.6.1 Case study 1: Identifying novel components of developmental regulatory networks—BREVIS RADIX in Arabidopsis roots 2077.6.2 Case study 2: Identifying potential targets of positive selection via a genomic scan in a nonmodel species—signatures of selection in sunflower SSRs 2097.6.3 Case study 3: Microevolution of a small gene family—phytochromes in Arabidopsis 2117.6.4 Phytochrome A 2127.6.5 Phytochrome B 2137.6.6 Phytochrome C 2137.6.7 Case study 4: Combining association mapping and population genomics—the Arabidopsis flowering time network 2157.7 Conclusion 219References 2208 Comparative Evolutionary Genomics of Land Plants 227Amy Litt8.1 Evolution of nuclear genome size 2298.1.1 Gene number 2328.2 Whole genome duplications 2338.2.1 Whole genome duplications in non-flowering plants 2368.2.2 Whole genome duplications in angiosperms 2378.2.3 Impact of whole genome duplications on plant evolution 2408.3 Transposable elements 2418.3.1 Retrotransposons 2428.3.2 DNA elements 2438.3.3 Transposable elements and genome size 2448.3.4 Dynamics of TE amplification and removal 2468.3.5 Distribution of transposable elements in plant genomes 2488.3.6 Impact of transposable elements on genome structure 2498.3.7 Impact on gene diversity, expression, and function 2508.4 Gene family expansions 2528.4.1 Land plant gene diversification 2528.4.2 Angiosperm gene diversification 2548.5 Tandem gene duplications 2578.6 Fern and gymnosperm genomes 2588.7 Arabidopsis genome 2608.8 Domestication 2618.9 Future directions 263References 2659 Development and the Evolution of Plant Form 277Barbara A. Ambrose and Cristina Ferrandiz9.1 Introduction 2779.1.1 A brief historical overview of evolutionary developmental biology 2789.1.2 General concepts in evolutionary developmental biology 2799.2 Plant evolutionary developmental biology 2809.2.1 The evolution and development of the flower 2819.2.2 The evolution and development of leaves 2939.3 Future directions 3019.3.1 Morphological features 3019.3.2 Alternation of generations 3019.3.3 Gametophytes 3039.3.4 Sporangia and spores 3049.3.5 Meristems 3059.3.6 Development of model organisms 3079.4 Conclusions 308References 30810 Development in the Wild: Phenotypic Plasticity 321Kathleen Donohue10.1 Development in the wild is phenotypic plasticity 32110.1.1 Why are some traits more plastic than others? 32310.1.2 Manifestations of phenotypic plasticity in plants 32410.2 Why are some traits more plastic than others? The evolution of phenotypic plasticity 32710.2.1 The adaptive value of plasticity: scales of environmental variation 32710.2.2 Genetic constraints on the evolution of plasticity 33210.3 The genetic basis of phenotypic plasticity and genetic constraints on plasticity 33210.3.1 Molecular mechanisms of phenotypic plasticity: gene–environment interactions 33310.3.2 How does the molecular mechanism of plasticity translate to genetic constraints on plasticity? 34110.4 Phenotypic plasticity and local adaptation 34310.4.1 Plasticity, niche width, and ecological isolation 34410.4.2 Phenotypic plasticity as an intermediate stage of specialization 34510.4.3 Does plasticity prevent or promote divergence? 34610.5 Conclusion 348References 34911 The Evolution of Plant Form: a Summary Perspective 357Michael PuruggananReferences 363Index 367A color plate section falls between pages 62 and 63

Barbara A. Ambrose is the Cullman Assistant Curator of Plant Genomics at The New York Botanical Garden, Bronx, New York, USA.Michael Purugganan is the Dorothy Schiff Professor of Genomics at the Department of Biology, Center for Genomics and Systems Biology, New York University, New York, USA, and at the Center for Genomics and Systems Biology, NYU Abu Dhabi Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.

“In summary, the very good introductory parts make the book more easily accessible for beginners, undergraduates, and teachers, while the up-to-date and in-depth discussions are highly useful for every scientist who is interested in the evolution of plant forms. Overall, I will finish with my congratulations to the authors for this extremely interesting, excellent, state-of-the-art, and well-prepared book.”  (Journal of Plant Physiology, 14 September 2013)“Overall I felt that this book will be a great first port of call for those interested in morphological evolution and it will be useful at all levels from undergraduate onwards. It will be particularly useful for molecular and developmental biologists wishing to move into a comparative approach.”  (Annals of Botany, 1 July 2013)

• List of Contributors xiii Preface xvAcknowledgments xvii1 Phylogenetic Analyses and Morphological Innovations in Land Plants 1James A. Doyle1.1 Introduction 21.2 Basic innovations in cell structure and life cycle: aquatic streptophytes 41.3 Invasion of the land: “bryophytes” 91.4 Origin of vascular plants: the importance of fossils 111.5 Early innovations within vascular plants: leaves, roots, and heterospory 131.6 Innovations on the line to seed plants: “progymnosperms” and “seed ferns” 181.7 Innovations within seed plants, especially conifers 221.8 Origin of angiosperms and their innovations 261.9 Innovations within angiosperms: monocots and eudicots 33Acknowledgments 36References 362 The Evolution of Body Form in Bryophytes 51Bernard Goffinet and William R. Buck2.1 Fundamental Bauplan of bryophytes 532.1.1 The apical meristem is unicellular and growth is modular 532.1.2 The architecture of the gametophyte varies within bryophytes 542.1.3 Bryophytes differ consistently in their sporophytes 542.2 Phylogenetic relationships of bryophytes 552.3 Evolution of plant form in liverworts 612.3.1 The gametophyte 612.3.2 The sporophyte 642.3.3 Evolutionary trends 652.4 Evolution of plant form in mosses 672.4.1 The gametophyte 672.4.2 The sporophyte 732.4.3 Evolutionary trends 762.5 Evolution of plant form in hornworts 782.5.1 The gametophyte 782.5.2 The sporophyte 802.5.3 Evolutionary trends 802.6 The ancestral developmental toolbox of land plants 80Acknowledgments 84References 843 The Morphology and Development of Lycophytes 91Barbara A. Ambrose3.1 Introduction 913.2 Vasculature 963.3 Shoot apical meristems 963.4 Sporophyte architecture 993.5 Microphylls 1013.6 Sporangia 1033.7 Roots 1053.8 Structural enigmas 1063.8.1 Ligules 1063.8.2 Rhizophores 1083.9 Conclusions 109Acknowledgments 110References 1104 Evolutionary Morphology of Ferns (Monilophytes) 115Harald Schneider4.1 Introduction 1154.2 Context of evolutionary plant morphology 1174.2.1 Perspective 1: rapid radiation versus stasis in the evolution of fern body plans 1204.2.2 Perspective 2: key structures and organs of fern body plans 1234.2.3 Perspective 3: genomics and evo-devo of ferns 132Acknowledgments 134References 1345 Gymnosperms 141Dennis Wm. Stevenson5.1 Introduction 1415.2 Architecture 1425.3 Shoots 1445.4 Leaves 1475.5 Roots 1505.6 Seeds 1525.7 Seedlings 1535.8 Embryology 154References 1596 Identifying Key Features in the Origin and Early Diversification of Angiosperms 163Paula J. Rudall6.1 Introduction: key features of flowering plants 1636.2 Patterning of flowers and inflorescences 1646.3 Eight extant lineages of flowering plants 1676.4 Origin of the angiosperms: the phylogenetic framework 1696.5 Resolving conflicting hypotheses of flower origin 1706.6 Evolution of the perianth 1746.7 Carpels, gynoecia, and organ fusion 1746.8 Origins of floral diversity: deep-node characters and genome duplications 1766.9 Contrasting floral ground plans 1786.10 Iterative origins of floral symmetry patterns and floral novelties 1796.11 Constraints and canalization in floral evolution 180Acknowledgments 181References 1817 Genomics, Adaptation, and the Evolution of Plant Form 189Kristen Shepard7.1 Overview 1897.2 The types of genetic variation present within species 1917.3 From phenotype to genotype: map-based approaches to identifying adaptive genes 1937.3.1 The genetic architecture of quantitative traits 1937.3.2 Family-based mapping 1937.3.3 Advantages and disadvantages of family-based QTL mapping 1947.3.4 Population-based mapping 1957.3.5 Advantages and disadvantages of populationbased QTL mapping 1967.3.6 Additional considerations in QTL mapping 1967.3.7 Emerging approaches for detecting QTL 1977.4 From genotype to phenotype: molecular population genetics and adaptive evolution 1977.4.1 Overview of molecular population genetics 1977.4.2 Signatures of selection on DNA sequences 1987.4.3 Demographic factors can complicate inferences of selection 1997.4.4 Gathering nucleotide sequence data 1997.4.5 Interpreting the sequence data: summary statistics and tests of neutrality 2007.4.6 Nucleotide diversity and divergence 2017.4.7 Analysis of the site frequency spectrum: Tajima’s D and similar tests 2017.4.8 Analyses of linkage disequilibrium: haplotype-based tests 2027.4.9 Comparing diversity to divergence: McDonald-Kreitman and HKA tests 2027.4.10 Detecting local adaptation: population differentiation and reduced variability 2037.5 Bringing it all together—the need for thorough testing of adaptive hypotheses 2047.5.1 Techniques for testing the functional consequences of polymorphisms 2047.5.2 Testing adaptive hypotheses 2067.6 Case studies in molecular population genomic approaches to the evolution of plant form 2077.6.1 Case study 1: Identifying novel components of developmental regulatory networks—BREVIS RADIX in Arabidopsis roots 2077.6.2 Case study 2: Identifying potential targets of positive selection via a genomic scan in a nonmodel species—signatures of selection in sunflower SSRs 2097.6.3 Case study 3: Microevolution of a small gene family—phytochromes in Arabidopsis 2117.6.4 Phytochrome A 2127.6.5 Phytochrome B 2137.6.6 Phytochrome C 2137.6.7 Case study 4: Combining association mapping and population genomics—the Arabidopsis flowering time network 2157.7 Conclusion 219References 2208 Comparative Evolutionary Genomics of Land Plants 227Amy Litt8.1 Evolution of nuclear genome size 2298.1.1 Gene number 2328.2 Whole genome duplications 2338.2.1 Whole genome duplications in non-flowering plants 2368.2.2 Whole genome duplications in angiosperms 2378.2.3 Impact of whole genome duplications on plant evolution 2408.3 Transposable elements 2418.3.1 Retrotransposons 2428.3.2 DNA elements 2438.3.3 Transposable elements and genome size 2448.3.4 Dynamics of TE amplification and removal 2468.3.5 Distribution of transposable elements in plant genomes 2488.3.6 Impact of transposable elements on genome structure 2498.3.7 Impact on gene diversity, expression, and function 2508.4 Gene family expansions 2528.4.1 Land plant gene diversification 2528.4.2 Angiosperm gene diversification 2548.5 Tandem gene duplications 2578.6 Fern and gymnosperm genomes 2588.7 Arabidopsis genome 2608.8 Domestication 2618.9 Future directions 263References 2659 Development and the Evolution of Plant Form 277Barbara A. Ambrose and Cristina Ferrandiz9.1 Introduction 2779.1.1 A brief historical overview of evolutionary developmental biology 2789.1.2 General concepts in evolutionary developmental biology 2799.2 Plant evolutionary developmental biology 2809.2.1 The evolution and development of the flower 2819.2.2 The evolution and development of leaves 2939.3 Future directions 3019.3.1 Morphological features 3019.3.2 Alternation of generations 3019.3.3 Gametophytes 3039.3.4 Sporangia and spores 3049.3.5 Meristems 3059.3.6 Development of model organisms 3079.4 Conclusions 308References 30810 Development in the Wild: Phenotypic Plasticity 321Kathleen Donohue10.1 Development in the wild is phenotypic plasticity 32110.1.1 Why are some traits more plastic than others? 32310.1.2 Manifestations of phenotypic plasticity in plants 32410.2 Why are some traits more plastic than others? The evolution of phenotypic plasticity 32710.2.1 The adaptive value of plasticity: scales of environmental variation 32710.2.2 Genetic constraints on the evolution of plasticity 33210.3 The genetic basis of phenotypic plasticity and genetic constraints on plasticity 33210.3.1 Molecular mechanisms of phenotypic plasticity: gene–environment interactions 33310.3.2 How does the molecular mechanism of plasticity translate to genetic constraints on plasticity? 34110.4 Phenotypic plasticity and local adaptation 34310.4.1 Plasticity, niche width, and ecological isolation 34410.4.2 Phenotypic plasticity as an intermediate stage of specialization 34510.4.3 Does plasticity prevent or promote divergence? 34610.5 Conclusion 348References 34911 The Evolution of Plant Form: a Summary Perspective 357Michael PuruggananReferences 363Index 367A color plate section falls between pages 62 and 63

Barbara A. Ambrose is the Cullman Assistant Curator of Plant Genomics at The New York Botanical Garden, Bronx, New York, USA.Michael Purugganan is the Dorothy Schiff Professor of Genomics at the Department of Biology, Center for Genomics and Systems Biology, New York University, New York, USA, and at the Center for Genomics and Systems Biology, NYU Abu Dhabi Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.

“In summary, the very good introductory parts make the book more easily accessible for beginners, undergraduates, and teachers, while the up-to-date and in-depth discussions are highly useful for every scientist who is interested in the evolution of plant forms. Overall, I will finish with my congratulations to the authors for this extremely interesting, excellent, state-of-the-art, and well-prepared book.”  (Journal of Plant Physiology, 14 September 2013)“Overall I felt that this book will be a great first port of call for those interested in morphological evolution and it will be useful at all levels from undergraduate onwards. It will be particularly useful for molecular and developmental biologists wishing to move into a comparative approach.”  (Annals of Botany, 1 July 2013)

• List of Contributors xiii Preface xvAcknowledgments xvii1 Phylogenetic Analyses and Morphological Innovations in Land Plants 1James A. Doyle1.1 Introduction 21.2 Basic innovations in cell structure and life cycle: aquatic streptophytes 41.3 Invasion of the land: “bryophytes” 91.4 Origin of vascular plants: the importance of fossils 111.5 Early innovations within vascular plants: leaves, roots, and heterospory 131.6 Innovations on the line to seed plants: “progymnosperms” and “seed ferns” 181.7 Innovations within seed plants, especially conifers 221.8 Origin of angiosperms and their innovations 261.9 Innovations within angiosperms: monocots and eudicots 33Acknowledgments 36References 362 The Evolution of Body Form in Bryophytes 51Bernard Goffinet and William R. Buck2.1 Fundamental Bauplan of bryophytes 532.1.1 The apical meristem is unicellular and growth is modular 532.1.2 The architecture of the gametophyte varies within bryophytes 542.1.3 Bryophytes differ consistently in their sporophytes 542.2 Phylogenetic relationships of bryophytes 552.3 Evolution of plant form in liverworts 612.3.1 The gametophyte 612.3.2 The sporophyte 642.3.3 Evolutionary trends 652.4 Evolution of plant form in mosses 672.4.1 The gametophyte 672.4.2 The sporophyte 732.4.3 Evolutionary trends 762.5 Evolution of plant form in hornworts 782.5.1 The gametophyte 782.5.2 The sporophyte 802.5.3 Evolutionary trends 802.6 The ancestral developmental toolbox of land plants 80Acknowledgments 84References 843 The Morphology and Development of Lycophytes 91Barbara A. Ambrose3.1 Introduction 913.2 Vasculature 963.3 Shoot apical meristems 963.4 Sporophyte architecture 993.5 Microphylls 1013.6 Sporangia 1033.7 Roots 1053.8 Structural enigmas 1063.8.1 Ligules 1063.8.2 Rhizophores 1083.9 Conclusions 109Acknowledgments 110References 1104 Evolutionary Morphology of Ferns (Monilophytes) 115Harald Schneider4.1 Introduction 1154.2 Context of evolutionary plant morphology 1174.2.1 Perspective 1: rapid radiation versus stasis in the evolution of fern body plans 1204.2.2 Perspective 2: key structures and organs of fern body plans 1234.2.3 Perspective 3: genomics and evo-devo of ferns 132Acknowledgments 134References 1345 Gymnosperms 141Dennis Wm. Stevenson5.1 Introduction 1415.2 Architecture 1425.3 Shoots 1445.4 Leaves 1475.5 Roots 1505.6 Seeds 1525.7 Seedlings 1535.8 Embryology 154References 1596 Identifying Key Features in the Origin and Early Diversification of Angiosperms 163Paula J. Rudall6.1 Introduction: key features of flowering plants 1636.2 Patterning of flowers and inflorescences 1646.3 Eight extant lineages of flowering plants 1676.4 Origin of the angiosperms: the phylogenetic framework 1696.5 Resolving conflicting hypotheses of flower origin 1706.6 Evolution of the perianth 1746.7 Carpels, gynoecia, and organ fusion 1746.8 Origins of floral diversity: deep-node characters and genome duplications 1766.9 Contrasting floral ground plans 1786.10 Iterative origins of floral symmetry patterns and floral novelties 1796.11 Constraints and canalization in floral evolution 180Acknowledgments 181References 1817 Genomics, Adaptation, and the Evolution of Plant Form 189Kristen Shepard7.1 Overview 1897.2 The types of genetic variation present within species 1917.3 From phenotype to genotype: map-based approaches to identifying adaptive genes 1937.3.1 The genetic architecture of quantitative traits 1937.3.2 Family-based mapping 1937.3.3 Advantages and disadvantages of family-based QTL mapping 1947.3.4 Population-based mapping 1957.3.5 Advantages and disadvantages of populationbased QTL mapping 1967.3.6 Additional considerations in QTL mapping 1967.3.7 Emerging approaches for detecting QTL 1977.4 From genotype to phenotype: molecular population genetics and adaptive evolution 1977.4.1 Overview of molecular population genetics 1977.4.2 Signatures of selection on DNA sequences 1987.4.3 Demographic factors can complicate inferences of selection 1997.4.4 Gathering nucleotide sequence data 1997.4.5 Interpreting the sequence data: summary statistics and tests of neutrality 2007.4.6 Nucleotide diversity and divergence 2017.4.7 Analysis of the site frequency spectrum: Tajima’s D and similar tests 2017.4.8 Analyses of linkage disequilibrium: haplotype-based tests 2027.4.9 Comparing diversity to divergence: McDonald-Kreitman and HKA tests 2027.4.10 Detecting local adaptation: population differentiation and reduced variability 2037.5 Bringing it all together—the need for thorough testing of adaptive hypotheses 2047.5.1 Techniques for testing the functional consequences of polymorphisms 2047.5.2 Testing adaptive hypotheses 2067.6 Case studies in molecular population genomic approaches to the evolution of plant form 2077.6.1 Case study 1: Identifying novel components of developmental regulatory networks—BREVIS RADIX in Arabidopsis roots 2077.6.2 Case study 2: Identifying potential targets of positive selection via a genomic scan in a nonmodel species—signatures of selection in sunflower SSRs 2097.6.3 Case study 3: Microevolution of a small gene family—phytochromes in Arabidopsis 2117.6.4 Phytochrome A 2127.6.5 Phytochrome B 2137.6.6 Phytochrome C 2137.6.7 Case study 4: Combining association mapping and population genomics—the Arabidopsis flowering time network 2157.7 Conclusion 219References 2208 Comparative Evolutionary Genomics of Land Plants 227Amy Litt8.1 Evolution of nuclear genome size 2298.1.1 Gene number 2328.2 Whole genome duplications 2338.2.1 Whole genome duplications in non-flowering plants 2368.2.2 Whole genome duplications in angiosperms 2378.2.3 Impact of whole genome duplications on plant evolution 2408.3 Transposable elements 2418.3.1 Retrotransposons 2428.3.2 DNA elements 2438.3.3 Transposable elements and genome size 2448.3.4 Dynamics of TE amplification and removal 2468.3.5 Distribution of transposable elements in plant genomes 2488.3.6 Impact of transposable elements on genome structure 2498.3.7 Impact on gene diversity, expression, and function 2508.4 Gene family expansions 2528.4.1 Land plant gene diversification 2528.4.2 Angiosperm gene diversification 2548.5 Tandem gene duplications 2578.6 Fern and gymnosperm genomes 2588.7 Arabidopsis genome 2608.8 Domestication 2618.9 Future directions 263References 2659 Development and the Evolution of Plant Form 277Barbara A. Ambrose and Cristina Ferrandiz9.1 Introduction 2779.1.1 A brief historical overview of evolutionary developmental biology 2789.1.2 General concepts in evolutionary developmental biology 2799.2 Plant evolutionary developmental biology 2809.2.1 The evolution and development of the flower 2819.2.2 The evolution and development of leaves 2939.3 Future directions 3019.3.1 Morphological features 3019.3.2 Alternation of generations 3019.3.3 Gametophytes 3039.3.4 Sporangia and spores 3049.3.5 Meristems 3059.3.6 Development of model organisms 3079.4 Conclusions 308References 30810 Development in the Wild: Phenotypic Plasticity 321Kathleen Donohue10.1 Development in the wild is phenotypic plasticity 32110.1.1 Why are some traits more plastic than others? 32310.1.2 Manifestations of phenotypic plasticity in plants 32410.2 Why are some traits more plastic than others? The evolution of phenotypic plasticity 32710.2.1 The adaptive value of plasticity: scales of environmental variation 32710.2.2 Genetic constraints on the evolution of plasticity 33210.3 The genetic basis of phenotypic plasticity and genetic constraints on plasticity 33210.3.1 Molecular mechanisms of phenotypic plasticity: gene–environment interactions 33310.3.2 How does the molecular mechanism of plasticity translate to genetic constraints on plasticity? 34110.4 Phenotypic plasticity and local adaptation 34310.4.1 Plasticity, niche width, and ecological isolation 34410.4.2 Phenotypic plasticity as an intermediate stage of specialization 34510.4.3 Does plasticity prevent or promote divergence? 34610.5 Conclusion 348References 34911 The Evolution of Plant Form: a Summary Perspective 357Michael PuruggananReferences 363Index 367A color plate section falls between pages 62 and 63