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In the Light of Evolution Volume III: Two Centuries of Darwin
Index
A
Abalone, 257, 258, 259, 261
Achatinellinae tree snails, 141
Acyrthosiphon pisum (Harris), 10, 13-17
Adaptation, Fisher-Orr geometric model, 52-53
Adaptive protein evolution, 150, 153, 159-163
Adaptive radiations
Aquilegia, 2-3, 23, 30-44
classic examples, 28
convergent evolution in, 30
defining features, 28
evolutionary trends, 29-30, 31-34
genetic dissection of adaptive traits, 27, 28, 29, 30, 42-44
phenotype-environment correlations, 28
research interests and trends, 28-29
research needs, 27-28, 44-45
trait directionality, 30, 31-34
trait utility, 28
African sleeping sickness, 66
Alfalfa, 13-17
Allendorf, Fred W., 86-87, 129-147
Allopatric speciation, 6, 9-10, 20, 22, 23, 24-25, 107
Altman, Sidney, 277
Altruism, 310-311, 338-339
Alveolata
cellular structures, 66, 68, 69-73
convergent evolution with Euglenozoa, 65-84
endosymbiosis, 77
gene expression, 66, 73-76
photosynthetic, 67-68
plastids, 77-78
RNA editing and processing, 66, 73-76, 81, 83
and stramenopiles, 68
subgroups and characteristics, 66-67
tree structure, 67
American Museum of Natural History, 294
Anisogamy theory, 231-232
Anthocyanidin reductase, 35, 36, 41
Anthocyanidin synthase, 34, 35, 37, 39, 40, 41, 42, 43
Anthocyanin biosynthetic pathway, 27, 32-33, 34, 35-36, 37-38, 39, 40-41, 42, 43
Anthocyanin GST, 35, 41
Antibiotic-resistance enzyme, 158
Antirrhinum, 42
AN2 gene, 36-37, 42
Apicomplexans, 66, 67, 77, 80-81
Apicoporus, 70, 71
Apple maggot (Rhagoletis pomonella), 54
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Aquaculture, 130
Aquilegia
A. brevistyla, 38
A canadensis, 33, 38
A. chrysantha, 37-38
A. coerulea, 32, 33, 38, 43
A. flabellata, 37-38
A. flavescens, 32, 34, 38
A. formosa, 32, 33, 38, 39, 42, 43-44
A. jonesii, 32
A. laramiensis, 34
A. longissima, 32, 37-38
A. pinetorum, 37
A. pubescens, 32, 38, 39, 43-44
A. saximontana, 32
A. scopulorum, 32, 43
A. vulgaris, 43
adaptive radiations, 2-3, 23, 30-44
anthocyanin production, 27, 32-33, 34, 35-36, 37-38, 39, 40-41, 42, 43
association mapping, 45
crossing studies, 27, 37-38
evolutionary trends, 31-34
flavonoid pathway, 27, 32-33, 35, 39-42, 43, 44
flower color evolution, 2-3, 32-37, 39-44
gene index, 27, 39, 40, 41, 43
genetic analyses, 2-3, 27-28, 32-37, 39-42, 44-45
genome sequencing, 44
orientation of flowers, 31-32, 34, 44
petal spur length, 30, 31, 34, 44
phylogeny, 33
pollinators, 31-34, 44
QTL analysis, 43, 44
research needs, 44-45
virus-induced gene silencing, 43
Arabian gazelle (Gazella gazelle), 102-103
Arabidopsis, 36, 39, 41, 119
Argument from design, xvi, 281, 282
Arnhart, Larry, 297
Arnold, Frances H., 67, 149-163
Arthur M. Sackler Colloquium, iv, viii, xvi, 26, 45, 190, 233-234, 266
Arthur M. Sackler Gallery of Asian Art, viii
Articulins, 72
Artificial selection.
See also Directed protein evolution;
Domestication;
Unnatural selection
Darwin’s legacy, xvi, 85, 90, 91-92, 99, 108, 293, 308, 321, 322, 334
defined, 89, 90, 91
prezygotic selection, 91
strong, 86, 91, 98, 101, 111, 119, 122, 123, 146
weak, 86, 91, 98
Asian elephant, 93
Association mapping, 45
Assortative mating, 9, 10, 25, 50-51, 54, 58, 89, 107, 108, 174-176
Atlantic cod (Gadus morhua), 134, 142, 146-147
Auroch (Bos primigenius), 96-97, 102-103
Avise, John C., iv, xiii-xiv, 26
Ayala, Francisco J., xiii-xiv, 26, 263-264, 267-285, 338
B
Bacon, Francis, 268, 272
Bactrian camel (Camelus bactrianus), 98-99, 102-103
Baltimore, David, 277
Barley, 94, 112
Barnacles, xv, 210, 271, 282, 283, 284, 335
Barred buttonquail (Turnix suscitator), 183
Bateman gradients, 184, 185, 186, 187-188, 192, 193, 197, 201
Beadle, George, 114, 116
Bees, 31, 32, 34, 311, 334
Bentham, Jeremy, 338
Bernard, Claude, 274-275, 279
Bernhardi, Friedrich von, 296
Bezoar (Capra aegagrus), 96-97, 102-103
Bighorn sheep (Ovis canadensis), 130, 140
Bindins, 258, 259
Biodiversity, defined, xiii
Biological species concept, 2, 6, 92
Black rat (Rattus rattus), 96-97, 102-103, 106
Bloom, Jesse D., 67, 149-163
Blyth, Edward, 291
Body size and complexity, 29, 55, 58
Bottlenecks, 21, 105, 115-116, 122, 123, 126-127, 153, 315
Bowerbird, 178
Bowler, Peter, 289, 304
Bradley, F. H., 338
Breasted, James Henry, 93-94
British Association for the Advancement of Science, 294
British Museum, 294
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Brown rat (Rattus norvegicus), 96-97, 102-103, 106
Brown trout (Salmo trutta), 130
Buckler, Edward S., IV, 86, 111-127
Buttonquail (Turnix), 172, 183
C
Caddis fly’s food sieve, 348-349
Caenorhabditis elegans, 76
Cape hare (Lepus capensis), 102-103
Caridean shrimp, 210
Cat (Felis silvestris catus) domestication
assortative mating, 89, 107, 108
context, 98-99
distribution of genotypes, 104-105
earliest human association, 98, 105
genetic analysis, 101, 104-106
genetic diversity, 105-106
oldest evidence, 105
preadaptive features, 102-103
selection mechanism, 85-86, 89, 99, 101, 108
selective breeding, 108-109
sympatric divergence and mitochondrial origins, 89, 92, 106-108
Catholic Church, 292, 296
Cattle, 85, 93, 94, 96-97, 102-103, 108
Cavalli-Sforza, Luigi, 326
CDPK3 gene, 50
Cech, Thomas, 277
Central dogma of molecular biology, 277
Cereal cultivation, 94, 106
Chagas’s disease, 66
Chalcone flavone isomerase, 34, 35, 41, 42
Chalcone synthase, 34, 35, 37, 41
Chambers, Robert, 291, 336
Cheetah (Acinonyx jubatus), 102-103
Chimpanzees, 115, 285, 350, 351, 353
Chinese mountain cats (Felis silvestris bieti), 104, 105
Chinook salmon (Oncorhynchus tshawytscha), 145, 147
Chromalveolata, 67, 68
Chromera, 66-67, 77
Chromosomal inversions, 16, 54
Church-Turing Thesis, 346
Cichlids, 28, 54, 176
Ciliates, 66, 67-68, 80
Climate change, 95, 132
Cnidarians, 210
cob gene, 79, 80
Coevolution, 83
flower spurs and pollinator tongues, 31
sexually antagonistic, 248-250, 252-261
Color.
See also Flower color patterns in butterflies, 50
Columbines. See Aquilegia
Common ancestry
Darwin’s principle, 315-318, 328
evidence of, 315-318, 319-321
exceptions to Darwin’s principle, 318-321, 324-325
natural selection and, 264, 312-315, 321-328
parsimony in reconstruction of, 325-327
Common fallow deer (Dama dama), 102-103
Complexity, 308-309, 325
Condition-dependent indicator (good genes) model, 178-179, 180, 217
Condition-independent indicator model, 179, 180
Conte, Gina L., 3, 47-64
Convergent evolution, 30, 3, 65, 66, 68-73, 82, 83
Copernican Revolution, 281, 299
Copernicus, Nicolaus, xv-xvi, 299, 329
Copper tolerance gene, 51
Courtship behavior, 243-244, 253-255
cox1 gene, 79, 80
cox3 gene, 79, 80
Creationists, 264, 265, 290, 296, 314, 344, 345, 346-347
Crops, 94-95, 106, 116.
See also Maize
Crossing studies, 27, 37-38, 334
Cryptic female choice, 166-167, 243, 244, 245, 247-248, 249, 250, 252, 256-257, 258, 259, 260, 261
Cryptosporidium, 67
Cyanidins, 33, 35, 36, 38
Cytochrome P450 enzyme, 151, 154-155, 156, 158, 160
D
Damselfly, 247
Darwin, Erasmus, 292, 330
Darwin, Robert Waring, 330
Darwin-Fisher model, 174-176
Darwin’s legacy
on altruism, 310-311, 338-339
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artificial selection, xvi, 85, 90, 91-92, 99, 108, 293, 308, 321, 322, 334
on common ancestry, 264, 312-328
early life, 330-332
on HMS Beagle, iv, xv, xvi, 263, 268-269, 279-280, 281, 282, 331
inductivism and, 267, 268, 269-271, 272
mate choice, 169, 173-174
mating system analyses, 166, 191, 192, 194-195
moral purpose of evolution, 264-265, 295-296, 297, 298, 310-312, 329, 330, 332-340
natural selection theory, xvi, 1-2, 28, 48, 214, 308, 271, 275-276, 280-284, 293, 296, 312-328, 334-340
Paley’s influence, xvi, 281
postcopulatory sexual selection, omission of, 166, 244-245
scientific methodology and thought processes, 263-264, 267-271, 272, 282-283, 318, 323-328
sexual selection, xi, 163, 165, 169, 170-171, 172, 173-174, 182-183, 189, 192, 193, 214
on species-variety boundary, 307-308
Transmutation Notebooks, 263, 268, 281, 282, 291, 329, 330, 332
unnatural selection in wildlife, 86-87, 130-131, 132
Darwin’s finches, 2, 28, 280
Darwinian debt, 134, 147
Darwinian revolution
conceptual nature of change, 264, 287, 299-304
metaphysical context, 264, 287, 290, 295-299
and scientific revolutions generally, 287, 288-289
scientific context, 264, 287, 289-295
Dawkins, Richard, 351
Delphinidins, 32, 35, 38
Dennett, Daniel, 265, 289, 329, 343-354
Derieg, Nathan J., 2-3, 27-45
Diderot, Denis, 292
Dihydroflavonol 4-reductase, 34, 35, 36, 37, 38, 41, 42
Dinoflagellates
cellular organization, 69-73
ecological role, 67
euglenid congergent evolution, 66, 67, 68, 69-73, 77, 80
feeding apparatuses, 72
flagellum, 71
gene expression and transcription, 73, 74-76
mitochondrion, 78-82
nuclear genome characteristics, 73-76
parasitic, 66
pellicle, 72-73
photoreceptors, 72
photosynthesis, 66-67, 73
plastids and protein targeting system, 67, 77-78
polycistronic mRNA processing, 74-76, 81, 82
predatory, 66, 69, 77
RNA editing and genome breakdown, 78-82, 83
spliced leaders (miniexons), 73-74, 82
trichocysts, 70, 71
Diplonema, 67
Diplonemids, 66, 67, 80, 81
Direct-benefits models, 176-177, 180
Directed protein evolution
antibiotic-resistance enzyme, 158
choosing next-generation parents, 153-154
cytochrome P450 enzyme, 151, 154-155, 156, 158, 160
empirical lessons from, 87, 149, 155-160
experimental design, 151-154
fitness landscapes, 156-157, 159
generalizability to natural evolution, 160-163
identifying improved mutants, 153, 158, 163
lactamase enzyme, 158
lactonase enzyme, 160
mutagenizing parent genes, 152-153
neutral mutations, 87, 149, 151, 153, 156, 157, 158, 159-160, 161, 162-163
neutral network view, 157
Pauling-Zuckerkandl hemoglobin experiment, 150, 151, 161
phosphotriesterase enzyme, 160
population bottlenecks, 153
promiscuous functions, 87, 149, 159-160, 162
single mutations, 149, 156-157, 159-160
stability-mediated epistasis, 87, 149, 157-159, 162
standing genetic variation, 153
thermostable chorismate mutase, 158
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Divergent selection
cats, 106-108
ecological speciation, 9, 11, 12, 19-22, 48, 49
Fst outlier analysis, 12-19, 21, 23-24
by genetic drift, 2, 10, 22-23, 24, 25, 160
genomic effects of, 5, 11, 12, 19-22
habitat choice and, 10, 11, 13, 15, 16, 19, 58
hitchhiking, 2, 5, 6, 14-19, 21-22, 23-24, 25, 153
for mate choice, 25, 50
under mutation, 49
and postzygotic isolation, 49, 51-53
potential vs. realized gene flow, 10-12
reproductive isolation, 9, 11, 12, 19-22, 28, 29, 49, 58
resource-based, 10, 11, 16, 19, 25
size of genomic hitchhiking regions, 17-19
in sympatry, 5, 13, 24-25, 89, 92, 106-108
DNA shuffling, 152-153
Dobzhansky, Theodosius, xiii, xiv, 6, 48
Dobzhansky-Muller incompatibilities, 6-7, 22-23, 24, 25, 53-54, 295
Doebley, John, 114
Dogs (Canis familaris), 85-86, 89, 93, 96-97, 98-101, 102-103, 338
Domestication.
See also Cat;
Maize
barnyard animals, 95-98, 99, 101
birds, 85, 96-97
bottlenecks, 115-116, 122, 126-127
characteristic traits, 92
commensal species, 96-97, 106
crops, 94-95, 106, 116
dogs, 89, 96-97, 98-101, 102-103
ecosystem effects, 90
natural selection and, 86, 89, 91, 96-99, 100
in Neolithic Fertile Crescent, 86, 89, 93-98, 106, 107-108
neoteny, 93
preadaptive characteristics, 98, 100
selection mechanism, 86, 89, 91, 96-99, 100, 101
standing variation, 92
sympatric divergence and mitochondrial origins, 89, 92, 106-108
taming compared, 93
tolerance of humans, 92-93, 106
Donkey (Equus asinus asinus), 98-99, 102-103
Dorcas gazelle (Gazella dorcau), 102-103
Doryrhamphus excisus, 182
Driscoll, Carlos A., 85-86, 89-109
Dromedary camel (Camelus dromedarius), 98-99, 102-103
Drosophila
D. hydei, 231
D. melanogaster, 123, 186, 187, 214-215, 249-250
D. pseudoobscura, 215
mating differentials, 186, 187, 214-215, 231, 249-250
reproductive isolation, 24, 51
Sod gene, 123
E
Eberhard, William G., 166-167, 243-261
Ecological factors
in intensity of sexual selection, 185-187, 197, 204, 208, 209
in mate choice, 9, 10-11, 25, 50, 166, 216
in mating, 185-187
Ecological speciation.
See also Reproductive isolation
allopatric vs sympatric speciation, 24-25
defined, 3, 47, 48
divergent selection, 9, 11, 12, 19-22, 48, 49
Fst outlier analysis, 12-19, 21, 23-24
with gene flow, 2, 3, 5, 6, 7, 9-12, 15, 16, 19-23, 24-25, 50, 53, 56, 59, 60, 62, 64
genetics of, 2, 5-6, 11, 12-13, 19-22, 47, 49, 49-51
geographic separation (allopatry) and, 6, 9-10, 20, 22, 23, 25, 28
hitchhiking and, 2, 5, 6, 14-19, 21-22, 23-24, 25
mutation-order speciation compared, 63-64
natural selection process in, 8-9
pea aphid model, 10, 13-17
postzygotic isolation and, 47, 49, 51-53
prezygotic isolation and, 47, 49-51, 55, 58, 63, 64
QTL analysis, 11, 12, 13, 14-25, 50
sexual selection, 9, 10, 50
stages of, 19-23
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from standing genetic variation, 3, 47, 49, 58-63, 64, 64
in sympatry or parapatry, 2, 5, 9, 13, 24-25
threespine stickleback model, 47, 49, 55-63
Ectodysplasin (Eda) gene, 56-57, 59, 60, 62-63, 64
Edwards, Anthony, 326
Egg-sperm molecular interactions, 243, 257-260
Egyptian New Kingdom, 105
Einkorn wheat, 94
Elephant seals, 176
Emmer wheat, 94
Endosymbiosis, 66, 73, 77, 345, 348
Epiplasmins, 72
Error-prone PCR, 152
Euglena, 70, 71
Euglenids, convergent evolution with dinoflagellates, 66, 67, 68, 69-73, 77, 80
Euglenophytes, 3, 47, 71, 77, 78
Euglenozoa
cellular structures, 66, 68, 69-73
convergent evolution, 65-84
endosymbiosis, 66, 77
gene expression, 66, 73-76
and heteroloboseans, 68
mitochondrion, 78-82
parasitic and commensalic, 66
photoautotrophic, 66
plastids, 77-78
predatory, 66, 69, 72, 77
RNA editing and processing, 66, 73-76, 83
subgroups and characteristics, 66, 69, 72, 77
on tree of eukaryotes, 67
Eukaryotes.
See also Protists
convergent evolution in, 68-69
nuclear gene expression, 74
phylogenetic diversity, 3, 67
tree, 67
European badger (Meles meles), 102-103
European otter (Lutra lutra), 102-103
Evolution, generally
arms races, 297-298
of language and culture, 350-352
moral purpose of, 264-265, 295-296, 297, 298, 310-312, 329, 330, 332-340
neutral theory of, 66, 69, 81-82, 83, 120, 122-123, 162
non-Darwinian contributions, 288-289, 292
postcopulatory sexual selection and, 243, 250-261
public acceptance of, 292-294
synthetic theory of, 292
trends, 29-30, 31-34
Excavata, 66, 67, 68.
See also Euglenozoa
Exploitation of wild animals. See Harvest of wild populations;
Unnatural selection
Eye evolution, 325-326
F
Fecundity, 13, 15-16, 134, 137, 173, 174, 175, 184, 185, 186, 193, 201, 203, 204, 217, 218, 220, 232, 245
Female-female combat, 172, 215
Ferrets, 101, 102-103
Fertile Crescent, domestication in, 86, 93-98, 106, 107-108
Fisher, Ronald A., 292, 316, 326
Fisher-Orr geometric model, 52-53
Fisher’s runaway hypothesis, 202
Fisherian model, 177-178, 180
Fishing/fisheries
Atlantic cod (Gadus morhua), 134, 142, 146-147
capture, 135
management, 135, 146-147
recreational, 136
salmon, 135, 136, 142, 143, 144-145, 147
selection effects, 86, 129, 130-131, 134-137, 142-143
and sexual selection, 142-143
Fitness
fecundity, 13, 15-16, 134, 137, 173, 174, 175, 184, 185, 186, 193, 201, 203, 204, 217, 218, 220, 232, 245
hybrids, 51, 52
mate choice and, 166, 213, 214-215, 216-217, 219-221, 224-227
migrants, 15
offspring viability, 166, 178, 184, 217, 218, 220, 232, 321
peaks in directed protein evolution, 156-157, 159
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productivity, 131, 134, 136, 142, 145, 146, 217, 218, 220, 232, 334
sex differences, 214-218
Flavanone-3-hydroxylase, 34, 35, 36, 37, 38, 39, 40, 41, 42
Flavonoid pathway, 27, 32-33, 35, 39-42, 43, 44
Flavonoid 3′-hydroxylase, 35, 36, 37, 38, 39-40, 42
Flavonoid 3′5′-hydroxylase, 35, 36, 38, 39-40, 42
Flower color evolution
Aquilegia, 32-44
carotenoid pigments, 34
flavonoid biosynthetic pathway, 34, 35, 36, 39-42
genetics of adaptation, 34-37
Mimulus, 29, 51
model, 37-38
molecular dissection, 42-44
pollinator preferences, 29, 51
trends, 35-37
Flowering plants
anthesis, 31, 44
cross-pollination, 195, 196, 251
dioecy, 195, 196, 210, 211
gynodioecy, 195, 196
heterochrony, 44
intrasexual conflict, 196-197, 260
mating systems, 166, 191, 192, 195-197
morphology of flowers, 196
nectar spurs, 30, 31, 34, 44
orientation of flowers, 31-32, 34, 44
outcrossing, 195-196, 210
petal spur length, 30, 31, 34, 44
pollinator preferences, 29, 30
self-incompatibility, 195, 196
selfing, 195-196, 210, 260
sexual selection, 191, 192, 195-197, 209-212, 243, 260-261
Fodor, Jerry, 346
Ford, E. B., 295
Forest elephant (Loxodonta Africana), 102, 130
Forest horse (Tarpan) (Equus ferus), 94, 98-99, 102-103
Fst outlier analysis, 12-19, 21, 23-24
G
Galapágos Islands, 2, 28, 280, 332
Galileo, xv, 329
Gasterosteus wheatlandi, 56
Gene expression, 66, 73-76
Gene flow
assortative mating and, 50
domestication and, 92
ecological speciation with, 2, 3, 5, 6, 7, 9-12, 15, 16, 19-23, 24-25, 50, 53, 56, 59-62, 64
as homogenizing force, 10, 11
in parallel selection, 53, 56, 59, 60
and recovery from selective harvest of wild populations, 146-147
transporter hypothesis, 59-62
Gene index, 27, 39, 40, 41, 43
Genetic analysis of speciation
adaptive radiations, 27-28, 27, 28, 29, 30, 42-45
Aquilegia flower color, 2-3, 27-28, 32-37, 39-42, 44-45
cats, 101, 104-106
Dobzhansky-Muller incompatibilities, 6-7, 22-23, 24, 25, 53-54, 295
ecological speciation, 2, 5-6, 11, 12-13, 19-22, 47, 49, 49-51
Fst outlier analysis of genomic regions, 12-19, 21, 23-24
hybridization and, 29, 30
magnifying glass (population) approach, 2, 7-8, 10, 26
pea aphids, 10, 13-17
population-level, 7-8
spyglass (retrospective) approach, 2, 5, 6-7, 17, 22, 23-24, 26
Genetic compatibility model, 179, 180
Genetic drift, 20, 59, 318
in adaptive protein evolution, 150, 153, 159, 160, 163
divergence by, 2, 10, 22-23, 24, 25, 160
gene flow and, 10
genomic effects, 10
human activities and, 100
mate-choice evolution, 179
neutral, 10-11, 150, 153, 159, 160, 163
rapid, 153
Genetic linkages
interrace disequilibrium, 14, 16, 21, 23-24, 25
performance and mating, 9
selective sweep, 14
Genital evolution, 243, 248-249, 250-253
Genome
hitchhiking regions, 17-19
sequencing, 44, 124
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Ghiselin, Michael, 283, 338
Glass sponges (Hexactinellidae), 210
Goats (Capra hircus), 94, 96-97, 102-103
Goethe, Johann Wolfgang von, 331
Goitered gazelle (Gazella subgutturosa), 102-103
Golden jackal (Canis aureus), 102-103
Gorillas, 93, 284-285, 297
Gould, Stephen J., 297, 298, 303, 307, 337
Gowaty, Patricia Adair, 166, 213-241
Gray, Asa, 294, 301, 322, 336, 341
Gray mouse (Mus musculus), 96-97, 102-103
Gray wolf (Canis lupus), 96, 99-101, 102
Green alga, 66, 77
Greg, Richard Rathbone, 339
gRNAs, 79, 81
Group selection hypothesis, 202, 310-311, 334, 338-339
Grunion, 210
Gryllus, 257
Gulf pipefish (Syngnathus scovelli), 182, 183
H
Habitat choice, 10, 11, 13, 15, 16, 19, 58
Habitat degradation, 132
Haeckel, Ernst, 294, 304, 305, 341
Haldane, J. B. S., 139, 292
Hard, Jeffrey J., 86-87, 129-147
Harvest of wild populations.
See also Fishing/Fisheries;
Hunting;
Unnatural selection
and intensity of sexual selection, 136, 143
management challenges, 132, 141, 145-146
and mate choice, 142-144
recovery from, 146-147
specimen collection, 141
sustainable, 131, 132, 134, 146
Haw fly, 54
Hawaiian silversword, 28
Hawkmoths, 31-32, 34
Helianthus paradoxus, 50
Heliconius butterflies, 50-51
Hemoglobin, 150, 312, 318
Hempel, C. G., 274, 299
Hennig, Will, 326
Herschel, John F. W., 293
Heterochrony, 44
Heteroloboseans, 68
Heterosis, 51
Hitchhiking
divergence, 2, 5, 6, 14-19, 21-22, 23-24, 25, 153
selective sweep, 15
Hodge, Jonathan, 288, 289, 304
Hodges, Scott A., 2-3, 27-45
Hofstadter, Douglas, 352
Honeycreeper birds, 28
Horse (Equus caballus), 85, 98-99, 102-103
House mouse (Mus domesticus), 96-97, 102-103, 106
House sparrow (Passer domesticus), 96-97, 102-103, 106
Hubbell, Stephen A., 166, 213-241
Human evolution, 115, 284-285, 290, 310, 311, 322-323
Humboldt, Alexander von, 331
Hummingbirds, 31, 34
Hunting
bighorn sheep, 140-141
deer, 138, 140, 143
fox, 139
game, 137
genetic effects of, 138-141
natural mortality, 134
no-take protected areas, 147
selection effects, 86, 129, 130, 134, 137-141, 142, 143
sexual selection, 130, 137-138, 142, 143
trophy, 130, 137, 138, 140, 147
Huxley, Thomas Henry, 288-289, 290, 292, 293, 294, 296, 298, 301, 302, 303, 341
Hybrids/hybridization
Dobzhansky-Muller incompatibilities, 53-54
fecundity, 16
fitness, 51, 52
genetic dissection of traits, 29, 30
Mimulus flower color studies, 29
selection against, 13, 14, 16, 19, 260-261
sterility genes, 18, 22
vigor, 51
Hypotheses
consistency with commonly accepted hypotheses and theories, 277-278
explanatory value, 276-277
falsifiability, 178-179, 283-284, 326
imagination and corroboration, 274-276
internal consistency, 276
law of likelihood, 316-318
revolutionary examples, 277
testing, 276-279
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Hypothetical-deductive method, 263-264, 273-276, 282-285
I
Ichneumon (Herpestes ichneumon), 102-103
Iltis, Hugh, 114
Indian elephant (Elephas maximus), 102-103
Indirect-benefits models, 177-179, 217, 218
Individual selection, 310
Induction and empiricism, 263, 264, 267, 268, 269-271, 272-273, 275, 276, 283, 293
Intelligent design, 296, 308, 325, 346, 354
Intensity of sexual selection
Bateman gradients, 184, 185, 186, 187-188, 192, 193, 197, 201
crowding of sexual receptivity, 191, 208-209
Darwin’s perspective, 163, 182-183, 192
ecological factors, 185-187, 197, 204, 208, 209
environmental potential for polygamy, 185, 186, 197, 204, 208, 209
harvesting of wild populations and, 136, 143
lineage differences in color and morphology and, 171, 182-183
mate searching algorithms and, 186
mating differentials, 184, 185-187
multiple mating rates, 187, 194, 215
nuptial gifts and, 187
parental investment theory, 185, 187, 192, 198, 201-202, 203-204, 215-216, 218, 232, 243
research advances, 169, 183-184, 189
research needs, 188-189, 190
secondary sexual characteristics, 182
selection coefficients, 184-187
sex difference in opportunity for selection, 191, 202-204, 208
sex ratios and, 142-143, 186, 188, 194, 197-201, 203, 204, 206-208
sex-role-reversed taxa, 193, 204, 205
sexual conflict and, 187, 201
sexual dimorphism and, 166, 171, 182-183, 192, 210
spatial and temporal distribution of matings, 192, 204-208
Intersexual selection. See Mate choice;
Postcopulatory sexual selection
Intrasexual conflict
female-female combat, 172, 215
male-male combat, 140, 166, 172, 173, 184, 212, 214
in plants, 196-197, 260
sexual dimorphism and, 192
sperm competition, 166, 194, 198, 243, 244, 247, 255, 256, 257, 258
Invasive species, 132
Ipomoea, 37
ISI Web of Science, 29
J
Jacob, François, 272, 275, 276
Jefferson, Thomas, 331
Jevons, William Stanley, 274
Joint Genome Institute, 44
Jones, Adam G., 165, 169-190
Judson, Olivia, 265-266
Jungle cat (Felis chaus), 102-103
K
Keeling, Patrick, 3, 65-84
Kekulé, Friedrich, 275
Kin selection, 311
Kinetoplast DNA, 78, 80
Kinetoplastids, 66, 67, 73-76, 77, 78, 79, 80, 81-82
Kitlg gene, 56-57, 59
Kuhn, Thomas, 288, 299, 301, 302, 303
L
Lactamase enzyme, 158
Lactonase enzyme, 160
Lake Malawi, 28
Lake Victoria, 28, 54
Lake whitefish (Coregonus clupeaformis), 14, 51
Lamarck, Jean Baptiste de, 308, 332, 336
Lamarckism, 292, 308, 311, 332
Land snail (Helix pomatia), 141
Lankester, E. Ray, 294
Largemouth bass (Micropterus salmoides), 136
Leafy sea dragon (Phycodurus eques), 182
Leander, Brian, 3, 65-84
Leishmania, 66
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Leopard (Panthera pardus), 102-103
Lepidoptera, 256
Lepocinclis, 67
Leptomonas, 67
Lewes, G. H., 314
Lewontin, Richard, 297, 303
Lion (Panthera leo), 102-103
Lloyd, Lisa, 297
Lock-and-key hypothesis, 251, 253
Lukeš, Julius, 3, 65-84
Lyell, Charles, 315, 332
Lysins, 258, 261
M
Macdonald, David, 85-86, 89-109
Maize (Zea mays ssp. mays) domestication
chromosome morphology and number, 114
data analysis, 126-127
evolutionary process, 86, 116-119
flowering time, 119
genome diversity of teosinte, 111, 115-116
genome sequencing, 124
HapMap, 124
kernel oil content, 119
landrace collections, 124
large-effect vs. small-effect loci, 112, 116-119
morphology, 86, 112-113, 116, 117-118
origins, 86, 112-115, 117, 118-119
plant materials and DNA sequencing, 125-126
QTL analysis, 116-117, 118, 119
research needs, 111, 123-125
selective sweep on chromosome 10, 86, 111, 119-123, 125-127
starch biosynthesis, 118-119
Teosinte Hypothesis, 114-115, 116
tomato domestication compared, 116
Tripartite Hypothesis, 113-114, 116
yellow color, 123
Male-male combat, 140, 166, 172, 173, 184, 212, 214, 246, 247-250
Malthus, Thomas Robert, 293, 332
Mangelsdorf, Paul, 113, 114
Marbled polecat (Vormela peregusna), 102-103
Mate choice
anisogamy theory, 231-232
assortative mating, 9, 10, 25, 50-51, 54, 58, 89, 107, 108, 174-176
condition-dependent indicator (good genes) model, 178-179, 180, 217
condition-independent indicator model, 179, 180
costs of, 181, 219
Darwin-Fisher model, 174-176
Darwin’s view, 169, 173-174
direct-benefits models, 176-177, 180
divergent selection for, 25, 50
ecological constraints, 9, 10-11, 25, 50, 166, 216
empirical examples, 176
Fisherian model, 177-178, 180
fitness distributions, 166, 213, 214-215, 216-217, 219-221, 224-227
genetic compatibility model, 179, 180
harvesting of wildlife and, 142-144
indirect-benefits models, 177-179, 217, 218
latency in mating, 166, 213, 215, 216, 219, 220, 225, 226, 227, 229, 234, 235, 236, 237-238, 240-241
ornaments and fancy traits, 173, 175, 177-178, 179, 180, 181, 186, 189, 214, 217-218, 232-233
parental investment theory and, 232
plant mating systems, 197-198
progress in research, 169, 174, 180, 189
reproductive compensation hypothesis, 217
research needs, 181, 190
sensory exploitation model, 179, 180
sex ratios, 198, 213, 225-226
sex role behavior and, 214-218, 231-232, 233
sexual conflict model, 179-180
survival probability, 166, 178, 213, 214, 215, 216, 219, 225, 226, 228, 234, 236, 240, 241
switch point theorem, 166, 218, 219-241
time available for mating and, 166, 213, 219, 227, 230
Mate searching algorithms, 186
Mating
compatibility measurement, 55
differentials, 184, 185-187, 214-215, 231, 249-250
ecological factors, 185-187
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latency, 166, 213, 215, 216, 219, 220, 225, 226, 227, 229, 234, 235, 236, 237-238, 240-241
mass, 210
multiple mating rates, 187, 194, 215
spatial and temporal distribution, 192, 204-208
time available for, 166, 213, 219, 227, 230
Mating system analyses
animal, 166, 191, 192-193, 197-200
common ground for plant and animal systems, 209-212
covariance methods, 201-202
crowding of sexual receptivity, 191, 208-209
Darwin’s contribution, 166, 191, 192, 194-195
mass matings, 210
molecular markers, 165, 189
plant, 166, 191, 192, 195-197
quantitative methodology, 191, 192, 201-212
research needs, 188
sex difference in opportunity for selection, 191, 202-204, 208
spatial and temporal distribution of matings, 192, 204-208
Mayr, Ernst, 6, 48, 251-252
Maximum likelihood methods, 30
Memes, 351
Mendel, Gregor, 34, 273, 274
Menidia menidia, 147
Mesolithic, animal domestication, 89
Mice, 51, 96-97, 102-103, 106, 176, 217, 227
Migration/migrants, 13, 15-17, 19, 49-50
Mill, James, 338
Mill, John Stuart, 263, 268, 272
Milton, John, 340-341
Mimulus
M. aurantiacus, 37
M. cardinalis, 29, 51
M. guttatus, 51, 53
M. lewisii, 29, 51
Miniexons, 73-74, 82
Minimum-evolution principle, 326
Mitochondrion, 78-82
Mockingbirds, 2, 28, 332
Molecular clock, 162
Molecular markers, 165, 189
Molecular phylogenetics, 29
Monkeyflowers, 29, 37, 51
Monophyletic clades, 2, 20, 28, 29, 39, 59, 66, 107
Morgan, Lloyd, 338
Morris, Simon Conway, 298, 346
Mouflon (Ovis orientalis), 94, 96-97, 102-103
mRNA, polycistronic processing, 74-76, 81, 82
Muller, H. J., 6
Multidimensional scaling analysis, 60, 62
Museum d’Histoire Naturelle, 298
Mutations
beneficial, 52, 149, 151, 153-154, 156, 157, 158-160, 161, 162
color variation in flowers, 37-38
deleterious, 52, 76, 117, 151, 153, 156, 157, 158, 161, 162, 312
divergent selection under, 49
duplications, 30, 39, 76, 83
gain of function, 36
global suppressor, 158
loss-of-function, 29, 35-37, 38
neutral, 87, 149, 151, 153, 156, 157, 158, 159-160, 161, 162-163, 252, 312, 318, 324
parallel selection, 53
pleiotropic, 52
selective sweeps, 14, 15, 24, 117
speciation by, 47, 49, 52, 53, 63-64
stability-mediated epistasis, 87, 149, 157-159, 162
substitutions, 22, 30, 81, 150-151, 154, 159, 160, 161, 162, 163, 285
transpositions, 30
Myoglobin, 150
Myzocytosis, 77
N
Nagel, Thomas, 346
Narwhals, 172
Natufians, 95
Natural selection
codiscovery claims, 290-291
and common ancestry, 264, 312-315, 321-328
and complexity, 308-309, 325
Darwin’s legacy, xvi, 1-2, 28, 48, 214, 271, 275-276, 280-284, 293, 296, 312-328, 334-340
defined, 91, 214
and domestication, 86, 89, 91, 96-99, 100
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genomic effects, 10
group selection hypothesis, 310-311, 334, 338-339
individual selection, 310
as intelligent and moral force, 264-265, 295-296, 297, 298, 310-312, 329, 330, 332-340
intensity, 136
process in ecological speciation, 8-9
“random” variation, 309
sexual selection combined, 132, 136, 165, 171, 248
stabilizing, 9, 22, 52, 154-155, 158, 159, 162-163
“survival of the fittest,” 308
tree thinking, 328
uniform or balancing, 9, 20, 25, 48, 22-23
Neolithic
domestication of animals, 86, 89, 90, 93-98, 106, 107-108
preadaptive features of fauna, 102-103
Neutral theory of evolution, 66, 69, 81-82, 83, 120, 122-123, 162
Newton, Isaac, xv, 269, 274, 275, 329, 343
Newton’s laws, 270
Newtonian mechanics, 277, 283, 304
Nicotiana tobacum, 36, 38
Nubian wild ass (Equus asinus africanus), 98-99, 102-103
Nuclear genome characteristics, 73-76
Nuptial gifts, 187
O
O’Brien, Stephen J., 85-86, 89-109
Odysseus (Ody) gene, 18
Offspring viability, 166, 178, 184, 217, 218, 220, 232, 321
Oken, Lorenz, 288
Opsin gene, 54
Orangutans, 285
Orchids, xv, 271, 282, 283, 284, 303
Osborn, Henry Fairfield, 288, 294
Outcrossing, 195-196, 210
Oxyrrhis, 80
P
Paley, William, xvi, 281, 282, 325
Pan-editing, 83
Pandalid shrimp, 210
Parallel selection
with gene flow, 53, 56, 59, 60
mutations, 53
of reproductive isolation, 53, 54, 55, 56, 59, 60, 63, 64
threespine stickleback, 55, 56, 59, 60, 63
Parasperm, 256-257
Parental investment theory, 184, 185, 187, 192, 198, 201-202, 203-204, 215-216, 218, 232, 243
Parker, Geoff, 244-245
Pascal, Blaise, 273
Pasteur, Louis, 274
Pauling, Linus, 150, 151, 161
Pea aphids, 10, 13-17, 50, 51
Peacocks, 165, 178, 214, 250
Peirce, Charles S., 274
Pelargonidins, 33, 35, 36, 38
Penrose, Roger, 346
Peranema, 70, 71
Persian fallow deer (Dama mesopotamica), 102-103
Persian onager (Equus hemionus hemippus), 102-103
Petunia, 36, 40-41, 42
P. axillaris, 36
Phacus, 70
Phosphotriesterase enzyme, 160
Photoreceptors, 72
Photosynthesis, 67-68, 73
Phylogeny
Aquilegia, 33
disciplines contributing to, 284
minimum-evolution principle for inferring, 326
tree thinking, 328
Pig (Sus domesticus), 94, 96-97, 108
Pigeon (Columba livia), 85, 96-97, 322
Plantinga, Alvin, 346-348, 353
Plants.
See also Flowering plants
herbivore resistance, 36
UV protection, 36
Plasmodium, 67
Plastids, 67, 77-78
Plato, 289, 296
Pleiotropy, 10, 25, 36, 42, 50, 51, 52, 64, 161, 251-252
Pleistocene, 93, 94, 96
Ploeotia, 70
Polar bears, 93, 308, 323
Pollinators, 31-34, 44, 51
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Polycistronic mRNA processing, 74-76, 81, 82
Polygamy, environmental potential for, 185, 186, 197, 204, 208, 209
Polykrikos, 70, 71
Polyploidy, 9
Polyspermy, 258
Popper, Karl, 274, 283, 326
Population genetic theory, 115
Population pressure, 332
Postcopulatory sexual selection
analysis of effects of, 205
courtship behavior during and after copulation, 243-244, 253-255
cryptic female choice, 166-167, 243, 244, 245, 247-248, 249, 250, 252, 256-257, 258, 259, 260, 261
Darwin’s omission, 166, 244-245
defined, 171
egg-sperm molecular interactions, 243, 257-260
evolutionary consequences, 243, 250-261
female effects on male-male competition, 246, 247-250
flowering plants, 243, 260-261
free-spawning species contrasted, 258
genital evolution, 243, 248-249, 250-253
male contact organs, 243, 253, 254
parasperm, 256-257
and parental investments, 184, 243
research needs, 189
seminal products, 243, 257
sensory traps, 248-249
sexually antagonistic coevolution, 248-250, 252-253, 254, 255, 257, 258-259, 260, 261
sperm competition, 166, 194, 198, 243, 244, 245, 247, 255, 256, 257, 258
sperm morphology, 255-257
Proanthocyanidins, 36
Productivity, 131, 134, 136, 142, 145, 146, 217, 218, 220, 232, 334
Prokaryotes, nuclear gene expression, 74
Prorocentrum, 70, 71
Protein evolution. See Adaptive protein evolution;
Directed protein evolution
Protists.
See also Alveolata;
Euglenozoa
convergent evolution in cellular organization, 3, 65, 66, 68-73
phylogenetic diversity, 3, 82
Protoperidinium, 67
Provine, William, 289
Pundamilia neyereri, 54
Pundamilia pundamilia, 54
Q
Quantitative methodology, mating system analysis, 191, 192, 201-212
Quantitative trait loci analysis
ecological speciation under divergent selection, 11, 12, 13, 14-25, 50
flower color, 43, 44, 51
maize origins, 116-117, 118, 119
R
Ratterman, Nicholas L., 165, 169-190
Red alga, 77
Red clover, 13-17
Red deer (Cervus elaphus), 102-103, 138, 140, 143
Red fox (Canis vulpes; Vulpes vulpes), 102-103, 139
Reeves, Robert, 113, 114
Reproductive compensation hypothesis, 217
Reproductive isolation.
See also Ecological speciation
assortative mating, 50-51, 89
behavioral, 89
divergent selection to alternate environments, 9, 11, 12, 19-22, 28, 29, 49, 58
Dobzhansky-Muller incompatibilities, 6-7, 22, 23, 24, 25, 53-54, 295
Fisher-Orr geometric model of adaptation, 52-53
genetics of, 49-53
immigrant inviability, 15-16, 49-50
intrinsic, 51, 52, 53, 63
mutation-order speciation, 63-64
parallel speciation, 53, 54, 55, 56, 59, 60, 63, 64
postzygotic, 3, 23, 24, 25, 47, 48, 49, 51-53, 58, 63
premating/prezygotic, 25, 47, 48, 49-51, 55, 58, 63, 64
Resource-based divergence, 10, 11, 16, 19, 25
Rice, 112, 123
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Richards, Robert J., 264-265, 288-289, 329-341
RNA editing and processing, 66, 73-76, 78-83
Roberts, Richard, 277
Rock dove, 96-97, 322
Roe deer, 140
ROSEA1 gene, 42
ROSEA2 gene, 42
R2R3-myb transcription factor, 36, 40, 41
Ruppell’s fox (Vulpes ruppellii), 102-103
Ruse, Michael, 264, 287-305, 329, 337-338
S
Sackler, Arthur M., vii-viii.
See also Arthur M. Sackler Colloquium
Sackler, Jillian, vii, viii
Salmon, 135, 136, 142, 143, 144-145, 147
Salt tolerance gene, 50
Sand cat (Felis margarita), 102-103, 104
Scarab beetles, 172
Schluter, Dolph, 3, 47-64
Scientific method.
See also Hypotheses
Darwin’s legacy, 263-264, 267-271, 272, 282-283, 318, 323-328
hypothetical-deductive method, 263-264, 273-276, 282-285
induction and empiricism, 263, 264, 267, 268, 269-271, 272-273, 275, 276, 283, 293
Sea urchins, 257, 258, 259
Searle, John, 346
Seahorses (Hippocampus), 182, 204
Sebright, John, 291
Secondary sexual characteristics, 182
Sebright, James, 291
Selective breeding, 108-109.
See also Domestication
Selenidium, 67
Self-incompatibility, 195, 196
Selfing, 195-196, 210, 260
Self-splicing introns, 77
Sensory exploitation model, 179, 180
Sensory traps, 248-249
Sex differences
in fitness, 214-218
in opportunity for selection, 191, 202-204, 208
Sex ratios, 142-143, 186, 188, 194, 197-201, 203, 204, 206-208, 213, 225-226
Sex roles, 193, 198, 203, 204, 205, 214-218, 230, 231-232, 233, 255
Sexual conflict.
See also Intersexual;
Intrasexual
and intensity of sexual selection, 187, 201
mate choice model, 179-180
Sexual dimorphism, 166, 171, 173, 175, 177-178, 179, 180, 181, 182-183, 186, 189, 192, 210, 214, 217-218, 232-233
Sexual receptivity, crowding of, 191, 208-209
Sexual selection.
See also Intensity of sexual selection;
Intrasexual conflict;
Mate choice;
Mating system analysis;
Postcopulatory sexual selection
age structure in, 188, 250
contextual models of multilevel selection, 202
Darwin’s legacy, xi, 163, 165, 169, 170-171, 172, 173-174, 182-183, 189, 192, 193, 214
defined, 91, 165, 170, 191
ecological factors, 185
Fisher’s runaway hypothesis, 202
group structure or membership and, 202
harvesting of wild animals and, 130, 137-139, 140, 142-145
in ecological speciation, 9, 10, 50
lock-and-key hypothesis, 251, 253
mechanisms, 172-181
monogamous, 174-175, 176
and natural selection, 132, 136, 165, 171, 248
plants, 191, 192, 195-197, 209-212, 260-261
pleitropism theory, 251-252
polygamous, 100, 183, 185, 186, 197, 204, 208, 209, 210, 211, 212, 215
precopulatory, 171, 185, 189
quantitative approaches, 193-194
research needs, 190
sex roles, 193, 198, 203, 214, 215-217, 218, 230, 231, 255
species isolation hypothesis, 251-252, 258-259, 260, 261
Sexually antagonistic coevolution, 248-250, 252-253, 254, 255, 257, 258-259, 260, 261
Sheep (Ovis aries), 94, 96-97, 102-103
Shuster, Stephen M., 166, 191-212
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Sialia sialis, 215
Sickle cell anemia, 150
Singer, Peter, 296-297
Skull sutures, 327
Sober, Elliott, 264, 297, 307-328
Social Darwinism, 296
Sockeye salmon (Oncorhynchus nerka), 136, 143, 144-145
Socrates, xvi
Sod gene, 123
Spandrels, 318
Speciation.
See also Ecological speciation
allopatric, 6, 9-10, 20, 22, 23, 24-25, 28, 107
defined, 15, 48
error-then-solution model, 83
mechanisms, 48-49
models, 48, 54
mutation-order, 47, 49, 53-54, 63-64, 83
rates, 53, 54
sympatric, 2, 5, 9, 13, 24-25, 51, 89, 92, 106-108, 259
Species isolation hypothesis, 251-252, 258-259, 260, 261
Spencer, Herbert, 270, 291-292, 296, 336, 341
Sperm
competition, 166, 194, 198, 243, 244, 245, 247, 255, 256, 257, 258
morphology, 255-257
Spliced leaders (miniexons), 74, 82
Spliceosomal introns, 74-75
Sponge shrimp (Spongocola spp.), 210
Stability-mediated epistasis, 87, 149, 157-159, 162
Standing genetic variation, 3, 47, 49, 58-63, 64, 64
Steppe polecat (Mustela eversmanni), 102-103
Stevens, Natalie M., 86, 111-127
Stramenopiles, 68
Sunflower, 50
“Survival of the fittest,” 308
Survival probability, 166, 178, 213, 214, 215, 216, 219, 225, 226, 228, 234, 236, 240, 241
Switch point theorem
alternative to anisogamy theory, 231-232
alternative to parental investment theory, 232
changing more than one parameter at a time, 227, 229
derivation, 222-224, 234-241
fitness distributions, 219-220, 224-225, 232
flexibile reproductive decisions in both sexes, 231
model description, 221-222, 227, 230
number of potential mates, 225-226
predictability of fancy male traits, 232-233
reproductive time budgets, 219
results, 224-227, 240-241
sensitivity analysis, 228, 240
sex role ecology, 233
survival probability, 226-227, 228
time available for mating, 219, 227, 230
Symbiodinium, 67
Sympatric speciation, 2, 5, 9, 13, 24-25, 51, 89, 92, 106-108, 259
Syngnathus typhle, 182, 201
Syrian onager (Equus hemionus hemionus), 102-103
T
Taurine cattle (Bos taurus), 96-97, 102-103
Temin, Howard, 277
Teosinte (Zea mays ssp. parviglumis).
See also Maize domestication
chromosome morphology and number, 114
Euchlaena classification, 113
genome diversity, 111, 115-116
hypothesis, 114-115, 116
morphology, 86, 112-113
mutation rate, 115
peopraphical distribution, 126
selective sweep on chromosome 10, 86, 111, 119-123
Teosinte branched1 (tb1) gene, 117-118, 122, 125
Teosinte glume architecture1 (tga1) gene, 116-117, 122, 123, 125, 127
Terrestrial slugs, 210
Tetrapody, 326-327
Thermostable chorismate mutase, 158
Threespine stickleback (Gasterosteus aculeatus)
assortative mating, 58
body size, 55, 58
defensive body armor, 55, 56-57, 58-59, 62-63
ecological speciation, 47, 49, 51, 55-63
freshwater-marine hybridization, 3
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gene flow, 56, 59, 60, 62
hybrid fitness, 51, 58
male parental care, 204
multidimensional scaling analysis, 60, 62
parallel speciation, 55, 56, 59, 60, 63
phylogenies of populations and genes, 56-57
postzygotic isolation, 58
premating isolation, 55, 58, 63
selection from standing genetic variation, 47, 58-63
skin pigmentation, 56-57, 59
transporter hypothesis, 59-63
Tian, Feng, 86, 111-127
Tigers, 93, 310
Tomato, 116
Toxoplasma, 67
Trans-splicing, 73, 74-75, 76, 78, 81
Tree snails (Liguus and Orthicalus spp.), 141
Trichocysts, 70, 71
Tripartite hypothesis, 113-114, 116
Tripsacum, 113-114, 121
T. dactyloides, 122, 126, 127
tRNA, 80
Trypanosoma, 66, 74
T. brucei, 76, 80, 83
Turing, Alan, 265, 343, 345-346, 348, 350, 353
2-ODDs gene family, 39-40
U
UDP flavonoid glucosyltransferse, 34, 35
Uniform or balancing selection, 9, 20, 25, 48
University of Cambridge, xvi, 279, 281, 298, 299, 331
Unnatural selection in harvested wildlife
artificial selection compared, 86, 87, 130, 135
Darwin’s legacy, 86-87, 130-131, 132
defined, 131-132
and dispersal/migration, 131, 143
fishing, 86, 129, 130-131, 134-137, 142-143
genetic effects on populations, 129, 130, 133, 138-141
history of, 132-141
hunting, 86, 129, 130, 134, 137-141, 142, 143
intensity, 134, 136-137
and management practices, 131, 145-147
recovery from overharvesting, 129-130, 146-147
and sexual selection, 130, 137, 138-139, 140, 142-145
from specimen collection, 141
and sustainability, 129
traits likely to be affected, 86, 129, 131
V
VENOSA gene, 42
Via, Sara, 2, 5-26
Virus-induced gene silencing, 43
W
Wallace, Alfred Russel, 271, 290-291, 293-294, 308, 335, 341
waxy gene, 123
Weasel (Mustela nivalis), 102-103
Whewell, William, 274, 293, 303
Wild boar (Sus scrofia), 93, 96-97, 102
Wildcat, 98-99, 101, 102-103, 104-106
Wilkes, H. G., 114
Wilson, Edward O., 296
Windermere pike (Esox lucius), 137
wingless gene, 50, 51
Wollaston, T. V., 336
Wright’s island model, 10
Y
Yeast, 51
Young, Robert M., 290
Young earth creationists, 296
Younger Dryas, 95
Z
Zeboid cattle (Bos indicus, Bos primigenius namadicus), 97-98
Zuckerkandl, Emile, 150, 151, 161
