Index

abiotic environment, 148 ABO blood group, 55 abortion, spontaneous, 118 acacia, mutualism in, 215 acclimatization, 76

acquired immunodeficiency syndrome (AIDS), 283, 288, 290-291. See also human immunodeficiency virus (HIV) adaptation acclimatization compared to, 76 description, 75-76

distinguishing from non-adaptive tract, 76 exaptation, 77 local, 116-117 preadaptation, 77 adaptation, examples of back to the sea animals, 330-331 cave blindness, 329-330 elephants, 331 endosymbiosis, 333 eye, 328-329 photosynthesis, 332 teeth, 327-328

thermal vent organisms, 332-333 trap-jaw ants, 334 vertebrate flight, 333-334 adaptive characters, 17-18 adaptive landscape, 95 additivity, 105, 106 adenine, 41 agave, blue, 155-156 aging, 151, 165, 166 agriculture antibiotic use in, 282 artificial selection, 15, 74 crop history, 21 crop variation, 20

evolutionary processes and, 20-21 quantitative traits, 101 AIDS. See acquired immunodeficiency syndrome allele description, 47-48 dominant, 48, 53 fixation, 86, 90-91 heterozygous, 48 homozygous, 48 linkage and hitchhiking, 78-79 recessive, 48 allele frequency allele fixation, 86, 90-91 founder effects, 94 genetic drift, 86, 89 Hardy-Weinberg equilibrium and,

69, 70-71 hitchhiking effects, 79 allopatric speciation, 118-119 alternative splicing, 241-242 altruism cooperative breeding, 175-177 eusociality, 179-181 kin selection, 169, 179 multicellularity, 181-182 reciprocal, 177-178 amber, 326

Ambystoma mexicanum, 227 amelioration, 278 amino acid, 45, 66 Amish, 94 analogy, 226 ancestral state, 135, 136 anemia, sickle cell, 19 ani, groove-billed, 177 antagonist interaction, 205 antelope co-evolution, 206, 208, 210 pronghorn, 208

antibacterial, 270-271, 272 antibiotic agricultural use, 282 changes in use of, 281-282 description, 270-271 designing new, 277 targets of, 275 antibiotic resistance as adaptation, 75-76, 79 battle against, 277-282 at cellular and biochemical levels, 275 compensatory mutation, 278-279 cost to host, 280

as example of evolution in action, 28-29 by gene transfer, 274-275 history of, 271-272 methicillin-resistant Staphylococcus aureus (MRSA), 276 by mutations, 273-274, 275 partial resistance, 276-277 tuberculosis, 280-281 antibody, 298 antifungal, 270, 272 antimalarial, 19, 270 antimicrobial, 270 antiviral, 270, 272 antlers, 190 ants mutualism and, 215 trap-jaw, 334 appendix, as vestigial organ, 342 apple maggot, 121-122 aquatic vertebrates, evolutionary history of, 330-331 Arabidopsis, 234, 237 Archaeopteryx, 34, 36, 319-320 Archea, 235, 237 argon, 31

Aristotle (philosopher), 126 artificial selection in animal husbandry and agriculture, 15, 74

in laboratory setting, 159

life span experiments, 152-153

in mice for speed, 82

natural selection compared, 74

testing evolutionary theories, 152

asexual reproduction, 68, 184, 195, 196

Asian flu, 306

atomic clock, 31

atoms, isotopes of, 30-31

attractive force, 24

Australopithecus (genus), 255

Australopithecus afarensis, 258-259

Bacillus subtilis, 280 back mutation, 279

bacteria. See also antibiotic resistance Bacillus subtilis, 280 back mutations, 279 backup genome copy, 52 breakdown of polychlorinated biphenyls, 341

chemosynthesis by, 332 commensal, 269

compensatory mutations, 278-279 conjugation, 275 cyanobacteria, 325 Deinococcus radiodurans, 52 DNA location in, 52 endosymbiosis, 333 Escherichia coli (E. coli), 49, 204,

237, 241, 274 Eubacteria, 235, 237 gene transfer, 274-275 microevolution, 12 microfossils, 33, 325-326 Neisseria meningitides, 124 number of genes, 50 photosynthesis, 332 plasmids, 275 reproduction in, 203-204 species concept for, 123-124 Staphylococcus aureus, 124, 269, 276 stromatolites, 324-325 thermal-vent organisms, 332-333 transduction, 275 transformation, 275 balancing selection, 75 Barber, Iain (biologist), 188 base pairs, 49-50

bats evolution of flight in, 333-334 vampire, 177-178 Bayesian analysis, 139 beak size, morphological variation in, 83 bees development, 222 eusociality in, 179-180 beetles, group selection in, 170-172 biogeography, 29, 35, 246-247 biological-species concept, 112 biology, evolutionary, 10 biotic environment, 148 bipedal locomotion, 256, 258, 259 bird flu, 302 birds adaptive characters in, 17 ani, groove-billed, 177 cooperative breeding in, 175-177 evolutionary history of, 34, 36, 318 finches, Galapagos Island, 82-83 group selection in chickens, 172-173 influenza in, 302-305 parental care, 164-165 peacocks, sexual selection in,

185-187, 189 ring species, 114 blood type, 47, 55 body plan, 229-231

Bohannan, Brendan (biologist), 280-281 bottleneck, population, 92-93 Brachiosaurus, 318 breed, 113 breeding in agriculture, 20-21 captive, 93 cooperative, 175-177 nonrandom mating, 70 broad-sense heritability, 106-107 Bull, J.J. (biologist), 217 Burgess Shale, 323-324 Bush, Robin (biologist), 311, 312, 313 butterfly, mate attraction by, 191

C value, 236

CA-MRSA (community associated methicillin-resistant Staphylococcus aureus), 276 cancer, 64, 182 Caribbean tree frog, 228 Case Study icon, 6

cave blindness, evolution of, 329-330 CCR5 receptor, 287, 294 CD4 molecule, as HIV receptor, 287 cell definition of life and, 284 structure, 51-52 cell division, 220, 238 Chao, Lin (biologist), 199-200 character adaptive, 17-18 ancestral, 135, 136 continuous quantitative, 102 Darwin's use of term, 14 definition, 135 derived, 135, 136-137 heritable, 14 homology, 137 homoplasy, 137-138 non-continuous quantitative, 102 polarizing, 135, 136, 139, 140 cheetahs co-evolution, 206, 208, 210 directional selection for speed, 75 genetic differences, 55-56 genetic drift effects, 86, 90 phenotypic differences, 54 chemosynthesis, 332 chickens advancements in breeding, 20 group selection in, 172-173 chimpanzees as HIV-1 origin, 289, 290 locomotion and posture, 257 phylogenetics, 252-254 chloroplast, 333

chromosome description, 41 HIV integration into, 287 linkage of genes, 78-79, 104 marker gene, 104

non-coding DNA function in, 238-239 nuclear location of, 51 Y, 264 clade, 133 class, 127

classification systems, 126-127 clock atomic, 31 molecular, 244-247 clonal reproduction, 196 clotting factors, 103 clown fish, mutualism and, 206-207 clutch size, 163-165 Cnox genes, 231 coalescence description, 261 in human evolution, 261-263 cocktail, DNA, 43 codon, 42, 45 co-evolution competition, 207-208 definition, 205-206 mutualism, 205-207, 209, 212-215 outcomes of, 209-210 parasites, 208, 213-214, 215-217 plant-animal interactions, 81, 210-215 predation, 208

species interactions, 206-209 Cohan, Fred (biologist), 280 coin toss, as random event, 87, 89 Colorado River, role in Grand Canyon formation, 30 commensal bacteria, 269 commensalism, 207

community associated methicillin-resistant Staphylococcus aureus (CA-MRSA), 276 competition indirect, 191 male-male, 189-192 scramble, 191

sneaky strategy, 192, 193 sperm, 191-192, 193 for sunlight, 207-208 complexity evolution of greater, 22 irreducible, 340 conjugation, 275 conservation applying evolution to, 19-20 captive breeding programs, 93 genetic diversity, importance of, 20, 92, 93 constraint, 80 convergence, 137 cooperative breeding, 175-177 co-receptor, 287 corn, domestication of, 21 cost-benefit analysis, evolutionary, 150 creationism, 343 crops genetic variation in, 20 history of, 21 crustaceans, development in, 226 cultural evolution, 267-268 C-value paradox, 236 CXCR4 receptor, 287, 293 cyanobacteria, 325 cytosine, 41

Darwin, Charles (father of evolutionary theory) artificial selection, 15, 74 biogeographical studies, 29, 35 The Descent of Man, and Selection in

Relation to Sex, 14 descent with modification concept, 14-15, 27

The Expression of the Emotions in Man and Animals, 14 on eye complexity, 340-341 fossil record and, 33 Galapagos Islands and, 35-36, 82-83 life of, 13-14

natural selection concept, 15, 27, 29, 36, 74

orchid pollination, 211 On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 14, 74, 319, 338 speciation, 16-17 darwin-online.org (Web site), 14 dating, radioisotopes, 30-32 Davis, Clara (biologist), 280-281 de Lope, Florentino (biologist), 189 decay, isotope, 31

deep-sea thermal-vent organisms, 332-333 deer antlers, 190 degree of relatedness, 168, 180 Deinococcus radiodurans, 52 deletion, 66-67 dentition, 257, 258 deoxyribonucleic acid (DNA) chromosomes, 41 coding, 240-242 description, 40-41 extraction, at-home, 43 fossil, 34, 245

isolation from mammoths, 42 junk, 50, 51, 253 mitochondrial, 52, 264 mutations, 63-68 Neanderthal, 252, 261 non-coding, 237-240 nucleotides, 41 parasitic, 239 proofreading of, 67 repair of damaged, 67 replication, 42, 63, 67 RNA compared to, 44 sequence, 10 stability of, 34, 63 structure, 41-42 transcription, 44 virus genome, 286 derived state, 135, 136-137 The Descent of Man, and Selection in

Relation to Sex (Darwin), 14 descent with modification, 14-15, 27 deterministic development, 219 deuterium, 31

development definition, 220 deterministic, 219 environmental effects, 221-223 heterochrony, 226-227 Hox genes,229-231 key ideas, 224-229 mutations, 223-224 process, 221 differentiation, 220 Dimetredon, 327 dinosaurs, 34, 317-318 diploid organism, 53, 68, 88 directional selection, 75 disease. See also specific diseases co-evolution in disease systems, 215-217 genetic interactions in, 101 population density, affect of, 266 DNA. See deoxyribonucleic acid DNA polymerase, 42 Dobzhansky, Theodosius (evolutionary biologist), 9 Dodd, Diane (biologist), 122 dog blue merle pattern in, 240 breeds, 113 domain, 127 dominant allele, 48, 53 driver gene, 174 Drosophila. See fruit flies

E. coli. See Escherichia coli, 350 Earth age of, 30-32 plate tectonics, 34 elephant, evolutionary history of, 331 elephant seals male-male competition in, 181 population bottleneck, 93 Eleutherodactylus coqui, 228 embryo, 220. See also development embryonic stem cells, 221 endangered species, protecting, 20 endosymbiosis, 333

Entamoeba histolytica, 235, 237 entropy, 336 environment abiotic, 148 biotic, 148

effects on development, 221-223 effects on fitness, 19 effects on genetic drift, 87-88 effects on life history, 148 effects on phenotype, 54, 221 effects on quantitative traits, 102, 103, 104 effects on speciation, 35-36 environmental variation, 106 enzyme, 42 epistasis, 100-101

erosion, role in Grand Canyon formation, 30 Escherichia coli (E. coli), 274 gene acquisition, 204, 274 genome size, 49, 235

lateral (horizontal) gene transfer, 241, 274 number of genes, 235, 237 O157:H7 strain, 204, 274 periodic selection, 124 Eubacteria, 235, 237 eukaryotes, 235, 237 eusociality, 179-181 evidence of evolution Darwin and, 27 experimental, 28

knowledge of DNA and genetics, 28 measurement of rates of change, 28-29 evo-devo. See development evolution arguments against, 335-343 definition, 27, 73 evidence of, 27-29 rate of, 35 timescales of, 12 evolutionary biologist, 10 exaptation, 77 exon shuffling, 241-242 experiment selection, 153 thought, 166 The Expression of the Emotions in Man and Animals (Darwin), 14

extinction co-evolution and, 210 gene, 12

loss of genetic diversity and, 93 eye evolution of, 328-329 reduction in cave-dwelling organisms, 22, 329-330

fact definition, 26 evolution as, 335-336 theory compared to, 24-25 falsifiable hypothesis/idea, 27 family, 127 feathers on Archaeopteryx, 319-320 evolution of, 77 fecundity, 153, 163 female choice, sexual selection and,

185-189 female-male conflict, 192-195 fetus, 220

Fiers, Walter (molecular biologist), 313 fig, reproduction in, 212-213 finches, Galapagos Island, 82-83 fish clown fish, mutualism and, 206-207 guppies, life-history studies of, 157-160 overfishing, effects of, 160-162 sequential hermaphrodism in, 203 stickleback, sexual selection in, 188 sturgeon, reproductive strategy of, 163-164

swordtails, mating preference in, 188 Fitch, Walter (evolutionary biologist), 311 fitness adaptive landscape, 95-98 consequences of variations in, 62 description, 184

as differential reproductive success, 17 environmental effects on, 19 epistatic interactions, 100-101 inbreeding, effect of, 70

inclusive, 167, 168, 175-176 natural selection and, 17 survival of the fittest, 16 fitness landscape, 95 fixation definition, 86

genetic drift effects on, 86, 200, 243 population size and, 90-91 flies apple maggot, 121-122 biogeography, 246-247 development, 229 developmental mutations, 223-224 divergence of lineages, 122 generation time, 28 genome size, 234 life span, 150-153 male-female conflict, 194 meiotic drive in, 174 non-continuous quantitative characters, 102

number of genes in genome, 50, 234 toxic seminal fluid, 192, 194-195 flight, evolution of, 77, 333-334 flour beetle, group selection in, 170-172 flower color in peas, 53-54 in snapdragons, 53 flowering time, 116-117, 120 flu. See influenza foraminifera, 325 forelimb, length of, 256, 257 fossil amber, 326

Archaeopteryx, 319-320 biological material, 34 Burgess Shale, 323-324 Darwin's collection of, 14 dating, 31 definition, 32 dinosaurs, 317-318 geological stratigraphy and, 30 hallucigenia, 324 hominid, 254-260 mammoths, 320 marine, 34

microfossils, 33, 325-326 missing links, 339 pterosaurs, 320-321 in sedimentary rocks, 32 stromatolites, 324-325 Tiktaalik rosea, 322-323 trilobites, 321-322 fossil record effect of geological processes, 34 incompleteness of, 33 information from, 32-33 microscopic fossils, 33, 325-326 molecular clock and, 245-246 transitional life forms, 35 founder effect, 94-95, 119 frogs, development in, 228 fruit flies biogeography, 246-247 development, 229 divergence of lineages, 122 generation time, 28 genome size, 234 life span, 151-153 male-female conflict, 194 meiotic drive in, 174 non-continuous quantitative characters, 102

number of genes in genome, 50, 234 toxic seminal fluid, 192, 194-195 fruit, seed dispersal and, 81 fungus, 270, 272

Gage, Matthew (biologist), 193 Gagneux, Sebastien (biologist), 280-281 Galapagos Islands, 35-36, 82-83 gametes of diploid organisms, 53, 88 meiotic drive, 173-174 mutations in, 63 nonfusion of, 117

number of variations in human, 89 random pairing of, 88-89

Garland, Theodore, Jr. (evolutionary biologist), 82 gazelles, adaptive characters in, 17 gene additivity, 105 bad,165

definition, 10, 47, 236 driver, 174 duplication, 242, 338 epistatic interactions, 100-101 extinction, 12 linkage, 78, 104 locus, 47 marker, 104

number in genome, 50-51, 237 pseudo-genes, 242 selection level, 173-174 gene expression, 46 gene flow definition, 63

Hardy-Weinberg equilibrium, deviation from, 69 physical barriers to, 118 population structure and, 63 speciation and, 115, 117, 118 variations between populations, 60 gene frequency change in response to change in environment, 12 description, 11 founder effects, 94 measuring changes in, 27, 28 role of chance in, 18 gene splicing, alternative, 241-242 gene transfer evolution via, 274-275 lateral (horizontal), 217, 240-241 vertical transfer, 217, 274 generation time, 28, 244 genetic code description, 45 redundancy in, 13, 18, 66 stop codons, 45 unity of, 127 genetic diversity maintaining, 20 species, 93

genetic drift definition, 85-86 as evolutionary force, 337 fixation and, 86, 200, 243 founder effects, 94-95, 119 Hardy-Weinberg equilibrium, effect on, 70 natural selection effects compared, 90-91 neutral mutations and, 90, 91 neutral theory of molecular evolution, 243

population bottleneck, 92-93 random events and, 86-89 shifting-balance hypothesis, 95-98 in small populations, 89, 92-93 genetic reassortment, 300-301 genetics. See also quantitative genetics description, 39

epistatic interactions, 100-101 genomics, 40 molecular, 40 population, 40 genome base pairs, 49-50 copies of, 52 description, 49 influenza, 300

number of genes in, 50-51, 237 organization, 51 sequencing of human, 50 size, 49-50, 234-236 viral, 285, 286 genomics, 40 genotype in adaptive landscape, 95-96 definition, 54

relationship to phenotype, 48, 54-55, 61 thrifty genotype hypothesis, 223 genotype frequency, 69-71 genotypic variation, 61, 93 genus, 127 geology gradualism, 29-30 plate tectonics, 34 rock types, 32 stratigraphy, 30 Gerhard, Walter, 313 gomphotheres, 81

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