Molecular systematics and plant evolution

Molecular Systematics and Plant Evolution......Page 1
The Systematics Association Special Volume Series......Page 2
Contents......Page 5
Contributors......Page 7
Preface......Page 10
1.1 Introduction......Page 16
1.2 Selectively neutral genetic variation in organelle genomes......Page 17
1.2.1 Levels of variation a t driftlmutation equilibrium......Page 18
1.2.2 Mutation rates in plant genomes......Page 19
1.2.4 Introduction of diversity through \'organelle capture\'......Page 20
1.2.5 Conclusions and implications......Page 21
1.3.1 Detecting evolutionary units and elucidating population history......Page 23
1.3.2 Measuring gene flow via pollen and seed......Page 27
1.3.3 Detecting and characterising hybridization between species......Page 28
REFERENCES......Page 30
2.1 Introduction......Page 35
2.3 Consequences of glaciation......Page 36
2.4.2 When the ice retreats......Page 38
2.4.3 Onset of the next glaciation......Page 40
2.5.1 Quercus......Page 41
2.5.2 Fagus......Page 42
2.5.3 Alnus......Page 44
2.6 Divergence and speciation......Page 45
REFERENCES......Page 47
3.1 Introduction......Page 50
3.2 Occurrence of cpSSRs and levels of polymorp detected......Page 51
3.3.1 Analysis of natural populations of Scots pine Pinus sylvestris......Page 53
3.3.2 Biosysternatics of wild and cultivated rice  Oryza spp.......Page 55
3.4 Problems and concerns associated with cpSSR analysis......Page 58
REFERENCES......Page 61
4.1 introduction......Page 66
4.2 The tools: aliozymes and DNA markers......Page 67
4.2.1 Disadvantages of RAPDs......Page 69
4.2.2 Quantitative analysis of RAPD variation......Page 70
4.2.3 Graphical display of RAPD variation......Page 71
4.3.1 Population substructure in Alkanna orientalis, an outcrossing plant......Page 72
4.3.2 Population structure and differentiation of Plantago major s.I.......Page 76
4.3.2.2 Morphology......Page 77
4.3.2.3 RAPD and inter-SSR DNA fragments: discrimination of taxa......Page 78
4.3.2.4 Hybridisation......Page 81
4.3.2.6 Distribution of variation......Page 82
REFERENCES......Page 84
5.1 Introduction......Page 89
5.2 General principles and levels of selection......Page 91
5.3 Self- and cross-fertilisation......Page 94
5.3.2 Population structure in tristyfous species......Page 95
5.3.3 Polymorphisms for selfing and outcrossing......Page 98
5.3.4 Reproductive assurance in a metapopulation......Page 101
5.4.1 Ecological and demographic associations......Page 104
5.4.2 Sex allocation......Page 105
5.5 Conclusions......Page 108
REFERENCES......Page 109
6.1 Introduction......Page 116
6.3.1 Cytological investigations......Page 118
6.3.2 Fixed heterozygosity......Page 120
6.3.3 Sample size and segregation analysis......Page 121
6.4.1 Asplenium adiantum-nigrum in northern America and Hawaii......Page 122
6.4.2 Hemionitis pinnatifida......Page 124
6.5 How many origins?......Page 125
6.6 Conclusions......Page 128
REFERENCES......Page 129
7.1 Introduction......Page 133
7.3 Clonal diversity......Page 136
7.3.1 Microspecies......Page 139
7.4 Origins of clonal diversity......Page 144
7.4.1 Sexual origins......Page 146
7.4.2 Asexual origins......Page 147
REFERENCES......Page 150
ABSTRACT......Page 154
8.1 introduction......Page 155
8.2 Hierarchic and reticulate descent systems......Page 158
8.3 Hennig\'s monophyly concept......Page 161
8.4 \'Species\' and monophyletic groups in hierarchic descent systems......Page 162
8.5 Phylogenetic structure within \'species\', phylogeography and the Phylogenetic Species Concept......Page 166
8.6 Monophyletic species concepts with populations as phylogenetic elements......Page 167
8.7 Monophyletic species concepts with organisms as phylogenetic elements......Page 171
8.8 Genealogical species......Page 175
8.9 Monophyly and molecular systematics......Page 178
8.10 Conclusions......Page 181
REFERENCES......Page 182
9.1 Introduction......Page 186
9.2 Phylogenetic systematics of the Mediterranean species complex of Senecio sect. Senecio......Page 189
9.3.1.2 CpDNA analysis......Page 190
9.3.1.3 nrDNA ITS sequence analysis......Page 192
9.3.1.4 RAPD analysis......Page 193
9.3.2 Results and Discussion......Page 194
9.4.1 The study species......Page 198
9.4.2.1 CpDNA analysis......Page 199
9.4.3 Results and Discussion......Page 202
9.5 Conclusions......Page 204
REFERENCES......Page 207
10.1 Introduction......Page 214
10.2.2 Genome identification......Page 216
10.2.3.2 Translocations or recombinations in cells containing two or more genomes......Page 217
10.2.4 Meiotic studies......Page 218
10.3 Taxonomic distance necessary for discrimination by GISH......Page 219
10.4 Partial labelling of genomes......Page 220
10.5 Conclusions......Page 222
REFERENCES......Page 223
11.2 What i s the basis of the RAPDs technique?......Page 226
11.3 How have RAPDs been used?......Page 227
11.5.2 Primer structure......Page 228
11.5.4 Product competition......Page 229
11.5.6 Allelic variation......Page 230
11.6 Methods of analysing RAPD data......Page 231
11.6.1 Similarity measures......Page 232
11.6.3 Frequency measures......Page 234
11.7 Conclusions......Page 235
REFERENCES......Page 237
12.1 Introduction......Page 244
12.2 Some problems with nuclear genes in systematic studies......Page 246
12.3 \'Single copy\' nuclear genes versus gene families......Page 248
12.3.1 Nuclear cox2: a relatively recent transfer t o the nucleus......Page 249
12.3.2 Leghemoglobin in Glycine subgenus Glycine: unexpected maintenance of paralogous clades......Page 250
12.4 Molecular criteria for homology determination: nodulation and nodulin gene evolution......Page 252
12.4.1 Glutamine synthetase: a complex gene family......Page 253
12.5 Studies of closely related species: the need for additional sources of characters......Page 255
12.5.1 Nuclear genes a t Sower taxonomic levels: introns as sources of characters......Page 256
12.5.2 Intron-containing nuclear protein-coding genes in use or under development, primarily in Glycine Leguminosae......Page 257
12.5.2.1 Histone H3-D in Glycine subgenus Glycine......Page 259
REFERENCES......Page 262
13.1 Introduction......Page 270
13.2 Spectral analysis - what i t i s and what it isn\'t......Page 271
13.2.1 Calculating a spectrum......Page 272
13.2.2 Detection of \'good\' and \'poor\' signal......Page 274
13.2.3 Spectra from different sources......Page 275
13.3 The Hadamard - matrix and conjugation......Page 276
13.3.1 Paths and branches......Page 277
13.5 Summary......Page 279
REFERENCES......Page 281
ABSTRACT......Page 283
4.2 Ribosomal gene exploitation in plant systematics......Page 284
14.2.1.1 18s sequencing in angiosperms......Page 286
14.2.1.2 Complementary value of 18s and r b c l......Page 287
14.2.1.3 Differences between 18.5 and rbcL gene trees and patterns of sequence evolution......Page 288
14.2.2 The r D N A I73 region, including the 5.8s rRNA gene......Page 300
14.2.2.1 Sequencing ITS......Page 301
14.2.2.2 Quantitylquality of ITS phylogenetic signal......Page 302
14.2.2.3 ITS polymorphism......Page 312
14.2.3 The rRNA 5\' external transcribed spacer 5\'-ETS......Page 315
14.2.4 The 26s rRNA gene......Page 316
14.2.5 The 5s rRNA gene......Page 318
14.3 Advances in phylogenetic analysis relevant to rDNA systematics......Page 319
14.3.1 r D N A sequence alignment......Page 320
14.3.2.1 Among-site rate variation in rDNA sequence evolution......Page 321
14.3.2.2 Base substitution bias in rDNA......Page 322
14.3.2.4 Accommodating complex substitution patterns in phylogenetic analysis......Page 323
14.3.3 Resolvability of rDNA data-sets......Page 325
14.4 Future prospects for rDNA in angiosperm systematics......Page 330
REFERENCES......Page 331
APPENDIX......Page 339
15.1 Introduction......Page 342
15.2 Determining common sets of genes across chloroplast genomes......Page 343
15.3 A rooted phylogeny for nine plastid genomes......Page 352
15.4 Individual proteins in comparison to the concatenate proteins......Page 353
15.5 The information content of the data......Page 354
15.6 Predominance of parallel gene losses in independent lineages......Page 359
15.7 Transfer of functional genes from the plastid to the nucleus......Page 360
15.8 The phylogeny of plastids reflected in complete genomes......Page 362
ACKNOWLEDGEMENTS......Page 363
16.1 Introduction......Page 368
16.2 Mediterranean-type vegetation and the Cape Floristic Region......Page 369
16.3 Pelargonium......Page 370
16.3.1 Growth forms in Pelargonium......Page 372
16.4.1 Data and analysis......Page 374
16.4.2 Patterns of substitution and insertionldeletion in trnL-F......Page 375
16.5 Phylogeny, karyology, growth form and biogeography in Pelargonium......Page 378
16.6 Evolutionary trends in the small-chromosome group of Pelargonium......Page 383
ACKNOWLEDGEMENTS......Page 385
REFERENCES......Page 386
ABSTRACT......Page 390
17.1 Introduction......Page 391
17.2.1.1 The \'genus\' data set......Page 393
17.2.1.2 The \'species\' data set......Page 394
17.2.5 Sequence analysis......Page 395
17.3.1.1 Sequence comparison between trni+F, ITS and cyc......Page 396
17.3.1.2 Phylogenetic reconstruction using three genes......Page 397
17.3.1.3 Comparative pairwise sequence divergence......Page 402
17.3.2.1 Sequence comparison between ITS and Gcyc......Page 404
17.3.2.2 Phylogenetic reconstruction: ITS vs Gcyc......Page 406
17.4.1 Comparative rates of gene evolution......Page 409
17.4.3 Gcyc and the evolution of floral symmetry patterns......Page 411
ACKNOWLEDGEMENTS......Page 414
REFERENCES......Page 415
18.1 Introduction......Page 418
18.2.1 An optimisation framework......Page 419
18.2.2 Distribution of epigyny among angiosperms......Page 420
18.2.3 Epigyny in the Asterales......Page 421
18.2.5 Fixation and instability of epigyny......Page 422
18.3 Covriation with other kinds of organ fusion/synorganisation......Page 426
18.4.1 Origins and spread of epigyny......Page 427
18.4.2 Ovary protection......Page 428
18.4.3 Morphological consequences for fruit morphology and diversity......Page 429
18.5.2 Conditions transitional to epigyny......Page 430
18.5.3 Evidence from floral vasculature......Page 432
18.5.4 Ontogeny and organogenesis......Page 433
18.5.5 Histology and tissue identity......Page 434
18.6 Loss of organ identity following fusion......Page 436
18.7.1 MADS box genes\'......Page 437
18.7.2 The ABC model......Page 438
18.7.3 Process orthology in the inferior ovary......Page 439
ACKNOWLEDGEMENTS......Page 441
REFERENCES......Page 442
ABSTRACT......Page 447
19.2.1 Conceptual framework for evolutionary radiations......Page 448
19.2.2 Intrinsic criteria i.e. reflecting phenotype andlor genotype......Page 450
19.2.3 Extrinsic criteria ecology s.I.......Page 453
19.2.4 Temporal context of radiations......Page 454
19.3.1 Both adaptive and non-adaptive processes can underlie punctuational patterns......Page 456
19.3.2 Punctuational patterns in morphological and molecular phylogenies......Page 459
19.4.1 Northern hemisphere Orchidinae......Page 461
19.4.2 Macaronesian Poteriae......Page 463
19.4.3 Hawaiian Asteraceae......Page 466
19.5.1 Preferred protocol for comparing molecular and morphological trees......Page 468
19.5.2 Inferring evolutionary process from phylogenetic pattern: Cross-matrix disparity as an under-used interpretative too!......Page 469
19.5.3 The perils of punctuation and implications for \' t o t a l evidence\' trees......Page 470
19.6.1 Supposed advantages of molecular data......Page 472
19.6.2 Uses and abuses of character \'mapping\'......Page 475
19.6.3 Morphology is dead - long live morphology!......Page 476
19.7 Conclusions......Page 477
REFERENCES......Page 479