List of Contributors ......................................... xiii
Preface ........................................................ xv
Acknowledgments .............................................. xvii
1 Phylogenetic Analyses and Morphological Innovations
in Land Plants ............................................... 1
James A. Doyle
1.1 Introduction ............................................ 2
1.2 Basic innovations in cell structure and life cycle:
aquatic streptophytes ................................... 4
1.3 Invasion of the land: "bryophytes" ...................... 9
1.4 Origin of vascular plants: the importance of fossils ... 11
1.5 Early innovations within vascular plants: leaves,
roots, and heterospory ................................. 13
1.6 Innovations on the line to seed plants:
"progymnosperms" and "seed ferns" ...................... 18
1.7 Innovations within seed plants, especially conifers .... 22
1.8 Origin of angiosperms and their innovations ............ 26
1.9 Innovations within angiosperms: monocots and eudicots .. 33
Acknowledgments ............................................. 36
References .................................................. 36
2 The Evolution of Body Form in Bryophytes .................... 51
Bernard Goffinet and William R. Buck
2.1 Fundamental Bauplan of bryophytes ...................... 53
2.1.1 The apical meristem is unicellular and growth
is modular ...................................... 53
2.1.2 The architecture of the gametophyte varies
within bryophytes ............................... 54
2.1.3 Bryophytes differ consistently in their
sporophytes ..................................... 54
2.2 Phylogenetic relationships of bryophytes ............... 55
2.3 Evolution of plant form in liverworts .................. 61
2.3.1 The gametophyte ................................. 61
2.3.2 The sporophyte .................................. 64
2.3.3 Evolutionary trends ............................. 65
2.4 Evolution of plant form in mosses ...................... 67
2.4.1 The gametophyte ................................. 67
2.4.2 The sporophyte .................................. 73
2.4.3 Evolutionary trends ............................. 76
2.5 Evolution of plant form in hornworts ................... 78
2.5.1 The gametophyte ................................. 78
2.5.2 The sporophyte .................................. 80
2.5.3 Evolutionary trends ............................. 80
2.6 The ancestral developmental toolbox of land plants ..... 80
Acknowledgments ............................................. 84
References .................................................. 84
3 The Morphology and Development of Lycophytes ................ 91
Barbara A. Ambrose
3.1 Introduction ........................................... 91
3.2 Vasculature ............................................ 96
3.3 Shoot apical meristems ................................. 96
3.4 Sporophyte architecture ................................ 99
3.5 Microphylls ........................................... 101
3.6 Sporangia ............................................. 103
3.7 Roots ................................................. 105
3.8 Structural enigmas .................................... 106
3.8.1 Ligules ........................................ 106
3.8.2 Rhizophores .................................... 108
3.9 Conclusions ........................................... 109
Acknowledgments ............................................ 110
References ................................................. 110
4 Evolutionary Morphology of Ferns (Monilophytes) ............ 115
Harald Schneider
4.1 Introduction .......................................... 115
4.2 Context of evolutionary plant morphology .............. 117
4.2.1 Perspective 1: rapid radiation versus stasis
in the evolution of fern body plans ............ 120
4.2.2 Perspective 2: key structures and organs of
fern body plans ................................ 123
4.2.3 Perspective 3: genomics and evo-devo of ferns .. 132
Acknowledgments ............................................ 134
References ................................................. 134
5 Gymnosperms ................................................ 141
Dennis Wm. Stevenson
5.1 Introduction .......................................... 141
5.2 Architecture .......................................... 142
5.3 Shoots ................................................ 144
5.4 Leaves ................................................ 147
5.5 Roots ................................................. 150
5.6 Seeds ................................................. 152
5.7 Seedlings ............................................. 153
5.8 Embryology ............................................ 154
References ................................................. 159
6 Identifying Key Features in the Origin and Early
Diversification of Angiosperms ............................. 163
Paula J. Rudall
6.1 Introduction: key features of flowering plants ........ 163
6.2 Patterning of flowers and inflorescences .............. 164
6.3 Eight extant lineages of flowering plants ............. 167
6.4 Origin of the angiosperms: the phylogenetic
framework ............................................. 169
6.5 Resolving conflicting hypotheses of flower origin ..... 170
6.6 Evolution of the perianth ............................. 174
6.7 Carpels, gynoecia, and organ fusion ................... 174
6.8 Origins of floral diversity: deep-node characters
and genome duplications ............................... 176
6.9 Contrasting floral ground plans ....................... 178
6.10 Iterative origins of floral symmetry patterns and
floral novelties ...................................... 179
6.11 Constraints and canalization in floral evolution ...... 180
Acknowledgments ............................................ 181
References ................................................. 181
7 Genomics, Adaptation, and the Evolution of Plant Form ...... 189
Kristen Shepard
7.1 Overview .............................................. 189
7.2 The types of genetic variation present within
species ............................................... 191
7.3 From phenotype to genotype: map-based approaches to
identifying adaptive genes ............................ 193
7.3.1 The genetic architecture of quantitative
traits ......................................... 193
7.3.2 Family-based mapping ........................... 193
7.3.3 Advantages and disadvantages of family-based
QTL mapping .................................... 194
7.3.4 Population-based mapping ....................... 195
7.3.5 Advantages and disadvantages of population-
based QTL mapping .............................. 196
7.3.6 Additional considerations in QTL mapping ....... 196
7.3.7 Emerging approaches for detecting QTL .......... 197
7.4 From genotype to phenotype: molecular population
genetics and adaptive evolution ....................... 197
7.4.1 Overview of molecular population genetics ...... 197
7.4.2 Signatures of selection on DNA sequences ....... 198
7.4.3 Demographic factors can complicate inferences
of selection ................................... 199
7.4.4 Gathering nucleotide sequence data ............. 199
7.4.5 Interpreting the sequence data: summary
statistics and tests of neutrality ............. 200
7.4.6 Nucleotide diversity and divergence ............ 201
7.4.7 Analysis of the site frequency spectrum:
Tajima's D and similar tests ................... 201
7.4.8 Analyses of linkage disequilibrium:
haplotype-based tests .......................... 202
7.4.9 Comparing diversity to divergence: McDonald-
Kreitman and HKA tests ......................... 202
7.4.10 Detecting local adaptation: population
differentiation and reduced variability ........ 203
7.5 Bringing it all together - the need for thorough
testing of adaptive hypotheses ........................ 204
7.5.1 Techniques for testing the functional
consequences of polymorphisms .................. 204
7.5.2 Testing adaptive hypotheses .................... 206
7.6 Case studies in molecular population genomic
approaches to the evolution of plant form ............. 207
7.6.1 Case study 1: Identifying novel components of
developmental regulatory networks - BREVIS
RADIX in Arabidopsis roots ..................... 207
7.6.2 Case study 2: Identifying potential targets
of positive selection via a genomic scan in
a nonmodel species - signatures of selection
in sunflower SSRs .............................. 209
7.6.3 Case study 3: Microevolution of a small gene
family - phytochromes in Arabidopsis ........... 211
7.6.4 PhytochromeA ................................... 212
7.6.5 PhytochromeB ................................... 213
7.6.6 PhytochromeC ................................... 213
7.6.7 Case study 4: Combining association mapping
and population genomics - the Arabidopsis
flowering time network ......................... 215
7.7 Conclusion ............................................ 219
References ................................................. 220
8 Comparative Evolutionary Genomics of Land Plants ........... 227
Amy Litt
8.1 Evolution of nuclear genome size ...................... 229
8.1.1 Gene number .................................... 232
8.2 Whole genome duplications ............................. 233
8.2.1 Whole genome duplications in non-flowering
plants ......................................... 236
8.2.2 Whole genome duplications in angiosperms ....... 237
8.2.3 Impact of whole genome duplications on plant
evolution ...................................... 240
8.3 Transposable elements ................................. 241
8.3.1 Retrotransposons ............................... 242
8.3.2 DNA elements ................................... 243
8.3.3 Transposable elements and genome size .......... 244
8.3.4 Dynamics of ТЕ amplification and removal ....... 246
8.3.5 Distribution of transposable elements in
plant genomes .................................. 248
8.3.6 Impact of transposable elements on genome
structure ...................................... 249
8.3.7 Impact on gene diversity, expression, and
function ....................................... 250
8.4 Gene family expansions ................................ 252
8.4.1 Land plant gene diversification ................ 252
8.4.2 Angiosperm gene diversification ................ 254
8.5 Tandem gene duplications .............................. 257
8.6 Fern and gymnosperm genomes ........................... 258
8.7 Arabidopsis genome .................................... 260
8.8 Domestication ......................................... 261
8.9 Future directions ..................................... 263
References ................................................. 265
9 Development and the Evolution of Plant Form ................ 277
Barbara A. Ambrose and Cristina Ferrándiz
9.1 Introduction .......................................... 277
9.1.1 A brief historical overview of evolutionary
developmental biology .......................... 278
9.1.2 General concepts in evolutionary developmental
biology ........................................ 279
9.2 Plant evolutionary developmental biology .............. 280
9.2.1 The evolution and development of the flower .... 281
9.2.2 The evolution and development of leaves ........ 293
9.3 Future directions ..................................... 301
9.3.1 Morphological features ......................... 301
9.3.2 Alternation of generations ..................... 301
9.3.3 Gametophytes ................................... 303
9.3.4 Sporangia and spores ........................... 304
9.3.5 Meristems ...................................... 305
9.3.6 Development of model organisms ................. 307
9.4 Conclusions ........................................... 308
References ................................................. 308
10 Development in the Wild: Phenotypic Plasticity ............. 321
Kathleen Donohue
10.1 Development in the wild is phenotypic plasticity ...... 321
10.1.1 Why are some traits more plastic than
others? ........................................ 323
10.1.2 Manifestations of phenotypic plasticity in
plants ......................................... 324
10.2 Why are some traits more plastic than others? The
evolution of phenotypic plasticity .................... 327
10.2.1 The adaptive value of plasticity: scales of
environmental variation ........................ 327
10.2.2 Genetic constraints on the evolution of
plasticity ..................................... 332
10.3 The genetic basis of phenotypic plasticity and
genetic constraints on plasticity ..................... 332
10.3.1 Molecular mechanisms of phenotypic
plasticity: gene-environment interactions ...... 333
10.3.2 How does the molecular mechanism of
plasticity translate to genetic constraints
on plasticity? ................................. 341
10.4 Phenotypic plasticity and local adaptation ............ 343
10.4.1 Plasticity, niche width, and ecological
isolation ...................................... 344
10.4.2 Phenotypic plasticity as an intermediate
stage of specialization ........................ 345
10.4.3 Does plasticity prevent or promote
divergence? .................................... 346
10.5 Conclusion ............................................ 348
References ................................................. 349
11 The Evolution of Plant Form: a Summary Perspective ......... 357
Michael Purugganan
References ................................................. 363
Index ......................................................... 367
A color plate section falls between pages 62 and 63
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