T. RYAN GREGORY -- ALTERNATE VERSION
TABLE OF CONTENTS
VOLUME ONE
Chapter One: The evolution of genome size: a historical, conceptual,
and terminological review
Abstract 2
Introduction: a word about words 3
A brief history of DNA 4
The DNA constancy hypothesis 7
“Une remarkable constance”
7
Constancy questioned
8
Constancy confirmed
11
“C” is for class!
14
Exceptions to the rule (?) 17
Polyteny and gene amplification
18
Chromatin diminution
20
Intraspecific variation
21
The evolution of “genome size” 25
From pangens to genomes
25
Genome size, C-value, and polyploidy
28
Cryptopolyploidy
34
The paradox that was 35
The C-value paradox
35
Of genes and genomes
39
Multiple strands and multiplied genes
42
The puzzle that is 43
Death of a paradox
43
The C-value enigma
45
Single-copy DNA 47
Introns 49
Types of chromatin 51
Satellite DNA 52
Transposable elements 54
Retroposons: LINEs and SINEs
56
LTR retrotransposons
58
DNA transposons 59
Pseudogenes 60
Processed pseudogenes
61
Classical pseudogenes
62
Numts 63
Junk DNA 64
The origin of junk DNA
64
Junk DNA and non-function
66
From pseudogenes to everything
67
Should “junk” be thrown out?
69
The new noun “nuon” and its nuances
(an exercise in confusion) 71
The primacy of “secondary”
73
Selfish DNA 74
The origin(s) of selfish DNA
74
The origin(s) of selfish DNA (again)
79
Selfish genes and abstract elephants
80
Objections to selfish DNA
82
From parasitism to mutualism
84
Junk versus selfish
86
Mutation pressure theories 88
The junk DNA theory
88
The selfish DNA theory
89
The DNA loss hypothesis
90
The desperate search for function 91
Cell size and optimal DNA 94
The nucleoskeletal theory
94
The nucleotypic theory
95
Concluding remarks 97
Chapter Two: DNA content and the cellular phenotype
Abstract 108
Introduction: the importance of cell size
109
DNA content and cell size 110
The karyoplasmic ratio
110
Polyploidy and cell size
110
Genome size and cell size 111
Reptiles 112
Amphibians 113
Fishes 114
Birds 116
Mammals 119
Coincidence? 125
Size-dependent threshold
126
Overall increase in DNA content
127
Inability to delete extra DNA
128
Coevolution? 131
Nuclear size and the nucleoskeleton
132
Nuclear pores and RNA transport
134
Return and reversal of the karyoplasmic
ratio hypothesis 135
The pros and cons of coevolution
139
Causation? 142
Challenges to the nucleotypic theory
143
In support of the nucleotype
145
Previous models of nucleotypic influence
149
The nucleotide sequestration model
149
The division-initiation model
151
The gene-nucleus interaction model 153
Eukaryotic cell cycle regulation
154
DNA content and cell cycle length
156
DNA content and cell cycle control
160
Issues awaiting resolution
166
Concluding remarks 169
Effect versus function
169
Chapter Three: Genome sizes of mammals and birds
Abstract 194
Introduction 195
Summary of the dataset 196
Patterns of variation 197
A digression on regression 200
Genome size and chromosome number 202
Genome size, cell size, and metabolism in mammals
204
Mammalian metabolism: analysis and
results 205
Mammalian metabolism: discussion
208
Genome size, cell size, and metabolism in birds
209
Avian metabolism: analysis and results
211
Avian metabolism: discussion
212
Genome size and flight 214
A causal connection?
214
Genomic baggage: lost or never loaded?
216
Genome size and developmental parameters
220
Sources of data 223
Avian development: dataset #1
224
Avian development: dataset #2
225
Mammalian development
228
Genome size, development, and body
size in homeotherms 229
Concluding remarks 230
Chapter Four: Genome sizes of amphibians and reptiles
Abstract 244
Introduction 245
Summary of the dataset 245
Patterns of variation 246
Genome size and chromosome number 249
Genome size, cell size, and development (a reply to Pagel
and Johnstone) 252
What Pagel and Johnstone did, didn’t, and couldn’t say
253
Summary of the study
253
A statistical aside
255
Difficulties with the data
256
Negating the nucleoskeleton?
258
Neglecting the nucleotype
259
Genome size, cell size, and metabolic rate (a reply to
Cavalier-Smith) 261
Cell size and cellular metabolism
261
Genome size and metabolic rate
262
Cell size and metabolic rate
264
Genome size and developmental complexity
266
The threshold concept: genome size and development in
plants 267
Developmental complexity in amphibians
271
Developmental rate and constant complexity
272
Developmental process: direct development
275
Developmental process: neoteny
278
Developmental products: big genomes
and simple brains 285
Development in amphibians: a summary
288
Amphibian genome size and the hierarchy of evolution
289
Chapter Five: Genome sizes of fishes
Abstract 305
Introduction 306
Summary of the dataset and patterns of variation
306
Agnathans 307
Chondrychthyes 307
Chondrosteans 308
Teleosts 309
Sarcopterygians 312
Genome size, chromosome number, and polyploidy
313
Genome size, metabolism, and swimming performance
315
Hinegardner’s rule and developmental complexity
318
Other factors that may (or may not) affect fish genome
sizes 322
Genome size evolution in vertebrates: a summary
324
References for Volume One 341
VOLUME TWO
Chapter Six: Is DNA loss rate a determinant of genome size?
Abstract 432
Introduction 433
The DNA loss hypothesis 433
Of mice and men 436
Relative versus absolute rates of loss
437
Deletion rate versus deletion size
438
Comparisons of related taxa 439
Example #1: Mammals
439
Example #2: Drosophila
441
Example #3: Nematodes
443
Example #4: Barley and maize
444
Example #5: Bacteria
449
Swapping junk for trash? 451
Alternative explanations 452
Selection for small genome size
452
Rapid replication and sloppy slippage
454
Unequal patterns of unequal crossing-over
455
Is Drosophila just a freak?
457
Concluding remarks 458
Chapter Seven: DNA quantification by Feulgen image analysis densitometry
Abstract 466
Introduction 467
DNA quantification: past and present
468
Densitometry 468
Fluorometry 471
Image analysis densitometry 473
Basic concepts 474
Guidelines for specimen preparation: vertebrates
475
Fishes 477
Amphibians 477
Reptiles 478
Birds 479
Mammals 479
Guidelines for specimen preparation: invertebrates
481
Crustaceans 481
Insects 483
Arachnids 487
Myriapods 489
Annelids 489
Molluscs 491
Echinoderms 492
Flatworms 493
Nematodes 493
Cnidarians 494
Miscellaneous invertebrates
494
Staining methods 495
The Feulgen reaction
495
Stain preparation
496
Staining protocol
497
Measurement protocol 498
Hardware and software
498
Microscope set-up and image capture
499
Choice of standards and calculation
of genome size 500
Concluding remarks 501
Chapter Eight: DNA content modulation and the evolution of the Crustacea
Abstract 517
Introduction 518
Genome size variation in crustaceans
518
Summary of the dataset
518
Patterns of variation
519
Intraspecific variation in genome size
520
Cryptopolyploidy, polyteny, and quantum
shifts 522
The significance of genome size variation
523
Genome size and body size
523
Genome size and developmental rate
525
Rapid evolution by quantum shifts in
genome size 527
Other ecological and evolutionary considerations
528
Good old-fashioned polyploidy 531
The prominence of polyploidy
531
Ecological significance of polyploidy
532
Endopolyploidy 533
Patterns of endopolyploidization
534
Ecological significance of endopolyploidy
536
Chromatin diminution 537
Characteristics of chromatin diminution
in copepods 537
On the adaptive value of chromatin
diminution 539
Chromatin diminution and rapid development:
mechanistic aspects 541
Endoreduplication, chromatin diminution
(or not), and quantum shifts 542
Summary and concluding remarks 545
Chapter Nine: Genome sizes of insects
Abstract 558
Introduction 559
Summary of the dataset(s) 559
Previously published data
559
New genome size estimates
560
Patterns of variation 560
Blattaria 561
Coleoptera 562
Collembola 567
Dermaptera 568
Diptera 568
Embiidina 572
Ephemeroptera 572
Hemiptera 573
Hymenoptera 576
Isoptera 576
Lepidoptera 577
Mantodea 578
Odonata 578
Orthoptera 578
Phasmida 581
Plecoptera 583
Siphonaptera 583
Thysanura 583
Trichoptera 584
Endopolyploidy and polyteny 584
Classic examples
584
Dosage compensation in Hymenoptera
585
Nurse cells 586
Developmental complexity in insects: more on metamorphosis
590
Concluding remarks 594
Chapter Ten: Genome sizes of spiders
Abstract 609
Introduction 610
Summary of the dataset 611
Spiders 611
Other arachnids 612
Patterns of variation 613
General patterns in spiders
613
A note on the spider mite
615
Prospects for future work 615
Comparisons with other arachnids
616
Developmental and ecological lifestyle
616
Endopolyploidy 617
Chapter Eleven: Genome sizes of miscellaneous invertebrates
Abstract 621
Introduction 622
Summary of the dataset(s) 622
Previously published data
622
New genome size estimates
622
Patterns of variation 623
Molluscs 623
Annelids 628
Flatworms 634
Echinoderms 636
Nematodes 637
Tardigrades 639
Gastrotrichs 640
Myriapods 640
Cnidarians 641
Rotifers 642
Sponges 643
Miscellaneous invertebrates
643
Genome size evolution in invertebrates: a summary
645
Chapter Twelve: Macroevolution, hierarchy theory, and the C-value enigma
Abstract 654
Introduction 655
Macroevolutionary theory for neontologists
656
What is macroevolution?
656
Critiques of the Modern Synthesis
658
Reductionism in biology
664
Group selection: new and improved and
no longer naïve 667
The concept of individuality
670
Punctuated equilibria and species as
individuals 673
Species selection in principle and
in practice 676
Aggregate versus emergent characters
678
Emergent fitness versus the effect
hypothesis (the Lloyd-Vrba debate) 680
Selection versus sorting
683
Hierarchical macroevolutionary theory:
a summary 685
Molecular macroevolution 688
Are genomes “individuals”?
688
The necessity of hierarchy theory for understanding genomes
(and vice versa) 692
Group selection and the origin of the
genome 692
Selfish DNA and the necessity of hierarchy
695
The C-value enigma from a hierarchical perspective
699
Genomes as phenotypes and genotypes
699
The evolution and ecology of transposable
elements 703
Selection, sorting, and genome size
708
Stasis and DNA constancy
709
Genome-level processes and the major transitions in evolution
713
Concluding remarks 722
References for Volume Two 725
VOLUME THREE
Appendix 2.1: Erythrocyte sizes of reptiles 786
Appendix 2.2: Erythrocyte sizes of amphibians 789
Appendix 2.3: Erythrocyte sizes of fishes 799
Appendix 2.4: Erythrocyte sizes of birds 810
Appendix 2.5: Erythrocyte sizes of mammals 827
Appendix 3.1: Genome sizes of mammals 849
Appendix 3.2: Genome sizes of birds 880
Appendix 4.1: Genome sizes of amphibians 896
Appendix 4.2: Genome sizes of reptiles 943
Appendix 5.1: Genome sizes of fishes 969
Appendix 8.1: Genome sizes of crustaceans 1063
Appendix 9.1: Genome sizes of insects (database) 1083
Appendix 9.2: Genome sizes of insects (original data) 1105
Appendix 10.1: Genome sizes of spiders 1123
Appendix 11.1: Genome sizes of miscellaneous invertebrates (original data)
1131
Appendix 11.2: Genome sizes of molluscs 1137
Appendix 11.3: Genome sizes of annelids (database) 1152
Appendix 11.4: Genome sizes of annelids (original data)
1161
Appendix 11.5: Genome sizes of flatworms 1165
Appendix 11.6: Genome sizes of echinoderms 1168
Appendix 11.7: Genome sizes of nematodes 1172
Appendix 11.8: Genome sizes of miscellaneous invertebrates (database)
1174
References for Volume Three 1179