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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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Index A Altruism, 310-311, 338-339 Alveolata Abalone, 257, 258, 259, 261 cellular structures, 66, 68, 69-73 Achatinellinae tree snails, 141 convergent evolution with euglenozoa, Acyrthosiphon pisum (harris), 10, 13-17 65-84 Adaptation, Fisher-orr geometric model, endosymbiosis, 77 52-53 gene expression, 66, 73-76 Adaptive protein evolution, 150, 153, photosynthetic, 67-68 159-163 plastids, 77-78 Adaptive radiations rnA editing and processing, 66, 73-76, Aquilegia, 2-3, 23, 30-44 81, 83 classic examples, 28 and stramenopiles, 68 convergent evolution in, 30 subgroups and characteristics, 66-67 defining features, 28 tree structure, 67 evolutionary trends, 29-30, 31-34 American Museum of natural history, 294 genetic dissection of adaptive traits, 27, Anisogamy theory, 231-232 28, 29, 30, 42-44 Anthocyanidin reductase, 35, 36, 41 phenotype-environment correlations, 28 Anthocyanidin synthase, 34, 35, 37, 39, 40, research interests and trends, 28-29 41, 42, 43 research needs, 27-28, 44-45 Anthocyanin biosynthetic pathway, 27, 32- trait directionality, 30, 31-34 33, 34, 35-36, 37-38, 39, 40-41, 42, 43 trait utility, 28 Anthocyanin GsT, 35, 41 African sleeping sickness, 66 Antibiotic-resistance enzyme, 158 Alfalfa, 13-17 Antirrhinum, 42 Allendorf, Fred W., 86-87, 129-147 AN2 gene, 36-37, 42 Allopatric speciation, 6, 9-10, 20, 22, 23, Apicomplexans, 66, 67, 77, 80-81 24-25, 107 Apicoporus, 70, 71 Altman, sidney, 277 Apple maggot (Rhagoletis pomonella), 54 

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400 / Index Aquaculture, 130 defined, 89, 90, 91 prezygotic selection, 91 Aquilegia A. brevistyla, 38 strong, 86, 91, 98, 101, 111, 119, 122, 123, A canadensis, 33, 38 146 A. chrysantha, 37-38 weak, 86, 91, 98 A. coerulea, 32, 33, 38, 43 Asian elephant, 93 A. flabellata, 37-38 Association mapping, 45 A. flavescens, 32, 34, 38 Assortative mating, 9, 10, 25, 50-51, 54, 58, A. formosa, 32, 33, 38, 39, 42, 43-44 89, 107, 108, 174-176 A. jonesii, 32 Atlantic cod (Gadus morhua), 134, 142, A. laramiensis, 34 146-147 A. longissima, 32, 37-38 Auroch (Bos primigenius), 96-97, 102-103 Avise, John C., iv, xiii-xiv, 26 A. pinetorum, 37 A. pubescens, 32, 38, 39, 43-44 Ayala, Francisco J., xiii-xiv, 26, 263-264, A. saximontana, 32 267-285, 338 A. scopulorum, 32, 43 A. vulgaris, 43 B adaptive radiations, 2-3, 23, 30-44 anthocyanin production, 27, 32-33, 34, Bacon, Francis, 268, 272 35-36, 37-38, 39, 40-41, 42, 43 Bactrian camel (Camelus bactrianus), 98-99, association mapping, 45 102-103 crossing studies, 27, 37-38 Baltimore, David, 277 evolutionary trends, 31-34 Barley, 94, 112 flavonoid pathway, 27, 32-33, 35, 39-42, Barnacles, xv, 210, 271, 282, 283, 284, 335 43, 44 Barred buttonquail (Turnix suscitator), flower color evolution, 2-3, 32-37, 183 39-44 Bateman gradients, 184, 185, 186, 187-188, gene index, 27, 39, 40, 41, 43 192, 193, 197, 201 genetic analyses, 2-3, 27-28, 32-37, 39-42, Beadle, George, 114, 116 44-45 Bees, 31, 32, 34, 311, 334 genome sequencing, 44 Bentham, Jeremy, 338 orientation of flowers, 31-32, 34, 44 Bernard, Claude, 274-275, 279 petal spur length, 30, 31, 34, 44 Bernhardi, Friedrich von, 296 phylogeny, 33 Bezoar (Capra aegagrus), 96-97, 102-103 pollinators, 31-34, 44 Bighorn sheep (Ovis canadensis), 130, 140 QTl analysis, 43, 44 Bindins, 258, 259 research needs, 44-45 Biodiversity, defined, xiii virus-induced gene silencing, 43 Biological species concept, 2, 6, 92 Arabian gazelle (Gazella gazelle), 102-103 Black rat (Rattus rattus), 96-97, 102-103, 106 Arabidopsis, 36, 39, 41, 119 Bloom, Jesse D., 67, 149-163 Argument from design, xvi, 281, 282 Blyth, edward, 291 Arnhart, larry, 297 Body size and complexity, 29, 55, 58 Arnold, Frances h., 67, 149-163 Bottlenecks, 21, 105, 115-116, 122, 123, 126- Arthur M. sackler Colloquium, iv, viii, xvi, 127, 153, 315 26, 45, 190, 233-234, 266 Bowerbird, 178 Arthur M. sackler Gallery of Asian Art, viii Bowler, Peter, 289, 304 Articulins, 72 Bradley, F. h., 338 Artificial selection. See also Directed protein Breasted, James henry, 93-94 evolution; Domestication; Unnatural British Association for the Advancement of selection science, 294 Darwin’s legacy, xvi, 85, 90, 91-92, 99, British Museum, 294 108, 293, 308, 321, 322, 334

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Index / 40 Brown rat (Rattus norvegicus), 96-97, 102- Cnidarians, 210 103, 106 cob gene, 79, 80 Brown trout (Salmo trutta), 130 Coevolution, 83 Buckler, edward s., iv, 86, 111-127 flower spurs and pollinator tongues, 31 Buttonquail (Turnix), 172, 183 sexually antagonistic, 248-250, 252-261 Color. See also Flower color patterns in butterflies, 50 C Columbines. See Aquilegia Common ancestry Caddis fly’s food sieve, 348-349 Darwin’s principle, 315-318, 328 Caenorhabditis elegans, 76 evidence of, 315-318, 319-321 Cape hare (Lepus capensis), 102-103 exceptions to Darwin’s principle, 318- Caridean shrimp, 210 321, 324-325 Cat (Felis silvestris catus) domestication natural selection and, 264, 312-315, assortative mating, 89, 107, 108 321-328 context, 98-99 parsimony in reconstruction of, 325-327 distribution of genotypes, 104-105 Common fallow deer (Dama dama), 102-103 earliest human association, 98, 105 Complexity, 308-309, 325 genetic analysis, 101, 104-106 Condition-dependent indicator (good genetic diversity, 105-106 genes) model, 178-179, 180, 217 oldest evidence, 105 Condition-independent indicator model, preadaptive features, 102-103 179, 180 selection mechanism, 85-86, 89, 99, 101, Conte, Gina l., 3, 47-64 108 Convergent evolution, 30, 3, 65, 66, 68-73, selective breeding, 108-109 82, 83 sympatric divergence and Copernican revolution, 281, 299 mitochondrial origins, 89, 92, Copernicus, nicolaus, xv-xvi, 299, 329 106-108 Copper tolerance gene, 51 Catholic Church, 292, 296 Courtship behavior, 243-244, 253-255 Cattle, 85, 93, 94, 96-97, 102-103, 108 cox1 gene, 79, 80 Cavalli-sforza, luigi, 326 cox3 gene, 79, 80 CDPK3 gene, 50 Creationists, 264, 265, 290, 296, 314, 344, Cech, Thomas, 277 345, 346-347 Central dogma of molecular biology, 277 Crops, 94-95, 106, 116. See also Maize Cereal cultivation, 94, 106 Crossing studies, 27, 37-38, 334 Chagas’s disease, 66 Cryptic female choice, 166-167, 243, 244, Chalcone flavone isomerase, 34, 35, 41, 42 245, 247-248, 249, 250, 252, 256-257, Chalcone synthase, 34, 35, 37, 41 258, 259, 260, 261 Chambers, robert, 291, 336 Cryptosporidium, 67 Cheetah (Acinonyx jubatus), 102-103 Cyanidins, 33, 35, 36, 38 Chimpanzees, 115, 285, 350, 351, 353 Cytochrome P450 enzyme, 151, 154-155, Chinese mountain cats (Felis silvestris bieti), 156, 158, 160 104, 105 Chinook salmon (Oncorhynchus tshawytscha), 145, 147 D Chromalveolata, 67, 68 Chromera, 66-67, 77 Damselfly, 247 Chromosomal inversions, 16, 54 Darwin, erasmus, 292, 330 Church-Turing Thesis, 346 Darwin, robert Waring, 330 Cichlids, 28, 54, 176 Darwin-Fisher model, 174-176 Ciliates, 66, 67-68, 80 Darwin’s legacy Climate change, 95, 132 on altruism, 310-311, 338-339

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40 / Index artificial selection, xvi, 85, 90, 91-92, 99, feeding apparatuses, 72 108, 293, 308, 321, 322, 334 flagellum, 71 on common ancestry, 264, 312-328 gene expression and transcription, 73, early life, 330-332 74-76 on hMs Beagle, iv, xv, xvi, 263, 268-269, mitochondrion, 78-82 279-280, 281, 282, 331 nuclear genome characteristics, 73-76 inductivism and, 267, 268, 269-271, 272 parasitic, 66 mate choice, 169, 173-174 pellicle, 72-73 mating system analyses, 166, 191, 192, photoreceptors, 72 194-195 photosynthesis, 66-67, 73 moral purpose of evolution, 264-265, plastids and protein targeting system, 295-296, 297, 298, 310-312, 329, 330, 67, 77-78 332-340 polycistronic mrnA processing, 74-76, natural selection theory, xvi, 1-2, 28, 48, 81, 82 214, 308, 271, 275-276, 280-284, 293, predatory, 66, 69, 77 296, 312-328, 334-340 rnA editing and genome breakdown, Paley’s influence, xvi, 281 78-82, 83 postcopulatory sexual selection, spliced leaders (miniexons), 73-74, 82 omission of, 166, 244-245 trichocysts, 70, 71 scientific methodology and thought Diplonema, 67 processes, 263-264, 267-271, 272, 282- Diplonemids, 66, 67, 80, 81 283, 318, 323-328 Direct-benefits models, 176-177, 180 sexual selection, xi, 163, 165, 169, 170- Directed protein evolution 171, 172, 173-174, 182-183, 189, 192, antibiotic-resistance enzyme, 158 193, 214 choosing next-generation parents, on species-variety boundary, 307-308 153-154 Transmutation notebooks, 263, 268, 281, cytochrome P450 enzyme, 151, 154-155, 282, 291, 329, 330, 332 156, 158, 160 unnatural selection in wildlife, 86-87, empirical lessons from, 87, 149, 155-160 130-131, 132 experimental design, 151-154 Darwin’s finches, 2, 28, 280 fitness landscapes, 156-157, 159 Darwinian debt, 134, 147 generalizability to natural evolution, Darwinian revolution 160-163 conceptual nature of change, 264, 287, identifying improved mutants, 153, 158, 299-304 163 metaphysical context, 264, 287, 290, lactamase enzyme, 158 295-299 lactonase enzyme, 160 and scientific revolutions generally, 287, mutagenizing parent genes, 152-153 288-289 neutral mutations, 87, 149, 151, 153, 156, scientific context, 264, 287, 289-295 157, 158, 159-160, 161, 162-163 Dawkins, richard, 351 neutral network view, 157 Delphinidins, 32, 35, 38 Pauling-Zuckerkandl hemoglobin Dennett, Daniel, 265, 289, 329, 343-354 experiment, 150, 151, 161 Derieg, nathan J., 2-3, 27-45 phosphotriesterase enzyme, 160 Diderot, Denis, 292 population bottlenecks, 153 Dihydroflavonol 4-reductase, 34, 35, 36, 37, promiscuous functions, 87, 149, 159-160, 38, 41, 42 162 Dinoflagellates single mutations, 149, 156-157, 159-160 cellular organization, 69-73 stability-mediated epistasis, 87, 149, ecological role, 67 157-159, 162 euglenid congergent evolution, 66, 67, standing genetic variation, 153 68, 69-73, 77, 80 thermostable chorismate mutase, 158

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Index / 40 Divergent selection Donkey (Equus asinus asinus), 98-99, cats, 106-108 102-103 ecological speciation, 9, 11, 12, 19-22, 48, Dorcas gazelle (Gazella dorcau), 102-103 49 Doryrhamphus excisus, 182 Fst outlier analysis, 12-19, 21, 23-24 Driscoll, Carlos A., 85-86, 89-109 by genetic drift, 2, 10, 22-23, 24, 25, 160 Dromedary camel (Camelus dromedarius), genomic effects of, 5, 11, 12, 19-22 98-99, 102-103 habitat choice and, 10, 11, 13, 15, 16, 19, Drosophila 58 D. hydei, 231 hitchhiking, 2, 5, 6, 14-19, 21-22, 23-24, D. melanogaster, 123, 186, 187, 214-215, 25, 153 249-250 for mate choice, 25, 50 D. pseudoobscura, 215 under mutation, 49 mating differentials, 186, 187, 214-215, and postzygotic isolation, 49, 51-53 231, 249-250 potential vs. realized gene flow, 10-12 reproductive isolation, 24, 51 reproductive isolation, 9, 11, 12, 19-22, Sod gene, 123 28, 29, 49, 58 resource-based, 10, 11, 16, 19, 25 E size of genomic hitchhiking regions, 17-19 eberhard, William G., 166-167, 243-261 in sympatry, 5, 13, 24-25, 89, 92, 106-108 ecological factors DnA shuffling, 152-153 in intensity of sexual selection, 185-187, Dobzhansky, Theodosius, xiii, xiv, 6, 48 197, 204, 208, 209 Dobzhansky-Muller incompatibilities, 6-7, in mate choice, 9, 10-11, 25, 50, 166, 216 22-23, 24, 25, 53-54, 295 in mating, 185-187 Doebley, John, 114 ecological speciation. See also reproductive Dogs (Canis familaris), 85-86, 89, 93, 96-97, isolation 98-101, 102-103, 338 allopatric vs sympatric speciation, 24-25 Domestication. See also Cat; Maize defined, 3, 47, 48 barnyard animals, 95-98, 99, 101 divergent selection, 9, 11, 12, 19-22, 48, birds, 85, 96-97 49 bottlenecks, 115-116, 122, 126-127 Fst outlier analysis, 12-19, 21, 23-24 characteristic traits, 92 with gene flow, 2, 3, 5, 6, 7, 9-12, 15, 16, commensal species, 96-97, 106 19-23, 24-25, 50, 53, 56, 59, 60, 62, 64 crops, 94-95, 106, 116 genetics of, 2, 5-6, 11, 12-13, 19-22, 47, dogs, 89, 96-97, 98-101, 102-103 49, 49-51 ecosystem effects, 90 geographic separation (allopatry) and, natural selection and, 86, 89, 91, 96-99, 6, 9-10, 20, 22, 23, 25, 28 100 hitchhiking and, 2, 5, 6, 14-19, 21-22, in neolithic Fertile Crescent, 86, 89, 93- 23-24, 25 98, 106, 107-108 mutation-order speciation compared, neoteny, 93 63-64 preadaptive characteristics, 98, 100 natural selection process in, 8-9 selection mechanism, 86, 89, 91, 96-99, pea aphid model, 10, 13-17 100, 101 postzygotic isolation and, 47, 49, 51-53 standing variation, 92 prezygotic isolation and, 47, 49-51, 55, sympatric divergence and 58, 63, 64 mitochondrial origins, 89, 92, QTl analysis, 11, 12, 13, 14-25, 50 106-108 sexual selection, 9, 10, 50 taming compared, 93 stages of, 19-23 tolerance of humans, 92-93, 106

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404 / Index from standing genetic variation, 3, 47, neutral theory of, 66, 69, 81-82, 83, 120, 49, 58-63, 64, 64 122-123, 162 in sympatry or parapatry, 2, 5, 9, 13, non-Darwinian contributions, 288-289, 24-25 292 threespine stickleback model, 47, 49, postcopulatory sexual selection and, 55-63 243, 250-261 Ectodysplasin (Eda) gene, 56-57, 59, 60, 62- public acceptance of, 292-294 63, 64 synthetic theory of, 292 edwards, Anthony, 326 trends, 29-30, 31-34 egg-sperm molecular interactions, 243, excavata, 66, 67, 68. See also euglenozoa 257-260 exploitation of wild animals. See harvest egyptian new Kingdom, 105 of wild populations; Unnatural einkorn wheat, 94 selection elephant seals, 176 eye evolution, 325-326 emmer wheat, 94 endosymbiosis, 66, 73, 77, 345, 348 F epiplasmins, 72 error-prone PCr, 152 Fecundity, 13, 15-16, 134, 137, 173, 174, 175, Euglena, 70, 71 184, 185, 186, 193, 201, 203, 204, 217, euglenids, convergent evolution with 218, 220, 232, 245 dinoflagellates, 66, 67, 68, 69-73, 77, Female-female combat, 172, 215 80 Ferrets, 101, 102-103 euglenophytes, 3, 47, 71, 77, 78 Fertile Crescent, domestication in, 86, 93- euglenozoa 98, 106, 107-108 cellular structures, 66, 68, 69-73 Fisher, ronald A., 292, 316, 326 convergent evolution, 65-84 Fisher-orr geometric model, 52-53 endosymbiosis, 66, 77 Fisher’s runaway hypothesis, 202 gene expression, 66, 73-76 Fisherian model, 177-178, 180 and heteroloboseans, 68 Fishing/fisheries mitochondrion, 78-82 Atlantic cod (Gadus morhua), 134, 142, parasitic and commensalic, 66 146-147 photoautotrophic, 66 capture, 135 plastids, 77-78 management, 135, 146-147 predatory, 66, 69, 72, 77 recreational, 136 rnA editing and processing, 66, 73-76, salmon, 135, 136, 142, 143, 144-145, 147 83 selection effects, 86, 129, 130-131, 134- subgroups and characteristics, 66, 69, 137, 142-143 72, 77 and sexual selection, 142-143 on tree of eukaryotes, 67 Fitness eukaryotes. See also Protists fecundity, 13, 15-16, 134, 137, 173, 174, convergent evolution in, 68-69 175, 184, 185, 186, 193, 201, 203, 204, nuclear gene expression, 74 217, 218, 220, 232, 245 phylogenetic diversity, 3, 67 hybrids, 51, 52 tree, 67 mate choice and, 166, 213, 214-215, 216- european badger (Meles meles), 102-103 217, 219-221, 224-227 european otter (Lutra lutra), 102-103 migrants, 15 evolution, generally offspring viability, 166, 178, 184, 217, arms races, 297-298 218, 220, 232, 321 of language and culture, 350-352 peaks in directed protein evolution, moral purpose of, 264-265, 295-296, 297, 156-157, 159 298, 310-312, 329, 330, 332-340

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Index / 40 productivity, 131, 134, 136, 142, 145, 146, Gasterosteus wheatlandi, 56 217, 218, 220, 232, 334 Gene expression, 66, 73-76 sex differences, 214-218 Gene flow Flavanone-3-hydroxylase, 34, 35, 36, 37, 38, assortative mating and, 50 39, 40, 41, 42 domestication and, 92 Flavonoid pathway, 27, 32-33, 35, 39-42, ecological speciation with, 2, 3, 5, 6, 7, 43, 44 9-12, 15, 16, 19-23, 24-25, 50, 53, 56, Flavonoid 3′-hydroxylase, 35, 36, 37, 38, 59-62, 64 39-40, 42 as homogenizing force, 10, 11 Flavonoid 3′5′-hydroxylase, 35, 36, 38, in parallel selection, 53, 56, 59, 60 39-40, 42 and recovery from selective harvest of Flower color evolution wild populations, 146-147 Aquilegia, 32-44 transporter hypothesis, 59-62 carotenoid pigments, 34 Gene index, 27, 39, 40, 41, 43 flavonoid biosynthetic pathway, 34, 35, Genetic analysis of speciation 36, 39-42 adaptive radiations, 27-28, 27, 28, 29, 30, genetics of adaptation, 34-37 42-45 Mimulus, 29, 51 Aquilegia flower color, 2-3, 27-28, 32-37, model, 37-38 39-42, 44-45 molecular dissection, 42-44 cats, 101, 104-106 pollinator preferences, 29, 51 Dobzhansky-Muller incompatibilities, trends, 35-37 6-7, 22-23, 24, 25, 53-54, 295 Flowering plants ecological speciation, 2, 5-6, 11, 12-13, anthesis, 31, 44 19-22, 47, 49, 49-51 cross-pollination, 195, 196, 251 Fst outlier analysis of genomic regions, dioecy, 195, 196, 210, 211 12-19, 21, 23-24 gynodioecy, 195, 196 hybridization and, 29, 30 heterochrony, 44 magnifying glass (population) intrasexual conflict, 196-197, 260 approach, 2, 7-8, 10, 26 mating systems, 166, 191, 192, 195-197 pea aphids, 10, 13-17 morphology of flowers, 196 population-level, 7-8 nectar spurs, 30, 31, 34, 44 spyglass (retrospective) approach, 2, 5, orientation of flowers, 31-32, 34, 44 6-7, 17, 22, 23-24, 26 outcrossing, 195-196, 210 Genetic compatibility model, 179, 180 petal spur length, 30, 31, 34, 44 Genetic drift, 20, 59, 318 pollinator preferences, 29, 30 in adaptive protein evolution, 150, 153, self-incompatibility, 195, 196 159, 160, 163 selfing, 195-196, 210, 260 divergence by, 2, 10, 22-23, 24, 25, 160 sexual selection, 191, 192, 195-197, 209- gene flow and, 10 212, 243, 260-261 genomic effects, 10 Fodor, Jerry, 346 human activities and, 100 Ford, e. B., 295 mate-choice evolution, 179 Forest elephant (Loxodonta Africana), 102, neutral, 10-11, 150, 153, 159, 160, 163 130 rapid, 153 Forest horse (Tarpan) (Equus ferus), 94, 98- Genetic linkages 99, 102-103 interrace disequilibrium, 14, 16, 21, 23- Fst outlier analysis, 12-19, 21, 23-24 24, 25 performance and mating, 9 selective sweep, 14 G Genital evolution, 243, 248-249, 250-253 Genome Galapágos islands, 2, 28, 280, 332 hitchhiking regions, 17-19 Galileo, xv, 329 sequencing, 44, 124

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40 / Index Ghiselin, Michael, 283, 338 hitchhiking Glass sponges (hexactinellidae), 210 divergence, 2, 5, 6, 14-19, 21-22, 23-24, Goats (Capra hircus), 94, 96-97, 102-103 25, 153 Goethe, Johann Wolfgang von, 331 selective sweep, 15 Goitered gazelle (Gazella subgutturosa), hodge, Jonathan, 288, 289, 304 102-103 hodges, scott A., 2-3, 27-45 Golden jackal (Canis aureus), 102-103 hofstadter, Douglas, 352 Gorillas, 93, 284-285, 297 honeycreeper birds, 28 Gould, stephen J., 297, 298, 303, 307, 337 horse (Equus caballus), 85, 98-99, 102-103 Gowaty, Patricia Adair, 166, 213-241 house mouse (Mus domesticus), 96-97, 102- Gray, Asa, 294, 301, 322, 336, 341 103, 106 Gray mouse (Mus musculus), 96-97, 102-103 house sparrow (Passer domesticus), 96-97, Gray wolf (Canis lupus), 96, 99-101, 102 102-103, 106 Green alga, 66, 77 hubbell, stephen A., 166, 213-241 Greg, richard rathbone, 339 human evolution, 115, 284-285, 290, 310, grnAs, 79, 81 311, 322-323 Group selection hypothesis, 202, 310-311, humboldt, Alexander von, 331 334, 338-339 hummingbirds, 31, 34 Grunion, 210 hunting Gryllus, 257 bighorn sheep, 140-141 Gulf pipefish (Syngnathus scovelli), 182, 183 deer, 138, 140, 143 fox, 139 game, 137 H genetic effects of, 138-141 natural mortality, 134 habitat choice, 10, 11, 13, 15, 16, 19, 58 no-take protected areas, 147 habitat degradation, 132 selection effects, 86, 129, 130, 134, 137- haeckel, ernst, 294, 304, 305, 341 141, 142, 143 haldane, J. B. s., 139, 292 sexual selection, 130, 137-138, 142, 143 hard, Jeffrey J., 86-87, 129-147 trophy, 130, 137, 138, 140, 147 harvest of wild populations. See also huxley, Thomas henry, 288-289, 290, 292, Fishing/Fisheries; hunting; 293, 294, 296, 298, 301, 302, 303, 341 Unnatural selection hybrids/hybridization and intensity of sexual selection, 136, Dobzhansky-Muller incompatibilities, 143 53-54 management challenges, 132, 141, 145-146 fecundity, 16 and mate choice, 142-144 fitness, 51, 52 recovery from, 146-147 genetic dissection of traits, 29, 30 specimen collection, 141 Mimulus flower color studies, 29 sustainable, 131, 132, 134, 146 selection against, 13, 14, 16, 19, 260-261 haw fly, 54 sterility genes, 18, 22 hawaiian silversword, 28 vigor, 51 hawkmoths, 31-32, 34 hypotheses Helianthus paradoxus, 50 consistency with commonly accepted Heliconius butterflies, 50-51 hypotheses and theories, 277-278 hemoglobin, 150, 312, 318 explanatory value, 276-277 hempel, C. G., 274, 299 falsifiability, 178-179, 283-284, 326 hennig, Will, 326 imagination and corroboration, 274-276 herschel, John F. W., 293 internal consistency, 276 heterochrony, 44 law of likelihood, 316-318 heteroloboseans, 68 revolutionary examples, 277 heterosis, 51 testing, 276-279

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Index / 40 hypothetical-deductive method, 263-264, intrasexual conflict 273-276, 282-285 female-female combat, 172, 215 male-male combat, 140, 166, 172, 173, 184, 212, 214 I in plants, 196-197, 260 sexual dimorphism and, 192 ichneumon (Herpestes ichneumon), 102-103 sperm competition, 166, 194, 198, 243, iltis, hugh, 114 244, 247, 255, 256, 257, 258 indian elephant (Elephas maximus), 102-103 invasive species, 132 indirect-benefits models, 177-179, 217, 218 Ipomoea, 37 individual selection, 310 isi Web of science, 29 induction and empiricism, 263, 264, 267, 268, 269-271, 272-273, 275, 276, 283, 293 J intelligent design, 296, 308, 325, 346, 354 intensity of sexual selection Jacob, François, 272, 275, 276 Bateman gradients, 184, 185, 186, 187- Jefferson, Thomas, 331 188, 192, 193, 197, 201 Jevons, William stanley, 274 crowding of sexual receptivity, 191, Joint Genome institute, 44 208-209 Jones, Adam G., 165, 169-190 Darwin’s perspective, 163, 182-183, 192 Judson, olivia, 265-266 ecological factors, 185-187, 197, 204, 208, Jungle cat (Felis chaus), 102-103 209 environmental potential for polygamy, K 185, 186, 197, 204, 208, 209 harvesting of wild populations and, Keeling, Patrick, 3, 65-84 136, 143 Kekulé, Friedrich, 275 lineage differences in color and Kin selection, 311 morphology and, 171, 182-183 Kinetoplast DnA, 78, 80 mate searching algorithms and, 186 Kinetoplastids, 66, 67, 73-76, 77, 78, 79, 80, mating differentials, 184, 185-187 81-82 multiple mating rates, 187, 194, 215 Kitlg gene, 56-57, 59 nuptial gifts and, 187 Kuhn, Thomas, 288, 299, 301, 302, 303 parental investment theory, 185, 187, 192, 198, 201-202, 203-204, 215-216, 218, 232, 243 L research advances, 169, 183-184, 189 research needs, 188-189, 190 lactamase enzyme, 158 secondary sexual characteristics, 182 lactonase enzyme, 160 selection coefficients, 184-187 lake Malawi, 28 sex difference in opportunity for lake victoria, 28, 54 selection, 191, 202-204, 208 lake whitefish (Coregonus clupeaformis), sex ratios and, 142-143, 186, 188, 194, 14, 51 197-201, 203, 204, 206-208 lamarck, Jean Baptiste de, 308, 332, 336 sex-role-reversed taxa, 193, 204, 205 lamarckism, 292, 308, 311, 332 sexual conflict and, 187, 201 land snail (Helix pomatia), 141 sexual dimorphism and, 166, 171, 182- lankester, e. ray, 294 183, 192, 210 largemouth bass (Micropterus salmoides), spatial and temporal distribution of 136 matings, 192, 204-208 leafy sea dragon (Phycodurus eques), 182 intersexual selection. See Mate choice; leander, Brian, 3, 65-84 Postcopulatory sexual selection Leishmania, 66

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40 / Index leopard (Panthera pardus), 102-103 assortative mating, 9, 10, 25, 50-51, 54, lepidoptera, 256 58, 89, 107, 108, 174-176 Lepocinclis, 67 condition-dependent indicator (good Leptomonas, 67 genes) model, 178-179, 180, 217 lewes, G. h., 314 condition-independent indicator model, lewontin, richard, 297, 303 179, 180 lion (Panthera leo), 102-103 costs of, 181, 219 lloyd, lisa, 297 Darwin-Fisher model, 174-176 lock-and-key hypothesis, 251, 253 Darwin’s view, 169, 173-174 lukeš, Julius, 3, 65-84 direct-benefits models, 176-177, 180 lyell, Charles, 315, 332 divergent selection for, 25, 50 lysins, 258, 261 ecological constraints, 9, 10-11, 25, 50, 166, 216 empirical examples, 176 M Fisherian model, 177-178, 180 fitness distributions, 166, 213, 214-215, Macdonald, David, 85-86, 89-109 216-217, 219-221, 224-227 Maize (Zea mays ssp. mays) domestication genetic compatibility model, 179, chromosome morphology and number, 180 114 harvesting of wildlife and, 142-144 data analysis, 126-127 indirect-benefits models, 177-179, 217, evolutionary process, 86, 116-119 218 flowering time, 119 latency in mating, 166, 213, 215, 216, genome diversity of teosinte, 111, 219, 220, 225, 226, 227, 229, 234, 235, 115-116 236, 237-238, 240-241 genome sequencing, 124 ornaments and fancy traits, 173, 175, hapMap, 124 177-178, 179, 180, 181, 186, 189, 214, kernel oil content, 119 217-218, 232-233 landrace collections, 124 parental investment theory and, 232 large-effect vs. small-effect loci, 112, plant mating systems, 197-198 116-119 progress in research, 169, 174, 180, morphology, 86, 112-113, 116, 117-118 189 origins, 86, 112-115, 117, 118-119 reproductive compensation hypothesis, plant materials and DnA sequencing, 217 125-126 research needs, 181, 190 QTl analysis, 116-117, 118, 119 sensory exploitation model, 179, 180 research needs, 111, 123-125 sex ratios, 198, 213, 225-226 selective sweep on chromosome 10, 86, sex role behavior and, 214-218, 231-232, 111, 119-123, 125-127 233 starch biosynthesis, 118-119 sexual conflict model, 179-180 Teosinte hypothesis, 114-115, 116 survival probability, 166, 178, 213, 214, tomato domestication compared, 116 215, 216, 219, 225, 226, 228, 234, 236, Tripartite hypothesis, 113-114, 116 240, 241 yellow color, 123 switch point theorem, 166, 218, 219-241 Male-male combat, 140, 166, 172, 173, 184, time available for mating and, 166, 213, 212, 214, 246, 247-250 219, 227, 230 Malthus, Thomas robert, 293, 332 Mate searching algorithms, 186 Mangelsdorf, Paul, 113, 114 Mating Marbled polecat (Vormela peregusna), compatibility measurement, 55 102-103 differentials, 184, 185-187, 214-215, 231, Mate choice 249-250 anisogamy theory, 231-232 ecological factors, 185-187

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Index / 40 latency, 166, 213, 215, 216, 219, 220, 225, Monophyletic clades, 2, 20, 28, 29, 39, 59, 226, 227, 229, 234, 235, 236, 237-238, 66, 107 240-241 Morgan, lloyd, 338 mass, 210 Morris, simon Conway, 298, 346 multiple mating rates, 187, 194, 215 Mouflon (Ovis orientalis), 94, 96-97, 102-103 spatial and temporal distribution, 192, mrnA, polycistronic processing, 74-76, 204-208 81, 82 time available for, 166, 213, 219, 227, 230 Muller, h. J., 6 Mating system analyses Multidimensional scaling analysis, 60, 62 animal, 166, 191, 192-193, 197-200 Museum d’histoire naturelle, 298 common ground for plant and animal Mutations systems, 209-212 beneficial, 52, 149, 151, 153-154, 156, covariance methods, 201-202 157, 158-160, 161, 162 crowding of sexual receptivity, 191, color variation in flowers, 37-38 208-209 deleterious, 52, 76, 117, 151, 153, 156, Darwin’s contribution, 166, 191, 192, 157, 158, 161, 162, 312 194-195 divergent selection under, 49 mass matings, 210 duplications, 30, 39, 76, 83 molecular markers, 165, 189 gain of function, 36 plant, 166, 191, 192, 195-197 global suppressor, 158 quantitative methodology, 191, 192, loss-of-function, 29, 35-37, 38 201-212 neutral, 87, 149, 151, 153, 156, 157, 158, research needs, 188 159-160, 161, 162-163, 252, 312, 318, sex difference in opportunity for 324 selection, 191, 202-204, 208 parallel selection, 53 spatial and temporal distribution of pleiotropic, 52 matings, 192, 204-208 selective sweeps, 14, 15, 24, 117 Mayr, ernst, 6, 48, 251-252 speciation by, 47, 49, 52, 53, 63-64 Maximum likelihood methods, 30 stability-mediated epistasis, 87, 149, Memes, 351 157-159, 162 Mendel, Gregor, 34, 273, 274 substitutions, 22, 30, 81, 150-151, 154, Menidia menidia, 147 159, 160, 161, 162, 163, 285 Mesolithic, animal domestication, 89 transpositions, 30 Mice, 51, 96-97, 102-103, 106, 176, 217, 227 Myoglobin, 150 Migration/migrants, 13, 15-17, 19, 49-50 Myzocytosis, 77 Mill, James, 338 Mill, John stuart, 263, 268, 272 N Milton, John, 340-341 Mimulus nagel, Thomas, 346 M. aurantiacus, 37 narwhals, 172 M. cardinalis, 29, 51 natufians, 95 M. guttatus, 51, 53 natural selection M. lewisii, 29, 51 codiscovery claims, 290-291 Miniexons, 73-74, 82 and common ancestry, 264, 312-315, Minimum-evolution principle, 326 321-328 Mitochondrion, 78-82 and complexity, 308-309, 325 Mockingbirds, 2, 28, 332 Darwin’s legacy, xvi, 1-2, 28, 48, 214, Molecular clock, 162 271, 275-276, 280-284, 293, 296, 312- Molecular markers, 165, 189 328, 334-340 Molecular phylogenetics, 29 defined, 91, 214 Monkeyflowers, 29, 37, 51 and domestication, 86, 89, 91, 96-99, 100

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40 / Index genomic effects, 10 Pandalid shrimp, 210 group selection hypothesis, 310-311, Parallel selection 334, 338-339 with gene flow, 53, 56, 59, 60 individual selection, 310 mutations, 53 as intelligent and moral force, 264-265, of reproductive isolation, 53, 54, 55, 56, 295-296, 297, 298, 310-312, 329, 330, 59, 60, 63, 64 332-340 threespine stickleback, 55, 56, 59, 60, 63 intensity, 136 Parasperm, 256-257 process in ecological speciation, 8-9 Parental investment theory, 184, 185, 187, “random” variation, 309 192, 198, 201-202, 203-204, 215-216, sexual selection combined, 132, 136, 218, 232, 243 165, 171, 248 Parker, Geoff, 244-245 stabilizing, 9, 22, 52, 154-155, 158, 159, Pascal, Blaise, 273 162-163 Pasteur, louis, 274 “survival of the fittest,” 308 Pauling, linus, 150, 151, 161 tree thinking, 328 Pea aphids, 10, 13-17, 50, 51 uniform or balancing, 9, 20, 25, 48, 22-23 Peacocks, 165, 178, 214, 250 neolithic Peirce, Charles s., 274 domestication of animals, 86, 89, 90, 93- Pelargonidins, 33, 35, 36, 38 98, 106, 107-108 Penrose, roger, 346 preadaptive features of fauna, 102-103 Peranema, 70, 71 neutral theory of evolution, 66, 69, 81-82, Persian fallow deer (Dama mesopotamica), 83, 120, 122-123, 162 102-103 newton, isaac, xv, 269, 274, 275, 329, 343 Persian onager (equus hemionus hemippus), newton’s laws, 270 102-103 newtonian mechanics, 277, 283, 304 Petunia, 36, 40-41, 42 Nicotiana tobacum, 36, 38 P. axillaris, 36 nubian wild ass (Equus asinus africanus), Phacus, 70 98-99, 102-103 Phosphotriesterase enzyme, 160 nuclear genome characteristics, 73-76 Photoreceptors, 72 nuptial gifts, 187 Photosynthesis, 67-68, 73 Phylogeny Aquilegia, 33 O disciplines contributing to, 284 minimum-evolution principle for o’Brien, stephen J., 85-86, 89-109 inferring, 326 Odysseus (Ody) gene, 18 tree thinking, 328 offspring viability, 166, 178, 184, 217, 218, Pig (Sus domesticus), 94, 96-97, 108 220, 232, 321 Pigeon (Columba livia), 85, 96-97, 322 oken, lorenz, 288 Plantinga, Alvin, 346-348, 353 opsin gene, 54 Plants. See also Flowering plants orangutans, 285 herbivore resistance, 36 orchids, xv, 271, 282, 283, 284, 303 Uv protection, 36 osborn, henry Fairfield, 288, 294 Plasmodium, 67 outcrossing, 195-196, 210 Plastids, 67, 77-78 Oxyrrhis, 80 Plato, 289, 296 Pleiotropy, 10, 25, 36, 42, 50, 51, 52, 64, 161, 251-252 P Pleistocene, 93, 94, 96 Ploeotia, 70 Paley, William, xvi, 281, 282, 325 Polar bears, 93, 308, 323 Pan-editing, 83 Pollinators, 31-34, 44, 51

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Index / 4 Polycistronic mrnA processing, 74-76, 81, Protoperidinium, 67 82 Provine, William, 289 Polygamy, environmental potential for, 185, Pundamilia neyereri, 54 186, 197, 204, 208, 209 Pundamilia pundamilia, 54 Polykrikos, 70, 71 Polyploidy, 9 Q Polyspermy, 258 Popper, Karl, 274, 283, 326 Quantitative methodology, mating system Population genetic theory, 115 analysis, 191, 192, 201-212 Population pressure, 332 Quantitative trait loci analysis Postcopulatory sexual selection ecological speciation under divergent analysis of effects of, 205 selection, 11, 12, 13, 14-25, 50 courtship behavior during and after flower color, 43, 44, 51 copulation, 243-244, 253-255 maize origins, 116-117, 118, 119 cryptic female choice, 166-167, 243, 244, 245, 247-248, 249, 250, 252, 256-257, 258, 259, 260, 261 R Darwin’s omission, 166, 244-245 defined, 171 ratterman, nicholas l., 165, 169-190 egg-sperm molecular interactions, 243, red alga, 77 257-260 red clover, 13-17 evolutionary consequences, 243, 250-261 red deer (Cervus elaphus), 102-103, 138, female effects on male-male 140, 143 competition, 246, 247-250 red fox (Canis vulpes; Vulpes vulpes), 102- flowering plants, 243, 260-261 103, 139 free-spawning species contrasted, 258 reeves, robert, 113, 114 genital evolution, 243, 248-249, 250-253 reproductive compensation hypothesis, 217 male contact organs, 243, 253, 254 reproductive isolation. See also ecological parasperm, 256-257 speciation and parental investments, 184, 243 assortative mating, 50-51, 89 research needs, 189 behavioral, 89 seminal products, 243, 257 divergent selection to alternate sensory traps, 248-249 environments, 9, 11, 12, 19-22, 28, 29, sexually antagonistic coevolution, 248- 49, 58 250, 252-253, 254, 255, 257, 258-259, Dobzhansky-Muller incompatibilities, 260, 261 6-7, 22, 23, 24, 25, 53-54, 295 sperm competition, 166, 194, 198, 243, Fisher-orr geometric model of 244, 245, 247, 255, 256, 257, 258 adaptation, 52-53 sperm morphology, 255-257 genetics of, 49-53 Proanthocyanidins, 36 immigrant inviability, 15-16, 49-50 Productivity, 131, 134, 136, 142, 145, 146, intrinsic, 51, 52, 53, 63 217, 218, 220, 232, 334 mutation-order speciation, 63-64 Prokaryotes, nuclear gene expression, 74 parallel speciation, 53, 54, 55, 56, 59, 60, Prorocentrum, 70, 71 63, 64 Protein evolution. See Adaptive protein postzygotic, 3, 23, 24, 25, 47, 48, 49, 51- evolution; Directed protein 53, 58, 63 evolution premating/prezygotic, 25, 47, 48, 49-51, Protists. See also Alveolata; euglenozoa 55, 58, 63, 64 convergent evolution in cellular resource-based divergence, 10, 11, 16, 19, organization, 3, 65, 66, 68-73 25 phylogenetic diversity, 3, 82 rice, 112, 123

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4 / Index richards, robert J., 264-265, 288-289, sex roles, 193, 198, 203, 204, 205, 214-218, 329-341 230, 231-232, 233, 255 rnA editing and processing, 66, 73-76, sexual conflict. See also intersexual; 78-83 intrasexual roberts, richard, 277 and intensity of sexual selection, 187, rock dove, 96-97, 322 201 roe deer, 140 mate choice model, 179-180 ROSEA1 gene, 42 sexual dimorphism, 166, 171, 173, 175, 177- ROSEA2 gene, 42 178, 179, 180, 181, 182-183, 186, 189, r2r3-myb transcription factor, 36, 40, 41 192, 210, 214, 217-218, 232-233 ruppell’s fox (Vulpes ruppellii), 102-103 sexual receptivity, crowding of, 191, ruse, Michael, 264, 287-305, 329, 337-338 208-209 sexual selection. See also intensity of sexual selection; intrasexual conflict; Mate S choice; Mating system analysis; Postcopulatory sexual selection sackler, Arthur M., vii-viii. See also Arthur age structure in, 188, 250 M. sackler Colloquium contextual models of multilevel sackler, Jillian, vii, viii selection, 202 salmon, 135, 136, 142, 143, 144-145, 147 Darwin’s legacy, xi, 163, 165, 169, 170- salt tolerance gene, 50 171, 172, 173-174, 182-183, 189, 192, sand cat (Felis margarita), 102-103, 104 193, 214 scarab beetles, 172 defined, 91, 165, 170, 191 schluter, Dolph, 3, 47-64 ecological factors, 185 scientific method. see also hypotheses Fisher’s runaway hypothesis, 202 Darwin’s legacy, 263-264, 267-271, 272, group structure or membership and, 282-283, 318, 323-328 202 hypothetical-deductive method, 263- harvesting of wild animals and, 130, 264, 273-276, 282-285 137-139, 140, 142-145 induction and empiricism, 263, 264, 267, in ecological speciation, 9, 10, 50 268, 269-271, 272-273, 275, 276, 283, lock-and-key hypothesis, 251, 253 293 mechanisms, 172-181 sea urchins, 257, 258, 259 monogamous, 174-175, 176 searle, John, 346 and natural selection, 132, 136, 165, 171, seahorses (Hippocampus), 182, 204 248 sebright, John, 291 plants, 191, 192, 195-197, 209-212, secondary sexual characteristics, 182 260-261 sebright, James, 291 pleitropism theory, 251-252 selective breeding, 108-109. See also polygamous, 100, 183, 185, 186, 197, 204, Domestication 208, 209, 210, 211, 212, 215 Selenidium, 67 precopulatory, 171, 185, 189 self-incompatibility, 195, 196 quantitative approaches, 193-194 selfing, 195-196, 210, 260 research needs, 190 self-splicing introns, 77 sex roles, 193, 198, 203, 214, 215-217, sensory exploitation model, 179, 180 218, 230, 231, 255 sensory traps, 248-249 species isolation hypothesis, 251-252, sex differences 258-259, 260, 261 in fitness, 214-218 sexually antagonistic coevolution, 248-250, in opportunity for selection, 191, 202- 252-253, 254, 255, 257, 258-259, 260, 204, 208 261 sex ratios, 142-143, 186, 188, 194, 197-201, sheep (Ovis aries), 94, 96-97, 102-103 203, 204, 206-208, 213, 225-226 shuster, stephen M., 166, 191-212

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Index / 4 Sialia sialis, 215 fitness distributions, 219-220, 224-225, 232 sickle cell anemia, 150 flexibile reproductive decisions in both singer, Peter, 296-297 sexes, 231 skull sutures, 327 model description, 221-222, 227, 230 sober, elliott, 264, 297, 307-328 number of potential mates, 225-226 social Darwinism, 296 predictability of fancy male traits, sockeye salmon (Oncorhynchus nerka), 136, 232-233 143, 144-145 reproductive time budgets, 219 socrates, xvi results, 224-227, 240-241 Sod gene, 123 sensitivity analysis, 228, 240 spandrels, 318 sex role ecology, 233 speciation. See also ecological speciation survival probability, 226-227, 228 allopatric, 6, 9-10, 20, 22, 23, 24-25, 28, time available for mating, 219, 227, 230 107 Symbiodinium, 67 defined, 15, 48 sympatric speciation, 2, 5, 9, 13, 24-25, 51, error-then-solution model, 83 89, 92, 106-108, 259 mechanisms, 48-49 Syngnathus typhle, 182, 201 models, 48, 54 syrian onager (Equus hemionus hemionus), mutation-order, 47, 49, 53-54, 63-64, 83 102-103 rates, 53, 54 sympatric, 2, 5, 9, 13, 24-25, 51, 89, 92, T 106-108, 259 species isolation hypothesis, 251-252, 258- Taurine cattle (Bos taurus), 96-97, 102-103 259, 260, 261 Temin, howard, 277 spencer, herbert, 270, 291-292, 296, 336, 341 Teosinte (Zea mays ssp. parviglumis). See also sperm Maize domestication competition, 166, 194, 198, 243, 244, 245, chromosome morphology and number, 247, 255, 256, 257, 258 114 morphology, 255-257 Euchlaena classification, 113 spliced leaders (miniexons), 74, 82 genome diversity, 111, 115-116 spliceosomal introns, 74-75 hypothesis, 114-115, 116 sponge shrimp (Spongocola spp.), 210 morphology, 86, 112-113 stability-mediated epistasis, 87, 149, 157- mutation rate, 115 159, 162 peopraphical distribution, 126 standing genetic variation, 3, 47, 49, 58-63, selective sweep on chromosome 10, 86, 64, 64 111, 119-123 steppe polecat (Mustela eversmanni), Teosinte branched1 (tb1) gene, 117-118, 122, 102-103 125 stevens, natalie M., 86, 111-127 Teosinte glume architecture1 (tga1) gene, 116- stramenopiles, 68 117, 122, 123, 125, 127 sunflower, 50 Terrestrial slugs, 210 “survival of the fittest,” 308 Tetrapody, 326-327 survival probability, 166, 178, 213, 214, 215, Thermostable chorismate mutase, 158 216, 219, 225, 226, 228, 234, 236, 240, Threespine stickleback (Gasterosteus 241 aculeatus) switch point theorem assortative mating, 58 alternative to anisogamy theory, 231-232 body size, 55, 58 alternative to parental investment defensive body armor, 55, 56-57, 58-59, theory, 232 62-63 changing more than one parameter at a ecological speciation, 47, 49, 51, 55-63 time, 227, 229 freshwater-marine hybridization, 3 derivation, 222-224, 234-241

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44 / Index gene flow, 56, 59, 60, 62 hunting, 86, 129, 130, 134, 137-141, 142, hybrid fitness, 51, 58 143 male parental care, 204 intensity, 134, 136-137 multidimensional scaling analysis, 60, and management practices, 131, 145-147 62 recovery from overharvesting, 129-130, parallel speciation, 55, 56, 59, 60, 63 146-147 phylogenies of populations and genes, and sexual selection, 130, 137, 138-139, 56-57 140, 142-145 postzygotic isolation, 58 from specimen collection, 141 premating isolation, 55, 58, 63 and sustainability, 129 selection from standing genetic traits likely to be affected, 86, 129, 131 variation, 47, 58-63 skin pigmentation, 56-57, 59 V transporter hypothesis, 59-63 Tian, Feng, 86, 111-127 VENOSA gene, 42 Tigers, 93, 310 via, sara, 2, 5-26 Tomato, 116 virus-induced gene silencing, 43 Toxoplasma, 67 Trans-splicing, 73, 74-75, 76, 78, 81 Tree snails (Liguus and Orthicalus spp.), 141 W Trichocysts, 70, 71 Tripartite hypothesis, 113-114, 116 Wallace, Alfred russel, 271, 290-291, 293- Tripsacum, 113-114, 121 294, 308, 335, 341 T. dactyloides, 122, 126, 127 waxy gene, 123 trnA, 80 Weasel (Mustela nivalis), 102-103 Trypanosoma, 66, 74 Whewell, William, 274, 293, 303 T. brucei, 76, 80, 83 Wild boar (Sus scrofia), 93, 96-97, 102 Turing, Alan, 265, 343, 345-346, 348, 350, Wildcat, 98-99, 101, 102-103, 104-106 353 Wilkes, h. G., 114 2-oDDs gene family, 39-40 Wilson, edward o., 296 Windermere pike (Esox lucius), 137 wingless gene, 50, 51 U Wollaston, T. v., 336 Wright’s island model, 10 UDP flavonoid glucosyltransferse, 34, 35 Uniform or balancing selection, 9, 20, 25, 48 University of Cambridge, xvi, 279, 281, 298, Y 299, 331 Unnatural selection in harvested wildlife yeast, 51 artificial selection compared, 86, 87, 130, young, robert M., 290 135 young earth creationists, 296 Darwin’s legacy, 86-87, 130-131, 132 younger Dryas, 95 defined, 131-132 and dispersal/migration, 131, 143 fishing, 86, 129, 130-131, 134-137, Z 142-143 Zeboid cattle (Bos indicus, Bos primigenius genetic effects on populations, 129, 130, namadicus), 97-98 133, 138-141 Zuckerkandl, emile, 150, 151, 161 history of, 132-141