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In the Light of Evolution, Volume I: Adaptation and Complex Design
Index
A
Acalyptratae, 113
Accommodations, 55-56
Actins, 50
Adaptation.
See also Coadaptation;
Color vision;
Temperature adaptation to altitude, see High-altitude adaptation to climate, 19-20
comparative studies, 183, 187-204, 227
to environmental challenges, xvii, 13, 15-16, 18-19, 225, 226-227
and evolution, 73-76, 83, 84, 95, 98, 101-103, 135, 184, 187-204, 226
fitness tradeoffs, 129, 130, 133-134, 137-138, 139, 140-142, 143, 225, 226, 227-238
functional, 14, 17, 73, 239-255
to habitat, 19-20, 74
Levins’ principle of allocation, 226, 233-234
local, 211
selection experiments, 227
symbiotic associations, 165-166, 169-170, 171-172, 180
Alternative splicing, 70, 71, 94
Altitude. See High-altitude adaptation
Altruism.
See also Reproductive altruism
defined, 134
gene, 134-136, 139, 143
American Civil Liberties Union, 297
Amoebae, 168
Answers in Genesis, 287
Anthropogenic selection, 214
Antibiotic resistance, 15-16
Ants, 54, 149, 150, 151, 152, 153, 154, 157, 158, 159, 160-161, 174, 177
Aphids, 155, 174, 176, 177, 178, 179, 181
Apoptosis, 59, 73-74, 133, 273, 279
Aquinas, Thomas, xv
Arabidopsis, 213, 223
Archaea, 170
Arginine biosynthesis, 178
Argument against chance, 5, 8-9, 20
Argument from design.
See also Intelligent Design
Paley’s, xv, 5, 6-8, 10, 14, 293, 294
Arkansas Education Association, 287
Army ants, 152
Arrow, Gilbert, 281
Arthropods, 50, 60, 93, 112, 115, 180, 188, 267-268, 269, 277
Arthur M. Sackler colloquia, iv, viii, xiii-xiv, xvii, 43
Arthur M. Sackler Gallery of Asian Art, viii
Artificial life models. See Avida populations
Artificial selection, 13, 14, 88, 183-184, 217.
See also Plant domestication
Atta ants, 160-161
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Auchenorrhyncha, 173-176
Avida populations
frequency and distribution of function, 35-37
functional information of, 26, 28, 30, 33-40, 41, 42, 43
islands of function, 36-40
measures of function, 34-35
software, 43
stepped behavior, 37-38, 39-40, 41
Avise, John C., iv, xiii-xiv, 43, 163, 181
Ayala, Francisco J., xiii-xiv, xvii, 3-21, 43, 68, 163, 181, 183, 296
B
Bacteria.
See also Escherichia coli
age of, 19
coadaptation, 171
evolution of multicellularity, 132
flagellum, 171, 285, 289-290, 291, 292, 293
genome analysis, 50, 170
horizontal gene transfer, 167, 168, 170-171, 172, 179
loss of function, 69, 167
pathogenic, 168, 170
phototrophic, 171
resistance to antibiotics, 15-16
symbiotic associations, 167, 170-171, 172, 174-179
toxins, 167
type-III secretory systems, 167
Bacteriocytes, 174
Bacteriomes, 174, 175, 176, 177, 179
Bacteriophages, 170, 179
Baldwin effect, 57, 58
Bananas, 206, 211, 212
Barley, 206, 209, 212, 213, 214
Bat wing evolution, 55-56, 73-74, 75
Baumania cicadellinicola, 175, 176, 177
Beall, Cynthia M., 184, 239-255
Beavis effect, 211
Bees, 50, 146, 148, 149, 152, 153, 154, 157, 159-160, 161, 162, 172
Beetle horn diversification
allometry, 257, 258, 262, 271, 272, 275, 277-279, 281
axis of outgrowth, 265-270, 275-276, 280
comparative studies, 277
developmental model, 258, 275-280
developmental stages, 267
dimorphism and, 257, 261, 262-265, 266, 275, 279, 280, 281
fossil record, 261
gains and losses, 257, 258, 261-262, 264, 280-281
insulin sensitivity, 272, 277-279, 280
morphology, 257, 260, 261, 262-265, 266, 273, 275-277, 279, 280, 281
mutations, 261, 280
natural history of scarabs, 184, 257, 259-265
nutrition-related modulation, 257, 270-273, 275, 277-279
origin, 185, 257, 275-276
patterning genes, 276-277, 279, 280
physical location of horns 262, 263, 273-277, 281
pupal remodeling, 265, 267, 273-275, 279
shape, 257, 262, 264, 276-277, 279, 281
stepwise evolution, 265-275
Behe, Michael, 288-289, 290, 291, 293, 295-296, 299
Bell, Charles, 10, 12
Bennett, Albert F., 183, 225-238
Bernard, Gary D., 187-204
Bess beetles (Passalidae), 259, 260
β-tubulins, 50
Bicyclus anynana, 191
Biocomplexity.
See also Avida populations;
Eusocial insect colonies;
Multicellular organisms
artificial, 26
behavioral, 28
competitive, 32
conserved core processes, 54-55
of cross-purpose, 147
developmental constraints, 65
dimensionality, 28
diversity, 27-28
hierarchical levels, 105-107
information content–function relationship, 27
measuring, 150-151
modeling emergent events, 26, 42-43
natural selection and, 16-17, 54, 55, 68, 69, 73, 85, 93, 95-96
nonadaptive forces, 90-95
origins and evolution of, xvii, 42, 83, 84, 93-95, 103
of purpose, 147
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quantifying, 25, 27-28;
see also Functional information
structural, 27
symbiosis and, 171-172
symbolic, 27-28
Biodiversity, xiii, 16, 83
Bioinformatics, 220, 221
Biological Sciences Curriculum Study, 287
Biopolymers, 25, 26, 40-41, 42
Bird, Wendell, 297, 299
Bliss, Dick, 293
Blochmannia, 177
bmp gene, 62
Bone morphogenic protein (Bmp), 49, 61, 62, 73-74
Bovine rhodopsin, 199-200, 200, 204
Bowtie effect, 60
Bradley, Walter, 298
Bricolage, 68, 69, 70, 73.
See also Evolutionary tinkering
Bridgewater Treatises, 9-10
Briscoe, Adriana D., 187-204
Britten, Roy H., 23, 66
Bryan, William Jennings, 286
Buchner, Paul, 173-174, 176
Buchnera, 174, 176, 177, 178, 179, 180
Buell, Jon, 297, 298
Busk, George, 12
Butterflies.
See also Color vision in butterflies
wing morphology, 124, 125, 279
C
Cajal bodies, 94
Calmodulin signaling, 61, 62, 73
Cambrian geological period, 16, 48, 50
Carothers, James M., 23, 25-43
Carpenter ants, 174, 177
Carroll, Sean B., 86, 88, 105, 109-127
Carsonella rudii, 178, 179
CD44, 71
Cell–cell signaling, 49, 59, 61, 95, 110
Cell death. See Apoptosis
Cell proliferation, 58, 59, 74, 80, 265, 267, 268, 269, 272-273, 274, 275, 276-277, 279, 280
Cell specialization, 49, 106, 107, 129, 131-133, 134, 137-139, 140-142, 150, 165, 174.
See also Multicellular organisms
Center for Science and Culture, 288
Clark University, vii
Ceroplophana modiglianii, 259
Chafers (Rutelinae), 259, 260
Chlamydomonas reinhardtii, 131, 132, 135
Christian fundamentalism, 286-287, 295,297
Chromophores, 188, 190, 199-201
Cicadas, 173
Cichlid fishes, Lake Malawi, 62
Cis-regulatory elements (CREs).
See also Transcription-factor binding sites
altered gene expression, 61, 62
cooption, 114, 123
evolutionary significance, 111
and fitness penalties, 118-120
functional conservation of, 111, 115
modularity, 110, 111
and novelty, 114-117, 120
transcription factor interactions with, 120-122
Climate change, 226
Coadaptation, 166, 171, 179, 180
Cockroaches, 174
Coevolution
regulatory changes and, 46, 52, 53, 54, 56, 61, 62
symbiotic associations, 169, 170-171
Colobopsis ants, 150
Color vision in butterflies
absorbance spectra, 191-194
bovine rhodopsin model compared, 199-200, 200, 204
branch-site models of selection, 195, 197, 198-199, 203-204
character mapping of L opsin λmax values, 187, 195-196, 197
chromophore binding pocket, 188, 190, 194
epimicrospectrophotometry, 187, 191-192, 193, 201
homology modeling, 188, 199-201, 204
humans compared, 200-201
L opsin sites, 188, 199-201
McDonald-Kreitman test for selection, 194-195, 196, 202-203
Nymphalid model, 190, 191-195
opsin sequences, 191-194
papilonid, 195
parallel and/or convergent evolution, 187, 190, 196-198, 199, 201, 203
PCR, cloning, and sequencing, 187, 202-203
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phylogenetic reconstruction, 187, 189, 195, 197, 198, 203
pierid, 195
primates compared, 183, 187, 188-190, 194, 200-201
red–green, 190, 193
sample collecting, 202
Compartmentation, regulatory, 49, 51, 59-60
Competitive systems, 32, 170, 209
Complexity. See Biocomplexity
Conserved core components and processes
adaptability, 51, 54, 55-56, 60, 61, 62, 63
appendage and limb formation, 50, 55-56, 115, 269
complexity, 54-55
exploratory behavior, 45, 51, 54-55, 60, 63
and facilitated variation, 45-46, 48-51
functional information, 36-37, 51, 61-62, 80
genetic change and, 60-61
genetic networks, 79, 80
and genome analysis, 50
origins and evolution of, 48-51, 62-63
in pigmentation patterns, 113, 116, 122
and regulation of gene expression, 24, 111, 115
regulatory compartmentation and, 49, 51, 59-60, 63, 122
robustness, 51, 54, 55-56, 60, 61, 62, 63
state selection, 52-53, 60
weak regulatory linkages and, 51-54, 60, 63
Convergent evolution, 79, 187, 189, 190, 194, 195, 196-198, 199
Copernican Revolution, xvii, 3, 4-5
Copernicus, Nicolaus, xvii, 4
Creation myths, 68
Creation science movement, 285, 287, 288, 293-302
Cretaceous, 154
Cuerna sayi, 175
Cuevas, Cristina I., 187-204
Cyanobacteria, 170
Cytoplasmic P bodies, 94
D
Dalrymple, G. Brent, 296
Danaus plexippus (Monarch butterfly), 191, 197
Darrow, Clarence, 286
Darwin, Charles, 188, 289
beetle collection, 184-185
on domestication, 183-184, 207-209
evidence of evolution, 5-6, 13, 46, 61, 132
and evolutionary tinkering concept, 68
natural selection theory, xvi, xvii, 3, 5, 6, 10-12, 13-16, 21, 68, 86, 146, 151, 153, 169, 226, 235
Origin of Species, 5-6, 12-15, 132, 183, 207
Paley’s influence, xv, 6, 10, 14, 146
and phenotypic variation, 46, 56, 57, 183-184
scientific method, 146
on sexual selection, 163, 254, 258, 260, 281
superorganism view, 151, 153
Darwinian Revolution, xvii, 3, 4
Davidson, Eric, 23, 66, 74
Davis, Percival William, 298-299
Dawkins, Richard, 293
Decapentaplegic gene, 268, 269, 277
Dembski, William, 288, 289, 290, 293, 296, 298, 301
Dictyostelium, 168
Diptera, 112-114, 124, 125, 126, 172.
See also Drosophila
Discovery Institute, 288, 303
Divergence.
See also Morphological evolution
acquisition of foreign genes and, 168
beetle horns, 257, 262, 279
functional, 199
of Galapagos finches, 46, 63, 73
obligate nutritional symbionts of insects, 177, 178
rate of, 262
regulatory elements and, 110, 111, 112, 114, 116, 124, 125, 127, 135, 136
silent-site level of, 91
of sticklebacks, 61, 73, 74-76, 119
tradeoffs and, 234
tryptophan pathways, 167
DNA sequences
changes in, see Genetic variation
noncoding, 111
nonfunctional intergenic, 90, 172
nontranscribed, 47
Dobzhansky, Theodosius, xiii, xiv, xviii
Drosophila
cis-regulatory evolution, 114, 115-117, 118, 119, 121, 124-125
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compartmentation, 60
conservation of DNA sequences, 50, 57-58, 60, 269
demographic models, 217
fitness, 118
gene loss, 172
haltere development, 124-126
Hox proteins, 121, 124-125
imaginal discs, 266, 268, 269, 276
insulin sensitivity, 278
kikkawai, 121
larval hairs, 119
melanogaster, 114, 120-122
patterning genes, 268, 269, 276
Pax6 gene, 70
phenotypic variation, 57-58, 61, 213
pigmentation patterns, 114-117, 118, 121, 124-125
regulatory networks, 61, 70
selection testing, 213, 217-218
willistoni, 121
Dung beetles (Scarabaeinae), 259, 260, 267, 269
E
Education. See Public school evolution education
Embryonic development
cell differentiation, 58
compartmentation, 59, 60
and facilitated variation, 62
forelimb development, 73
phylotypic stage, 59-60
placenta and, 16-17
Embryonic induction, 53
Emlen, Douglas J., 185, 257-281
Enhancer binding proteins, 53
Environmentally induced change.
See also High-altitude adaptation;
Temperature adaptation
persistence of traits, 57;
see also Heritibility;
Natural selection
sex differentiation, 54
Epistasis, 87, 95-100.
See also Genetic networks
Erythropoietin, 246, 252-253
Escherichia coli, 50, 184
horizontal gene transfer, 168
tradeoffs in temperature adaptation, 225, 227-238
Eudorina elegans, 131, 132
Eukaryotes
conserved sequences, 50
genome architecture, 86, 90, 91, 92, 98
horizontal gene transfer, 165, 166, 168
multicellular, 90, 91, 93, 102, 132, 165, 166, 171-172
number of genes, 51
symbiosis, 171-172
unicellular, 51, 90, 91, 93, 168
Eukaryotic cells, 49, 50, 94, 102, 130, 147,171
Eusocial insect colonies
castes, 150, 159, 160, 161
complexity, 26, 145, 148, 150-151, 163
cooperation and common purpose, 106, 145, 147, 148-149, 152, 163
cross-purpose and conflicts, 106, 145-146, 147-148, 158, 159-161, 162, 163
dance language, 152
dispersion, 153
division of labor, 148-150, 151-152, 154-155
fortress defenders, 145, 155-157, 159
haplodiploid hypothesis, 106, 154-155
kin selection theory, 155-158, 159, 162, 163
kinship ties, 106, 145, 147-148, 153-154, 157, 161
life insurers, 145, 155, 157, 159
mobility, 150, 151
multicellular organism compared, 149-152
origins of sociality, 154
parental care, 155
queenless, 157, 161
queens, 145, 148, 149, 150, 153, 155, 157, 158, 159-161, 162
reproductive altruism, 106, 148, 154, 155, 157
sex ratio conflict, 154, 158, 159, 163
success of, 152-153
superorganism view of, 147, 149-152, 153, 158, 159
worker reproduction and policing, 161-162, 163
Evolution.
See also Humans;
Phenotypic variation
acceptance of theory, 302-304
adaptive, 73-76, 83, 84, 95, 98, 101-103, 135, 184, 187-204, 226;
see also Divergence
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behavioral, 54, 57, 95, 101, 106, 148, 149, 161, 240
of complexity, xvii, 42, 83, 84
conserved core processes, 48-51, 62-63
convergent, 79, 187, 189, 190, 194, 195, 196-198, 199
Darwin’s evidence, 13
directionality, 83, 85, 87, 88-89
diversification (cladogenesis), 14, 17;
see also Beetle horn diversification
education, see Public school evolution education
genetic variation and, 47, 54, 86, 118, 258
geographic evidence, 11
gradualness, 54, 75
interval vs. external forces, 88-89
Lamarckism, 56-5763
metaphors, 67-69
microevolutionary scale, 24, 65, 76-80, 85, 86, 123, 294-295
misconceptions about, 84, 85-86
Modern Synthesis, 57, 86
molecular reconstruction of, 17, 85, 176
morphological changes, see Morphological evolution
mutations and, 15, 54, 83, 85, 87, 88-89, 90-92
natural selection and, 14-15, 84, 85, 87, 92, 93, 95, 118
network perspective, 66, 67-69
neutral model, 90-92, 195
nonadaptive forces, 83, 86-87;
see also Genetic drift;
Genetic recombination;
Mutations
parallel, 56, 60, 79, 174, 176, 178, 188, 190, 194, 196-198, 199, 201, 203-204, 209, 223
pre-Darwinian theories, 11
population genetic environment and, 24, 83, 84-88
predictions of alternative trajectories, 24, 65
process, 3-4, 15, 18, 129
theory of, 5-6, 21, 62
tradeoffs, 68, 129, 130, 133-134, 137-143, 225-238
transitions, 129-143, 174
Evolutionary tinkering
concept, 68-69
in functional adaptation, 239, 255
molecular constraints on, 51, 69-73
morphological, 68
Evolvability, 83, 100-102, 103, 130
Ewen-Campen, Ben, 185, 257-281
Exploratory processes, 54-55, 91
Eye.
See also Color vision in butterflies
butterfly, 191, 192, 201
complexity argument, 7-8, 9, 146
dioptric distortion, 7-8
evolutionary tinkering, 70
fruit fly, 70
image-resolving, 188
molluscan, 17-18, 183, 188
rhabdom structure, 191, 201
stepwise evolution, 16, 17-18, 70, 132, 183
F
Facilitated variation, theory of
compartmentation, 59-60
conserved core processes and, 45-46, 48-56
and evolution, 62-63
experimental evidence, 60-62
exploratory processes, 54-55
favorable sources and paths, 56-59
steps, 47-48
weak regulatory linkages and, 48, 51-54
Falciprum malaria, 254
Finches, beak morphology, 46, 61-62, 73, 74, 75
Fish.
See also Stickleback fish
cis-regulatory evolution, 119
facilitated variation, 61, 62
functional adaptations, 7
placental, 17
sex determination, 54
vision, 188
Fitness.
See also Reproductive s
artificial life models, 35, 37
cis-regulatory elements and, 118-120
components, 133-134
covariance effect, 140-142
Darwinian fitness coefficient, 254
heritability, 130, 133
horizontal gene transfer and, 170
reorganization of, 130, 134
sociality and, 155-157
symbiotic associations and, 170
temperature adaptation in E. coli and, 225, 227-238
tradeoffs, 129, 130, 133-134, 137-138, 139, 140-142, 143, 225, 226, 227-238
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Flax, 223
Flower beetles (Cetoniinae), 259, 260
Forelimb evolution, 88, 90, 146
Formica exsecta, 158
Forrest, Barbara, 301
Fossil record, 20, 86, 153, 174, 176, 294
Foundation for Thought and Ethics, 297-298
Foxtail millet, 214
Frentiu, Francesca D., 183, 187-204
Functional information
applications, 42-43
of Avida populations, 26, 28, 30, 33-40, 41, 42, 43
and biopolymers, 25, 26, 28, 30, 33, 40-41, 42
calculation, 28-30
conserved sequences, 37
defined, 23, 25
discontinuities, 36-40
in higher-dimensional systems, 41-42
of letter sequences, 25, 26, 28, 30-33, 37, 40, 42
in statistically random systems, 39
G
Gain of function, 77-78, 90, 114
Galileo, xvii, 4
Gammaproteobacteria, 168, 175, 176
Gaut, Brandon S., 184, 205-223
Genes
cooption/recruitment, 69-70, 71, 75, 105, 115, 116, 122, 123, 129, 134, 135, 136, 142, 189
duplication, 82, 86, 94, 96-97, 98, 99, 111, 124, 126, 168, 172, 189, 190, 193, 201
interactions, 24, 87;
see also Genetic networks
loss, 50, 165, 166, 167, 169, 172
subfunctionalization, 92, 94, 97, 98, 100, 123
regulation, 24;
see also Genetic networks
transfer, see Horizontal gene transfer
Genetic assimilation, 57-58
Genetic drift, 24, 79, 83, 85, 86-87, 89, 90, 91, 96, 99, 103, 127, 194, 214
Genetic networks, 24
analysis, 67
complex morphological traits, 65, 268
conceptual framework, 66, 57-59
conserved, 79, 269
enhancer/silencer units, 71-72
evolutionary metaphors and, 67-69
evolutionary process, 75-76
and experimental research, 73-76
feedback loops, 77
forcing structure, 77
functional connectivity patterns, 76-77
general properties, 76-77
modularity, 65, 70-72, 74, 75, 76, 77, 79-80, 81, 83, 85, 92, 94, 95-100, 135-136, 268, 269, 270, 275, 292
and mutational events, 69, 71, 72
and natural selection, 72, 86, 95-96
passive emergence, 95-100
pathways, 77, 78-79
predictive capability, 65, 67, 76-80
regulatory, 66, 71-72, 78, 92, 95-100, 105-106, 109
schematic, 71
in systems biology, 66
Genetic recombination, 86, 87, 88, 93, 102, 103, 127, 178, 179, 180, 216, 217
Genetic variation.
See also Mutations
in adaptive traits, 215, 218, 234, 255
cis-regulatory changes, 47
and complex morphological changes, 123-126, 258
and evolution, 47, 54, 86, 118, 258
and gene regulation, 47
lethality, 48, 56, 61
nonadaptive mechanisms in, 86, 90, 101
and phenotypic variation, 45, 46-47, 56, 58, 59, 60-61, 205-223
in protein regulatory regions, 48
sources, 15, 47
at transcription sites, 47-48
Genome analysis, xvi
artificial life, see Avida populations
bacteria, 50, 170
comparative sequencing, 50, 166, 169, 176-177
Genomes
evolution of, 90-92
mobile elements, 88, 90, 92, 94, 102
plasticity, 179-180
Genomic imprinting, 148
Gerhart, John, 24, 45-63, 81, 84
Gish, Duane, 295
God, xv, 6-7, 9-10, 293, 294, 301
Gompel, Nicolas, 105, 109-127
Gonium pectoral, 131, 132
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Gould, Stephen Jay, 296
Graphocephala atropunctata, 177
Gray, Asa, 12
Griffin, Patrick L., 23, 25-43
H
Hamilton, W. D., 153-154
Hamiltonella defensa, 179
Haplodiploid hypothesis, 106, 154-155
Haplotype blocks, 212
HapMap project, 223
Hazen, Robert M., 23, 25-43
Hedgehog gene, 268, 277
Heliconius erato, 191
Heliconius sara, 197
Hemoglobin, 240, 244-246, 250, 252-253
Heritability
of adaptations, 57
defined, 100
of fitness-related traits, 130, 133-134
genetic variance and, 101
of high-altitude adaptation, 239-340, 250-255
of phenotypic variations, 46, 57, 60-61
of regulatory change, 45, 53
of symbiotic associations, 106, 165, 169, 179-180
Herschel, John, 11
High-altitude adaptation
arterial oxygen, 246, 247, 250, 252-253
basal metabolic rate, 242, 243
blood flow rates, 246-250, 254
blood oxygen levels, 241, 244-246, 250, 251, 254
candidate gene approach, 239, 254-255
capillary density, 249, 250, 252-253
Darwinian fitness coefficient, 254
effect size, 250
energy production, 242-243
erythropoietin concentrations, 246, 252-253
evolutionary tinkering, 239
genetic admixture analysis, 239, 251
H1F1 transcription factor, 254-255
hemoglobin concentration, 246, 252-253
hemoglobin oxygen saturation, 240, 244-246, 250, 252-253
heritability, 239-340, 250-255
hypoxic pulmonary vasoconstriction, 247-248
hypoxic ventilator response, 243, 245, 251, 252-253
mitochondrial volume, 241-242, 249, 250, 252-253, 254
myoglobin gene, 254
nitric oxide synthesis, 248, 250, 252-253, 254
offspring survival, 239, 248, 254
oxygen diffusion rates, 241, 246-250, 254
oxygen dissociation from hemoglobin, 249
points of, 242-250
pulmonary hypertension, 248, 250, 252-253, 254
quantitative genetic approach, 239, 250-251, 252-253
Tibetan-Andean population differences, 184, 240-241, 244-255
uteroplacental oxygen delivery, 248
ventilation, 243-244, 245, 251, 252-253
High-throughput analysis, 220
Histidine, 177
Hitchhiking effect, 88, 222
Homalodisca coagulata, 176
Homo sapiens, 19
Homology modeling, 188, 199-201, 204
Honey bees, 50, 146, 148, 149, 152, 159-159, 162, 172
Honeypot ants, 150
Hooker, Joseph, 11
Horizontal gene transfer
in bacteria, 167, 168, 170-171, 172, 179
barriers to, 168, 170-171, 172
in eukaryotes, 165, 166, 168, 172-173
evolutionary motivation, 166-167
and fitness, 170
and novelty, 106, 166, 168
in plants, 168
in prokaryotes, 106, 165, 167-168, 170
rates, 168
symbiotic associations and, 166, 169, 170-171, 172-173, 178-179
vectors, 170
Hox genes, 60
Hox proteins, 110, 121, 122, 124, 125
Human genome, 172
Humans
color vision, 200-201
oxygen transport cascade, 241-242
selection testing, 217-218
Hume, David, xv-xvi
Hymenoptera, 154, 155
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Hypoxia. See High-altitude adaptation
Hypoxic pulmonary vasoconstriction, 247-248
Hypoxic ventilator response, 243, 245, 251, 252-253
I
Imaginal discs, 266, 268, 269, 271, 272, 273, 275, 276, 277, 278
Immune system, 50, 133, 285
Inachis io, 197
Individuality
cost of reproduction and, 136-140
covariance effect, 140-142
fitness tradeoffs and, 134, 137
group size and, 129, 131, 136
origins, 147
reproductive altruism and, 134-136
Information theory, xvii
Insects.
See also Beetle horn diversification;
Color vision in butterflies;
Drosophila
apoptosis in, 279
colonies. See Eusocial insect colonies
compartmentation, 59
eye, 189
fat bodies, 272
fossil record, 153, 174, 176
limb and appendage development, 60, 266, 268, 269, 271, 272, 273, 275, 276, 277, 278, 279
symbiotic associations, 165, 173-178
Institute for Creation Research, 287, 295
Insulin sensitivity, 272, 277-279, 280
Intelligent design, 102
arguments for, xvii, 9-10, 12, 13, 146, 288-290, 292, 293, 294
artifact analogy, 5, 9, 289-293
and common ancestry of humans and apes, 295-296
creation science movement and, 285, 287, 288, 293-302
and educational policy, xviii, 285, 296-297, 299, 302-304
emergence of, 287, 296-302
landmark court decisions, 287-288, 291, 296-297, 298-299, 301, 302
microevolution/macroevolution distinction, 294-295
modern proponents, xviii, 286, 288-289, 294, 295-296, 301
Paley’s Natural Theology, xv, 6-8, 9, 10, 146, 294
scientific failure of, xviii, 286, 288, 289-290, 291, 292-293, 296, 304
special creation, 295-296
“teach the controversy” strategy, 303-304
textbooks, 298-299
Wedge Document, 288
Introns, 90, 91, 92, 94, 102, 193, 202
Invertebrates, 91, 94, 173, 290, 295
Irreducible complexity argument, 9-10, 13, 288-289, 293, 294
Ishikawaella capsulata, 178
J
Jacob, Francois, 68, 69, 93
Junonia coenia, 195, 197, 198, 199
Jurassic, 261, 276
K
Kansas Board of Education, 296
Kauffman, S., 66, 77, 103
Kenyon, Dean, 298-299
Kepler, Johann, xvii, 4
Kin selection
in behavioral evolution, 101
in eusocial insect colonies, 106, 145, 147-148, 155-158, 159, 162, 163
and individuality, 130, 143
King, Mary-Claire, 23
Kirschner, Marc, 24, 45-63, 81, 84
L
Lamarckism, 56-57, 63
Lavine, Laura Corley, 185, 257-281
Leafhoppers, 173-175
Lenski, Richard E., 183, 225-238
Leptothorax ants, 152
Life-history
evolution, 130, 143, 226
theory, 140
tradeoff genes, 129, 134, 135, 136, 137, 139, 140, 142
Limenitis spp., 187, 191-204
Limpets, 17, 18
Lingula, 12, 15
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Linnean Society of London, 11-12
Liostenogaster flavolineata, 159
Living fossils, 12, 15
Lizards and salamanders, 94, 149
Loss of function traits, 69, 74, 76, 77, 78, 79, 100, 114, 118, 167, 178
Lyell, Charles, 11, 146
Lynch, Michael, 24, 83-103
M
Maize, 206, 209, 210, 211, 213, 217, 218, 219, 220, 221, 222, 223
Malthus, Thomas, 146
Mammals
coat colors, 16, 66
ear, 68
evolutionary tinkering, 68
immune system, 285
placenta, 16-17, 248
relatedness and helping behavior, 157
vision, 183, 188, 189, 190
Manduca sexta, 203
Marsupials, 16, 79
Matzke, Nicholas J., 185, 285-304
May and June beetles (Melolonthinae), 259, 260
MC1R (melanocortin-1 receptor) gene, 16
McDonald-Kreitman test for selection, 194-195, 196, 202-203
McLean, Bill, 296
Melipona, 160
Metazoa, 172
Methanogenesis, 167
Michigan State University, Digital Evolution Laboratory, 43
Michod, Richard E., 106, 129-143
Microevolutionary theory, 24, 65, 76-80, 85, 86, 123, 294-295
Microtubules, 49, 54-55
Miller, Kenneth R., 293
Mitochondria, 147, 165, 168, 171, 172, 241-242, 249, 250, 252-253, 254
Molecular biology.
See also DNA sequences;
Genes
reconstruction of evolutionary history, 17, 85
technology, 87
Molecular clock, 67
Mollusks, 9
eye evolution, 17-18, 183, 188
Monte Carlo simulations, 42
Moran, Nancy, 42, 106-107, 165-181
Morowitz, Harold, 296
Morphological evolution, 68, 94.
See also Divergence;
Pigmentation patterns
bat wings, 55-56, 73-74, 75
beetle horns, 257, 260, 261, 262-265, 266, 273, 275-277, 279, 280, 281
developmental system drift, 96
finch beaks, 46, 61-62, 73, 74, 75
gains and losses of traits, 122-123
genetic networks, 65, 96
genetic variation, 118, 123-126, 258
insect wing, 113, 279
novelty, 50, 80, 105, 112
pleiotropy and, 119
regulatory evolution and, 105-106, 110, 111, 112-114, 115, 118-119, 120-126
sexual dimorphism, 257, 260, 261, 262-263, 266, 273, 275, 280
simplification, 84
tinkering, 68
Morrell, Peter L., 184, 205-223
Morris, Henry M., 287, 295, 299
Mouse genome, 50
Müller, H. J., 66, 173
Müller’s ratchet, 67
Multicellular organisms
complexity, 27, 106, 150-151
conflict mediation, 133
conflicts and cross-purposes, xvii, 133, 147
conserved functional components and processes, 49
cooperation and, xvii, 133, 135
division of labor, 133, 149
eusocial insect colony analogy, 149-152
fitness tradeoffs, 106, 129, 134, 136-140, 142
genome complexity, 90-92, 102
germ soma specialization, 131-132
group formation, 129, 142
hallmarks of, 94-95
horizontal gene transfer, 165, 166
individuality trait, 129, 131, 132, 142-143
interactions of systems, 105
kinship relationships, 101, 106, 131-132, 133, 142, 153
life-cycle stages, 27
modular gene structure, 94, 96-98
mutation rates, 91, 93
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nonadaptive evolutionary forces, 85, 86, 90-92, 93-98, 102
origins, 93-95, 132
reproductive altruism, 106, 129, 133, 134-136, 142
specialization of cells, 49, 106, 107, 129, 131-133, 134, 137-139, 140-142, 150, 165, 174
structure, 149
symbioses, 106-107, 165, 166, 171-180
transition from unicellularity, 106, 129-143
unicellular organisms compared, 91, 92, 102
Murex, 17
Mutations
accumulation, 19, 94, 126, 194, 212, 235-236
bias, 88, 89
complexity-increasing, 19, 61, 135
degenerative, 86, 90, 92, 96, 97, 98, 99
deleterious, 85, 87, 90, 93
and evolution, 15, 54, 83, 85, 87, 88-89, 90-92
examples, 15-16
fixation, 89, 194, 195
gain of function, 77-78, 90, 123
and genetic network modules, 69, 71, 72
in life-history traits, 139
loss of function, 77, 79, 100, 118, 122-123
molecular evidence of evolution, 17
and natural selection, 3, 13, 15-18, 20-21, 85, 86, 194, 195
neutral, 194
and phenotypic changes, 166
process, 15, 21
randomness, 20-21
rates, 89, 90, 93, 101, 102
and regulatory evolution, 115, 122-123, 124, 126
selective breeding, 13
single-gene, 16, 139
Mutualism, 179-180
Myoglobin gene, 254
Myrmica, 160
Mystery of Life’s Origin, 298
Myxobacteria, 132
N
Natural laws, 3, 4-5, 14, 21
Natural selection
adaptation, 3, 6, 13, 18, 101
artificial selection analogy, 183-184, 207-209
Baldwin effect, 57, 58
branch-site models, 195, 197, 198-199, 203-204
color vision, 189, 194-203
and complex design, 16-17, 54, 55, 68, 69, 73, 85, 93, 95-96
as creative process, 4, 16, 18, 20-21, 57
Darwin’s discovery, xvi, xvii, 3, 5, 6, 10-12, 13-16, 21, 86, 146, 151, 153, 169, 226, 235
and evolution, 14-15, 84, 85, 87, 92, 93, 95, 118
and genetic modularity, 72, 86, 95-96, 98
homology modeling, 188, 199-201, 204
important features, 18
levels of selection, 72, 100-102
MK test, 194-195, 196, 202-203
mutations and, 3, 13, 15-18, 19, 20-21, 85, 86
opportunism vs. design, 19-20
and reproductive success, 11, 13, 14, 17, 20, 120
stepwise process, 13, 16, 17, 166
symbiosis and, 169
Wallace’s discovery, 11-12
Nautilus, 12, 15, 17
Nematodes, 93, 94, 172, 180
Nerve growth factor, 55
Networks.
See also Genetic networks;
Neural networks
biological importance, 66
evolutionary dynamics, 66
graph theory analyses, 66
scale-free, 66
Neural crest cells, 50, 58-59, 62
Neural networks, biological, 26, 37, 54, 55, 56
Neuronal transmission, 52-53
New World monkeys, 190, 194, 200-201
New York University, vii
Newton, Isaac, xvii, 4
Newtonian dynamics, 28
Nitric oxide synthesis, 248, 250, 252-253, 254
No Child Left Behind Act, 302
Nonsense-mediated decay pathway, 94
Norm of reaction, 57
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Novelty.
See also Beetle horn diversification;
Phenotypic variation
conserved core processes and, 50
cooption and, 114-117, 275
gene duplication and, 111
horizontal gene transfer and, 106, 166
morphological, 50, 80, 105, 112
natural selection and, 16
origins of, 58, 83, 105, 107, 109
pigmentation patterns, 114-117
recruitment from available components, 117
regulatory evolution and, 58, 109, 112, 114-117, 120, 126-127
symbiotic associations and, 107
Nucleotide sequences
conservation, 90
functional information, 28-29, 30, 33, 40, 41, 42, 195
mutations, 91, 98, 196, 254
reconstruction, 195, 197, 198-199, 203-204
silent-site substitutions, 92
Nymphalis antiopa, 197
O
Octopus, 17, 18
Of Pandas and People, 298, 299-301
Olsen, Roger B., 298
Onthophagus spp., 261, 263, 264, 265, 266, 267, 269, 271, 277, 278, 279, 280
Ontogeny. See Morphological evolution;
Regulatory evolution
Operons, 90, 92, 94
Opsin genes and proteins, 187-204
Organelles. See Mitochondria;
Plastids
Organisms, characteristics of, 149
Origin of life, 84
Otoferlins, 50
P
Paley, William, 162
argument against chance, 5, 8-9
argument from design, xv, 5, 6-8, 10, 14, 293, 294
biological knowledge, 7, 9
influence on Darwin, xv, 6, 10, 14, 146
irreducible complexity argument, 9, 146
Natural Theology, xv, 6-8, 9, 10, 146, 294
Palm trees, 206, 211, 212
Papilio xuthus, 197
Parallel evolution, 56, 60, 79, 174, 176, 178, 188, 190, 194, 196-198, 199, 201, 203-204, 209, 223
Peking University, viii
Permian, 174
Pest resistance to pesticides, 15, 16
Phenotypic variation.
See also Facilitated variation
characterization, 46
constraints on, 24
genetic components, 23-24;
see also Facilitated variation;
Genes;
Genetic drift;
Genetic variation;
Mutations;
Population genetics
growth-related, 80, 279
measuring, see Functional information
and natural selection, 54, 55
nutrition-related, 257, 270-273, 275, 277-279
origins of, 57
paths of change, 46, 53-54, 56-59, 61, 63
pigmentation-related, 80
plasticity, 55, 58, 59, 61, 270-272, 278-279
symbiotic associations and, 107, 169-170
Photoperiod sensitivity, 209, 213
Photopigments, 184, 187, 188, 189, 190, 191-194, 197, 199, 201
Photoreceptors, 18, 188, 189, 191, 192, 200
Photosynthesis, 20, 132, 135, 170, 171, 209
Phototrophy, 167, 171
Phylogenetic
reconstruction, 17, 176, 187, 189, 195, 197, 198, 203, 260, 261-262
variation, xvi, 101-102, 171, 173-174
Phylogeographic methods, 207
Pieris rapae, 197
Pigmentation patterns.
See also Photopigments
abdominal, 120-123, 126
black, 114, 120
and body plan diversification, 112, 123-126
conserved components in, 80, 116, 122
eye, 17, 18
and fitness, 118-120
gene cooption and, 122
insect wings, 112-122, 126
and phenotypic variation, 80
and regulatory evolution, 112-122
sexual dimorphism in, 121-122
yellow, 114-117, 118, 119, 120-122, 123
Pitx1 gene, 74, 75
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Placenta, evolution of, 16-17, 248
Plant domestication
analogy to natural selection, 183-184, 207-209
approaches to finding adaptive genes, 184, 207, 209-223
artificial vs. natural selection, 183-184, 207-209, 221, 223
bottlenecks, 215, 216, 219
crops, 205-206, 209
demographic considerations, 215, 216-218
domestication syndrome, 208-209, 223
empirical ranking of genes, 218-220
genetic history, 214-216, 221
genome-wide association studies, 213
genotype-phenotype association, 212, 213, 214, 220-221
linkage disequilibrium mapping, 184, 209, 210, 212-214, 215, 221, 222, 223
methodical selection, 208
phenotypic changes, 208-209
phylogeographic methods, 207
population genetic analyses, 205, 209, 210, 215-221
quantitative trait loci mapping, 184, 205, 209, 210-212, 213, 214, 218, 221, 222, 223
testing hypotheses, 215-216
transgenic analyses, 210, 221
unconscious selection, 205, 208, 209, 215
Planthoppers, 173
Plants.
See also Plant domestication
desert adaptations, 19-20
genome evolution, 92
horizontal gene transfer, 168
Plastids, 165, 168, 171, 172
Pleiotropy, 59, 60, 98, 119-120, 214, 235-236
Pleodorina californica, 131, 132
Pocket mice (Chaetodipus intermedius), 16
Poeciliopsis, 17
Polistes wasps, 159
Polybia wasps, 152
Polyploidy, 222
Popper, Karl, 76
Population genetics, xvii, 83.
See also Genetic drift;
Genetic recombination;
Mutations
artificial life models, see Avida populations
epistasis, 87, 95-100, 101, 212
and evolution, 24, 83, 84-88
natural selection and, 57
polyploidy and, 222
standards of inquiry, 103
symbiotic associations, 170
Primates, 16, 19, 183, 187, 188-190, 201
Proagoderus (Onthophagus) lanista, 271
Probe Ministries, 297
Prosimians, 190
Prokaryotes
cell architecture, 93, 94
conserved core processes, 49, 50
genetic drift, 91
genomic architecture, 86, 90, 91
horizontal gene transfer, 106, 165, 167-168, 170
microbial consortia, 170-171
origins of multicellularity, 93, 95
symbiotic associations, 171
tryptophan pathway inactivation, 167
Protists, 50, 132, 167, 170
Prud’homme, Benjamin, 71, 105, 109-127
Prudic, Kathleen L., 187-204
Psyllids, 174, 178
Public school evolution education
bans on, 286-287
history of fundamentalist opposition, 286-287
intelligent design and, 297-298, 302-304
legislative attempts to promote ID, 302-303
Pulmonary hypertension, 248, 250, 252-253, 254
Q
Queller, David C., 42, 106, 145-163
R
Ray, John, xvi, 6
Red Queen hypothesis, 67
regA gene, 134-136, 139, 143
Regulatory evolution.
See also Cis-regulatory elements;
Conserved core components and processes;
Genetic networks
compounding of changes, 123-126
defined, 110
experimental systems, 111-112
gains vs. losses of traits, 122-123
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and morphological evolution, 105-106, 109, 110, 111, 112-114, 123-126
pigmentation patterns as models, 112-117
principles, 109-110, 126-127
research needs, 127
transcription factor–CRE interactions, 120-122
Regulatory linkages and networks.
See also Genetic networks
accumulation of, 117
bowtie effect, 60
compartmentation, 49, 51, 59-60, 122
and novelty, 58, 105, 122
opportunism in, 120, 122
plug-in modules, 74
stabilization, 59
weak, 48, 51-54, 58
Reproductive
altruism, 106, 129-131, 133, 134-136, 142, 148, 152, 164, 155, 157
isolation, 180
success, 11, 13, 14, 17, 20, 118-120, 239, 248, 254;
see also Fitness
Reptiles, 54, 68
Reverse genetic methodologies, 220, 221
Rhabdomeric photoreceptor cells, 189
Rhinoceros beetles (Dynastinae), 259, 260, 269-270, 274
Rhodopsins, 199-200, 201, 202
Ribozymes, 40
Rice, 206, 209, 211, 212, 213, 214, 220, 222, 223
RNA, 105, 107
aptamers, 25, 26, 28, 30, 33, 40-41, 42
functional, 49, 51
GTP-binding, 41
interference methods, 221, 270
messenger (mRNA), 62, 92, 191, 192
microRNA processing, 48
regulatory regions, 45, 47-48
ribosomal (rRNA), 87, 177
sequences/sequencing, 40, 87, 177
Ross-Ibara, Jeffrey, 184, 205-223
S
Sackler, Arthur M., vii-viii.
See also Arthur M. Sackler colloquia
Sackler, Jillian, vii, viii
Salmonella typhimurium, 289
SAND-like domain, 135-136
Scale insects, 174
Schwarziana quadripunctata, 160
Scientific Revolution, 3, 4
Scopes Monkey Trial, 286
Scott, Eugenie C., 185, 285-304
SCPP proteins, 50
Sea anemone (Nematostella), 50
Self-regulating processes, 52, 56, 99, 100
Selfish genetic elements, 135, 148
Sex chromosomes, 92
Sex differentiation, 53-54
Sexual dimorphism, 185
apoptosis and, 279
in beetle horn morphology, 257, 260, 261, 262-263, 266, 273, 275, 280
in insect wing morphology, 279
in pigmentation patterns, 121-122
regulatory processes, 60, 121-122
Sharpshooters, 174-176, 177, 178
Signal transduction pathways, 52, 70, 74, 272
Siproeta stelenes, 195, 197
Sison-Mangus, Marilou P., 187-204
Social amoebas, 41
Social behaviors, xvii.
See also Eusocial insect colonies
chemical signaling, 42
Social evolution, 130, 134, 143
Social genes, 136
Solenopsis, 160
Sorghum, 222, 223
Special creation, 295-296
Species
diversification, 6, 15, 17, 60, 110, 111, 113, 120, 123-126, 167, 160, 187, 201, 257-281
evolvability, 100-102
extinction, 19, 20, 21, 79, 83, 153, 294
inventory, 19
Specified complexity argument, 288-289, 290, 294
Spittlebugs, 173
Spliceosomes, 92, 102
Squid, 17, 200
Stag beetles (Lucanidae), 259, 260
Stenogastrine wasp, 157, 159
Stickleback fish, 61, 73, 74-76, 119
Stinkbugs, 174, 178
Strassmann, Joan E., 42, 106, 145-163
Sulcia, 174, 175-178
Sulfur fixation, 178
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Sunflower, 214
Superorganisms, 147, 149, 150-152, 153, 158, 159
Switch proteins, 52, 54, 66, 80
Symbiosis
in arthropods, 180
bacteria, 167, 170-171, 172, 174-179
bacteriophage and, 170
cell and organ specialization, 107
and coadaptation, 165-166, 169-170, 171, 180
coevolved associations, 170-171
cooperation in, 42
and eukaryotic adaptation and
complexity, 171-172
function topologies, 37, 42
gene loss and deterioration, 165, 167, 169, 172, 178
and genome plasticity, 179-180
genome sequencing, 176-177
genomic decay, 177-179
heritability, 106, 169, 171, 172, 173-174, 179-180
horizontal gene transfer, 166, 169, 170, 171, 178-179
insects, 165, 172-179, 180
intergenerational transmission, 107, 165, 172, 173, 176, 178, 179
metabolic interdependencies, 170-171
microbial consortia, 170-171
multipartite, 165-166, 174-176
mutualism, 179-180
nutritional, 173-179
obligate, 107, 165, 169-170, 171-172, 174, 177-179, 180
and phenotypic novelty, 107, 165, 169-170
reproductive isolation, 180
Systems biology, xvii
artificial life models, see Avida populations
and evolutionary biology, 66-67
Szostak, Jack W., 23, 25-43
T
Tajima’s D, 216, 218, 219, 220
Tbx genes, 60
Tel Aviv University, vii
Temperature adaptation in E. coli
at 20°C, 184, 225, 227-229
at 40°C, 184, 225, 228-231, 232-233
analyses, 238
antagonistic pleiotropy and, 235-236
experimental measurements, 237-238
generality of tradeoff effect, 225, 226, 227, 231
genetic basis, 235
historical thermal environment and, 226, 227, 228-229, 234-235, 238
mutation accumulation and, 235-236
nature of tradeoffs, 234, 235-236
power of experimental approach, 236
qualitative aspects of tradeoff hypothesis, 231-233
quantitative relationships in magnitude of fitness, 226, 227, 232, 233-234
study organisms, 230, 236-237
tradeoffs, 184, 226-227
universality of tradeoff effect, 225, 227, 231-232, 233
Teosinte, 211, 217, 218, 219, 220
Termites, 149, 153, 154, 155
TGF-β, 73, 74
Thaxton, Charles B., 298
Theodosia viridaurata, 259
Thermal stress, 179.
See Temperature adaptation in E coli
Thrips, 155
Tomato, 210, 221
Trans-regulatory landscape, 115-117
Transcription-factor binding sites, 53, 69, 90, 96, 97, 114, 115, 123
Transcription factors
allele-specific utilizations, 96, 97, 99
B, 99
compartmentation of regulation, 59
conserved, 60, 110, 122
demographic model, 218
down regulation, 74
engrailed, 115, 122
evolution of, 49
gene recruitment event, 69, 116
H1F1, 254-255
Hox proteins, 110, 120-122
interactions between CREs and, 105, 117, 120-122, 124-125
loss of function, 69, 74, 114
and morphological evolution, 111, 112, 114, 116
network modules, 69-70
Ubx, 124-125
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Transcriptional
networks, 66
regulation, 52, 59
Transposons, 148
Treehoppers, 173
Triassic, 153
Trypoxylus [Allomyrina] dichomata, 274
Tryptophan biosynthesis, 167, 168, 178
Tsetse flies, 174
Tufts University, vii
Turbulent flows, functional information of, 26, 42
U
Ubiquitin signaling pathway, 94
Ubx protein, 124-126
Unicellular organisms
fitness tradeoffs, 137
transition to multicellularity, 129-143
Uniformitarianism, 146
University of Cambridge, 10
University of Texas at Austin, 139
V
Vanessa atalanta, 191
Vanessa cardui, 191, 197
Vasculogenesis, 56
Vertebrates
blood clotting cascade, 290
compartmentation, 59, 60
conserved core processes, 50
eye evolution and color vision, 17, 189, 199, 201
immune system, 64, 290
insulin receptor pathway, 272
limb development, 266, 279, 290
neural crest cells, 58-59
nonadaptive processes in evolution, 91, 93-94
regulatory linkages, 53
sex determination, 54
Vision. See Color vision in butterflies;
Eye
Vitreochlamys, 132
Volvocine groups
colony size, 136, 137, 139, 142
conflict mediation, 133
fitness tradeoffs, 129, 136-142
flagellation constraint, 137
group formation, 132-133
individuality, 131, 132, 142-143
motility, 136-137, 139-140, 141
palintomy, 137
reproductive altruism, 134-135
Volvox aureus, 131
Volvox carteri, 129, 131, 134-135, 139
W
Waddington, C. H., 56, 57, 66
Wallace, Alfred Russel, 11-12, 207-208
Wasps, 149, 157, 159, 179
Wells, Jonathan, 301
Wheat, 206, 209, 211, 213, 214
Whiteflies, 174, 178
Wilder-Smith, A. E., 294, 299
Wilkins, Adam S., 24, 65-81
Wilson, Allan, 23
Wilson, E. O., 150, 151
Wingless gene, 268, 269, 277, 281
Wolbachia, 180
Wright, Sewell, 59, 66, 67
Wright–Fisher model, 216
