INDEX
A
Acanthomorphs, 73
Acritarchs
across Varanger ice age, 73, 74, 75-76
cladogenetic evolution, 75, 78-79
cohort survivorship in Proterozoic, 76
fossil record, 69-73
morphological diversification, 73
Precambrian evolution, 67-69
Proterozoic-Cambrian evolution, 74-80
Adaptive landscape
analysis of walks in, 158-164
depth of valley in, 28
morphospace in, 149
phenotype fitness, modeling of, 153-154
in phenotypic transformation, 146-147
plant model, 147-154
point of origin for walks in, 154
quantitative analysis in, 145-146
single vs. multi-task walks, 155-158
task demands in, 146-147
unimpeded walks in, 147-149
Adenosine triphosphatase, archaebacterial subunits, 13, 19
African replacement model, 203, 205
Amino acids
covarion model of replacement, 235-236
in major histocompatibility complex, 189
replacement in RuBisCo protein, 223-227
replacement in SOD, 235
replacement patterns, 213, 230
in replication in RNA world, 1, 35, 36, 37
in SOD molecular clock, 244, 246-247
See also Superoxide dismutase
Amphibians, in Cretaceous-Tertiary mass extinction, 118-119
Amylase, in Drosophila pseudoobscura, 289, 290-291
Annelids
late Precambrian form, 103
phylogenic lineage, 97-98
Archaea, 15-16
Archaebacteria
characteristics, 11-12
in eubacteria-eukaryotic-prokaryotic lineage, 4, 12-16
ribozymology, 4-5
RNA polymerase subunits, 20
Arthropods
late Precambrian form, 102-103
phylogenetic lineage, 95, 96-97
Asexual reproduction, 53
Atmospheric conditions
in Cambrian explosion, 102
primordial cyanobacteria, 55-56
B
Background selection, 276, 277-282
Bacteria
chloroplast-mitochondria lineage in, 9
as prokaryotes, 6
reproductive rate, 251
See also E. coli
Bacteriophages
P1. See Framework P1 map
Qß, replication strategy, 28-29, 30, 33-34
Balanced selection, 196-197, 199
Bilaterians
body plan evolution, 101
Biometrical science, iv
Bipedalism, 173-175
Bottleneck effect, 188-189, 197-201, 206
Brachiopods, 98
Bradytelic evolution, 43
Brome mosaic virus, 29
Burgess Shale
cnidarians in, 90
middle Cambrian diversity in, 91
C
Cambrian Period, 85
acritarch evolution, 69-80
annelids, 97-98
boundaries of explosion, 88-89, 91
environmental factors in explosion, 102
gene expression in explosion, 103
metazoan diversity before explosion, 85, 99
metazoan faunas, 89-91
skeletal fossils, 90-91
Candelabra model, 202-203
Cauliflower mosaic virus, 33
CCA terminus, 3, 28, 31, 35-37
Cell-type number, 92-93
Cenancestor
definition, 6
in eukaryote-prokaryote lineage, 10-11
genome structure, 18
macromolecular synthesis in, 25-26
obstacles to understanding, 20-22
Cephalopods, body plan, 98
Chloroplast
amino acid replacement in, 223-227
complexity of genome evolution in, 229-231
eukaryote-prokaryote lineage, 7, 9, 21
in eukaryotic cell, 215
genome conservation, 216-217
genome structure, 213, 215, 216
genomic deletion events, 217-219
intron evolution, patterns of, 228-229
mutation patterns, 217-220
noncoding DNA in, 217-220, 229
nucleotide substitution rate, 221-223
protein coding genes in, 220-223
pseudogenes, 217
research role, 230
Chromosomes
Drosophila polymorphism, 251-252, 283
Drosophila polytene, 299-300, 307, 310
mapping, 252
telomerase, 34
Chroococcaceans
fossil-modern comparisons, 49-50, 52
ranges of growth/survivability, 53-55
Classification systems
cenancestor in, obstacles to, 20-22
prokaryote-eukaryote-archaebacteria, 6-7, 11, 14-16
Cnidarians, 89-90
Coalescence theory, 196-197, 206
Codons
concomitantly variable. See Covarions
in molecular clock, 243-244
Color vision, 205-206
Comparative sequence analysis, 230, 231
Competition, as extinction factor, 111-112, 117-118
Complexity
body plan, cell-type number and, 92-93
Cambrian metazoa, 92
morphological diversity and, 86
Precambrian worms, 99
Covarions
in molecular clockwork, 243, 246, 248
in SOD simulation, 236-237, 240, 243
theory of, 235-236
Cretaceous-Tertiary mass extinction, 110, 114-115, 118-119, 121
Cyanobacteria, 9
classification, 6
ecological distribution, 53
hypobradytelic evolution in, 47-53, 57
living vs. fossil morphology, 44, 47-50, 48, 57
paleoenvironment, 50-52
Precambrian evolution, 42, 57-58
Precambrian fossil record, 43, 44-46
ranges of growth/survivability, 53-56
reproduction, 53
specialization and survivability, 53, 56
tempo of evolution, 43-44
Cytoskeletal proteins, 16
D
on extinction, 109-111, 117-118, 137
Lyell and, 126
uniformitarianism in thought of, 126-127, 137
Dinosaurs
fossil record, 113
species susceptibility in extinction, 120
taxonomic selectivity in extinction of, 118
Diplomonads, 19
Discontinuous variation, iv
Diversity peaks
Cambrian explosion, 85, 87-91, 93, 99, 102-103
Middle Cambrian body plans, 91
Proterozoic protistans, 77-78, 79, 80
DNA
Drosophila, extraction and sequencing of, 289-290
Drosophila polymorphism, patterns of, 251, 283
in Drosophila polytene, 300
evolutionary complexity in chloroplast genome, 229
evolutionary data in, 188
human mitochondrial evolution, 203-204, 206
mitochondrial polymorphism, 189
non-primer synthesis, 33
noncoding, in chloroplast genome, 217-220, 229
RNA ancestry in, 4-6
selective sweeps effects, 277
sequence data base, 275
tRNA in replication of, 31-33
Dobzhansky, Theodosius, 252, 287-288
Domains, classification of, 14-15, 16
Drosophila
amylase in, 290-291
ancestor chromosomes, 252
ancestor gene in pseudoobscura, 288-297, 310-311
chromosome mapping, 252
chromosome polymorphism, patterns in, 251
cytogenetic phylogeny, 288
early chromosomal studies, 287-288
extraction and sequencing of genomic DNA, 289-290
mutation rate, 280-282
polytene chromosome, 299-300, 307, 310
recombination-polymorphism correlation, 276, 282-283
reproductive rate, 251
research advantages, 299-300
restriction site polymorphism, 289, 292-294
virilis, 311
yeast artificial chromosome map, 300
See also Framework P1 map
Duration of species, 195-196
E
adaptive landscape, 262-264, 267-268
assessment of mean fitness in, 255, 259-260
cell size evolution, 256-259
chance events in experimental evolution, 267
environmental factors in, 268
evolutionary stasis in experimental populations, 268-269
experimental evolutionary method, 255-256
fitness evolution in experimental population, 260-261
in Framework P1 map, 301-302
limitations of experimental evolution, 270
measurement of cell size, 255, 256, 264
natural selection in experimental population, 256, 257, 259, 264-266
outcomes of experimental evolution, 271
parallel evolution in experimental populations, 266-268
punctuated equilibrium in experimental evolution, 269
reproductive rate, 251
size-fitness relationship, 264-266
Elongation factors
in Qß RNA genome replication, 30
Tu, RNase P and, 29
Endosymbiont hypothesis, 7, 9, 21
Environmental factors
in acritarch evolutionary tempo, 79
in Cambrian explosion, 79, 102
cyanobacterial growth tolerances, 53-56
in E. coli experimental evolution, 268
in morphological research, 254-255
in prokaryotic evolution, 42
Eosynechococcus moorei, 47
genome sequencing, 21
operans in, 18
origins of, 13-14
Eukaryotes
ancestral ribosome, 9
chloroplast genome, 215
endosymbiont hypothesis, 7, 9, 21
as Eucarya, 15
evolution of, 4-6
evolutionary model, 7-12
evolutionary pathway, 12-16
fossil record, 7
introns, 78
nuclear genome evolution, 18-19
Precambrian acritarchs, 67-73
prokaryotes vs., 6-7
Proterozoic algae, 78
rate of evolution, 2
RNA polymerase subunits, 20
tRNA production, 30
Evolutionary theory
bipartite model, 56-57
cellular information systems in, 4-6
eukaryotes-prokaryote lineage, 7-12
eukaryotes-prokaryote split, 12-16
genomic diversity of viruses, 30-31
historical development, iii-vi
human origins, 201-205
Modern Synthetic, 129
molecular research in, 22
paleontology and, 127-131
precellular evidence, 27
RNA in, 25-26
significance of extinction, 85-86, 109, 122-123
See also Darwin, Charles
See also Macroevolutionary theory
Exon theory, 11
Extinction
body size and, 119
Cretaceous-Tertiary event, 110, 114-115, 118-119, 121
Darwin on, 109-111, 117-118, 137
environmental factors in, 121, 122
episode analysis, 114-117
evolutionary significance, 85-86, 109, 122-123
geographic distribution and, 119
interspecies competition in, 111-112, 117-118
kill curve, 115-117
mass episodes, 110, 112, 114-115, 117, 123, 137
natural selection and, 120
role of, 121-122
selectivity mechanisms in, 117-120, 123
Simpson on, 111-112
species susceptibility, 119-120
taxonomic susceptibility, 118-119
trait susceptibility, 119
F
Fitness as evolutionary factor
E. coli cell size and, 264-266
E. coli evolutionary trajectory, 260-264
measuring, in E. coli, 255-256, 259-260
modeling evolutionary morphology of vascular land plants, 149-154, 158-164
modeling of task demands for plants, 155-158
modeling requirements, 147-149
in morphological transformation, 146-147
obstacles to analysis, 145-146
phenotypic maxima vs. phenotypic optima, 157-158
plants as object of study, 147
task demands and, 146
Fossil record
acritarchs, Proterozoic-Cambrian, 69-73
annelid, 97-98
brachiopod, 98
correspondence of computer simulations, 160-162
cyanobacterial hypobradytely, 47-53
discontinuities in, v
earliest metazoan, 89-90
earliest skeletal, 90-91
Early Cambrian, 87
eukaryote, 7
H. erectus, 202
hominid, 169, 173-175, 202, 203
hypobradytelic evolution, 44-46
marine animal survivorship analysis, 113
molecular fossils, 27, 43, 44-46
in morphological research, 254-255
Paleoproterozoic, 2
pre-cellular, 1
prokaryote, 7
Proterozoic-Cambrian, 64-73
Simpson's use of, 41
Founder effect theory, 188-189, 197-201, 206
Framework P1 map
cloning vectors, 301-302
contig assembly, 306-307
cytological analysis, 302, 307
D. virilis in, 311
depth of coverage, 300
distribution of clones, 304-305
Drosophila library, 303-304
Drosophila strains, 300-301
dual hybridizations, 304
electronic mail access, 300
in evolution studies, 307-311, 312
insert sizes, 300
ligated DNA packaging, 301-302
PCR amplification of insert-vector junctions, 302-303
PCR screening, 303
plasmid DNA extraction, 302
STS markers, 299, 303, 306-307
X chromosome, 305
G
Genetic information transfer
allele selectivity, 195
archaebacterial, 14
in Cambrian explosion, 103
chloroplast rp123 pseudogene, 217-219
chloroplast to eukaryotic nuclear genome, 215-216
coalescence theory, 196-197
human polymorphisms, population size in, 197-201
lateral events, 21
metazoan body plan evolution, 99-101
molecular clocks, 240-243
in multiregional model of human evolution, 205-206
in natural selection, 140-141
recombination-polymorphism correlation, 276-283
trans-specific polymorphisms, 191-196
Genetic science
comparative sequence analysis in, 230, 231
in evolutionary theory, iii-iv
in phylogenetic reconstruction, 252
population processes in, 275-276
role of phylogeny research in, 216
in species research, 187-188
Genotype
mapping, 145-146
Geographic distribution
extinction and, 119
in human origins, 202-207
Gloethece coerulea, 47
Haloferax volcanii, 18
H
Halophiles, 11
genome structure, 18
Hedgehog gene, 100-101
Hitchhiking effects, 276, 277, 282-283
Horotelic evolution, 43, 131, 132
Human evolution
allele phylogeny in, 191-193
ancestral population size, 197-201
ancestral species overlap, 181
body size, 175-177
color vision in, 205-206
DRB1 gene, 193
food consumption, 177-178
gene coalescence in, 196-197, 203-204, 206
geographic models, 202-206
hand structure, 175
histocompatibility complex allele complexity, 167
lipid metabolism in, 206
morphological course, 167, 182
most primitive hominid, 170, 173, 177
multiregional model, 204-206
phylogeny, 169-173
population bottlenecks in, 188-189, 197-201, 206
single ancestor theory, 189, 203
theory of origins, 201-205
trans-specific polymorphism in speciation, 193-196
within-species variation, 182
Human Genome Project, 299
Human leukocyte antigen complex. See Major histocompatibility complex
Hypobradytelic evolution
in cyanobacteria, 43-44, 46-56
fossil evidence, 44-46
I
Immune system, major histocompatibility complex in, 189
in situ hybridization, in chromosome mapping, 300
evolutionary patterns in chloroplast genome, 228-229
L
Light conditions, for early cyanobacteria, 55
Lipid metabolism, 206
Lobopods, 97
Lyell, Charles, 126
M
Macroevolutionary theory, 85-86
causality in, 136
experimental E. coli evolution and, 270-271
hierarchical selection theory in, 137-142
mass extinction in, 137
punctuated equilibrium in, 136-137
Simpson and, 132-136
Macromolecules
evolutionary pathways of synthesis, 25
social coevolution, 27-28
Major histocompatibility complex
action of, 189
allelic diversity, 189-191
allelic phylogeny, 196-197
DRB1 gene, 191-193, 196-197, 206
maintenance of polymorphisms, population size in, 197, 201, 206-207
trans-specific polymorphisms, 191-193
Mapping, genomic, 145-146
framework map, definition of, 300
human, 299
hybridization technique in, 300
role of, 299
yeast artificial chromosome map, 300
See also Framework P1 map
Mauriceville plasmid, 31-34
Metazoans
body-plan complexity, 91-93
Cambrian faunas, 90-91
Cambrian/Precambrian body plans, 87
earliest fossils, 89-90
genetic regulation in body plan evolution, 99-102
Hox/HOM genes in, 100
late Precambrian body plans, 95-99
Precambrian diversity, 99
Precambrian phylogeny, 95, 102-103
Methanogens, 11
Microsporidia, 19
Mitochondria
eukaryote-prokaryote lineage, 7, 9, 21
Mauriceville plasmid of Neurospora, 31-33
Mode of evolution
corresponding tempos, 132
definition, 3
in molecular research, 3
paleontological research, 130-131
quantum, 134
Molecular fossils, 27, 43, 44-46
Mollusks, 98
extinction record, 119
N
Natural selection. See Selection
Neurospora, Mauriceville plasmid, 31-33
Noah's Ark model, 203
Nucleotide substitution
in chloroplast genome, 221-223
as molecular clock, 242-243
recombination rate and, 278-279
O
Operons, in archaebacterial/eubacterial lineage, 18-19
Oscillatoriaceans
fossil-modern comparisons, 49-50, 52
ranges of growth/survivability, 53-55
P
Paleontology
in evolutionary science, 129-131, 142-143
phyletic data in, 133
professional status, 127-129
Paleoproterozoic, 2
Paleozoic era, time scale, 64
Paralogy, 20-21
Phanerozoic eon
rate of evolution, 52-53
worms, 99
Phenotype
cell-type number in body plan complexity, 92-93
genotype mapping, 145-146
identifying trends in, 254
modeling fitness transformations, 147-149, 160
Photosynthesis, 216
endosymbiont hypothesis, 7
Phycodes pedum, 88
Phycomata, 67-68
Phylogeny
algal eukaryotes, 78
alleles in reconstruction of, 191
amino acid replacement, 224, 226, 230
archaebacteria-eukaryote-prokaryote, 6-20
chloroplast genome, 229-230
Drosophila pseudoobscura ancestor gene, 288-297
eukaryote, 26
experimental reconstruction in bacteria, 255-256
genetics in reconstruction of, 252
hominid cladogram, 169-173
metazoan body plans, 93-99
Precambrian branching sequences, 93-95
precenancestral, reconstruction of, 20-22
prokaryote, 6-20
reconstruction process, 292
research role, 216
Simpson's emphasis on, 133-134
SOD amino acids, 237
Plants
chloroplast genome, 213, 215, 216
intron evolution, 228-229
modeling evolutionary morphology of, 149-154, 158-164
modeling of task demands, 155-158
tracheophyte evolution, 149, 154, 160-162
Pleistocene epoch
extinction in, 121
human population growth in, 198
Pleurocapsaceans, 51-52
Polymerase chain reaction, 302-303
Polymerases, domain structure, 33-34
Population size
cyanobacteria, 53
in fixation of neutral allele, 195
in founder effect theory of speciation, 188
in human evolution, 197-201, 203-207
in maintenance of polymorphism, 197
Postmodern thought, 135-136, 143
Precambrian era
arthropod evolution, 95, 96-97
clade diversity, 69
cyanobacterial hypobradytely in, 47-53, 57-58
evolution in, 57-58
life of, 41-42
metazoan body plans, 95-99
molecular fossil record, 43, 44-46
phylogenetic models, 93-95
prokaryote evolution, 41-42
vascularized worms, 95-96, 98-99, 102-103
Vendian fauna, 89-90, 95-96, 97
Progenote, 1
definition, 6
ribosomal structure, 9-10
templated protein synthesis in, 26
Prokaryotes
distinguishing features, 6-7
eukaryotes vs., 6-7
evolutionary forces, 41-42
evolutionary model, 7-12
evolutionary pathway, 12-16
fossil record, 7
introns in, 11
Precambrian, 41-43
rate of evolution, 1-2
Protein coding genes, 220-223
Proteobacteria, 9
Proterozoic eon
acritarch evolution in, 73-80
clade diversity in, 69
eukaryotes in, 72
paleontological data base, 69-72
time scale, 64-66
Protistan
Paleoproterozoic evolution, 2
Proterozoic diversity peaks, 77-78, 79, 80
Protostomes, phylogenetic lineage, 95, 96
Punctuated equilibrium, 136-137, 269
R
rDNA, 9
Recombination rate, correlation with polymorphism, 276-283
Reef communities, 117
Replication
earliest RNA genomes, 28-29
Mauriceville plasmid of Neurospora, 31-33
as selectivity criteria, 140-141
transitional genomes in, 31-33
Reproduction
asexual, 53
evolutionary dynamics, 253
rate of, 251
tracheophyte model, 152-153
Restriction site polymorphism, 289, 292-294
Retroviruses, replication strategy, 31, 33
Ribonucleotide reduction, in RNA-DNA ancestors, 4-5
Ribosomal RNA
arthropod, 96
eukaryote-prokaryote lineage, 8-10, 11
as molecular chronometer, 22
RNA
3' terminal sequence, 28-30
archaebacterial/eukaryotic linkage, 20
earliest genomic tags, 28-29
evolutionary role, 25-26
introns early hypothesis, 11
origins of, 26
See also Transfer RNA
S
Seaweeds, pre-Ediacaran, 68
Segment-polarity genes, 100-101
Selection, iv
in adaptive landscape, 145-147, 261-262
of alleles, 195
in amino acid replacement, 230
background selection model, 277-282
in chloroplast codon use, 220
codical domain in, 140-142
in E. coli cell size, 257, 259, 264-266
emergent fitness hypothesis in, 140
emergent trait hypothesis in, 139-140
in experimental E. coli populations, 256
extinction and, 86, 110-111, 117-120, 120, 123
hierarchical theory, 137-142
macroevolutionary theory, 86
in species extinction, 86, 119-120
in stasis of E. coli experimental populations, 268-269
Simpson, George Gaylord, iii-iv, v-vi, 3, 41, 287-288
on bradytelic evolution, 53
contributions of, 129-132
evolutionary rate classification, 43
on extinction, 111-112
on human evolution, 167
macroevolutionary theory and, 132-136, 142-143
Skeletal fossils, 90-91
hominid evolution, 173-181
SOD. See Superoxide dismutase
Sonic hedgehog gene, 100-101
Specialization
in cyanobacterial evolution, 53-56
in Precambrian microbes, 41-42
rate of evolution and, 53
Speciation
definition, 187
founder effect theories, 188-189, 197-201, 206
gene polymorphism in, 193-196
as mode of evolution, 131
obstacles to research, 187-188
Simpson on, 133
Species
definition, 187
duration, 195-196
as paleontological unit of study, 69
in selective extinction, 119-120
trans-specific polymorphisms in, 191-193
Sulfolubus, 18
Superoxide dismutase
action of, 237
amino acid replacement in, 235
as molecular clock, 213-214, 243-248
phylogeny, 237
sequence analysis, 236-237
structure, 237
T
Tachytelic evolution, 43, 131, 132
Taq DNA polymerase, 30
Telomerase, tRNA, 28, 30, 34-35, 37
Templated protein synthesis
origins of tRNA replication before, 26, 28
in progenote, 26
Tempo and Mode in Evolution, iii, v, 3, 41, 111-112
human evolution in, 167
significance of, 129-132
theory in, 132-134
Tempo of evolution
amino acid replacement in SOD, 235-236
chloroplast genome, 229-231
chloroplast introns, 228-229
constancy model, 213-214
corresponding modes, 132
cyanobacterial hypobradytely, 47-53
definition, 3
in detecting trans-specific polymorphisms, 192-193
determinants of, v
in experimental E. coli population, 266-269, 271
hitchhiking hypothesis, 277
hypobradytelic, 43-44
introns in acceleration of, 78
in molecular research, 3
nucleotide substitution in chloroplast genome, 221-223
Paleoproterozoic, 2
Phanerozoic, 52
Proterozoic-Cambrian acritarchs, 74-76, 78-80
Proterozoic-Cambrian database, 67-69
role of paleontology in, 130-131
Simpson's model, v-vi, 131-132
specialization and, 53
Tetrahymena, 34
Thermophiles, 12
ranges of growth, 55
tryptophan operans in, 18
Trace fossils
early Cambrian, 91
Transcription, tRNA, 29
Transfer RNA
5' processing, 29-30
earliest genomic tags, 28-29
evolutionary phylogeny, 26, 34-38
nucleotidyltransferase, 28, 29, 30
in replication, 31-33
as replication primer, 33-34
Triassic coal gap, 117
tRNA. See Transfer RNA
Tryptophan operans, 18
Turnip yellow mosaic virus, 29, 31, 33
U
Ultraviolet light, 55
Uniformitarianism, 126-127, 137, 229
V
Varanger ice age, acritarch evolution across, 72, 73, 74, 75-76
Vendian fauna, 89-90, 95-96, 101
segmented bilaterians, 97, 98-99
Viruses
genomic diversity, 30-31
replication strategies, 31-34
W
Worms
late Precambrian, 95-96, 98-99
in metazoan evolutionary phylogeny, 102
