References in italics refer to figures.
abiotic factors, 282, 283, 289, 290, 292, 485
Acoelomorpha, 162
adaptation, 28, 29, 30, 48, 191, 230, 268, 276, 452, 466, 471, 473, 600–601, 691; adaptation environments and time variance, 236; adaptive acclimation, 285–286; biochemical mechanisms informing physiological adaptation, 284; contributions of ancestry, selection, and chance to, 234–235; definition of, 95–96, 194; distinction between group adaptation and fortuitous group benefit, 201–202, 203; evolution and, 231; experimental studies of adaptive evolution, 294–295; frequency and magnitude of local adaptation, 243; gain or loss of function and, 232–233; in the genome, 466–473; as gradual or saltational, 232; is adaptation predictable, 233–234; is adaptation repeatable, 233; is adaptation reversible, 234; limit of, 232; local adaptation, 238, 321, 521; local adaptation and population divergence, 241–245; natural selection and, 193–194; physiological variation and, 283; to population density, 302; as a process, 89, 466; recognition of, 198–199; sex and the acceleration of, 231–232. See also adaptive dynamics; adaptive evolution; adaptive plasticity; adaptive radiation; adaptive zone; biotic environment, adaptation to; character adaptation
Adaptation and Natural Selection (Williams), 201
adaptive dynamics, 628
adaptive evolution, 221, 378, 442, 748
adaptive plasticity, 261–262, 426
adaptive radiation, 486, 559–565, 567, 572, 594, 595, 596; of Anolis lizards, 602; ecological theory and, 560–561; experimental adaptive radiation, 565; future studies of, 565; origin and development of, 560; testing of, 566
adaptive zone, 594
Afradapis fossils, 836
Africa, 186, 241, 311, 761, 805, 807; African Great Lakes, 509, 560; early humans in, 787, 788; equatorial Africa, 803; natural selection in sub-Saharan Africa, 811; traditional societies of, 684, 685
Agassiz, Louis, 19
aging, 718; as adaptation, 720–721; age-specific mortality in the United States, 719; as constraint, 721–722; definition of, 719; examples of long-lived species, 720; genetic architecture of, 725; in humans, 720; limits to the human life span, 724–725; as maladaptation, 721; model systems of, 719–720; question of why males die sooner than females, 725; the wall of death and, 724. See also senescence
agriculture, 814–815. See also domestication, and the evolution of agriculture; Malaysia, agriculture in
AIDS, 7, 8–9, 37, 752. See also HIV
Alcock, J., 636
alcohol dehydrogenase (Adh), 407, 410, 411
algae, 136, 230; algal grazing in fish, 594; charophycean green algae, 144–145; Chlamydomonas reinhardtii, 673; green algae, 139, 145; multicellular algae, 142; red algae, 139; volvocine algae, 673
Allee effect, 288
alleles, 40, 215, 232, 233, 287, 309–310, 328, 340, 345, 458, 529, 547, 801; additive effect of, 688; allele frequencies, 57, 209, 212, 310, 312–313, 472; alleles of human leukocyte antigens (HLA), 736, 739; change in allele frequency (cline), 206, 467; codominant alleles, 46; deleterious alleles, 212; dominant alleles, 46, 253; evolution of sex-specific alleles, 638; frequency-matched alleles, 443; hitchhiking and, 328, 467; inbreeding and, 336; linkage and, 44–45, 331–332; modifier alleles, 156, 260; mutation of to new alleles, 305; natural selection and, 514; neutral alleles, 328, 809; recessive alleles, 46, 212; recombination between multiple alleles, 329; reinforcement and allele mechanisms, 517–518; relatedness and, 697; sorting of into reciprocally monophyletic groups, 85–86, 85; wild-type alleles, 255
allometry, 436; evolutionary constraints and patterns of, 437–438, 440; forewing:hindwing allometry in butterflies, 441
allo-parapatric speciation, 507
allopatric speciation, 20, 489, 496, 504, 507, 508, 509;
allopatry, 87, 238, 520, 551, 555, 559
alternative mating strategies, 643–644
altruism, 197, 200–201, 202, 677, 678, 710, 723; fraternal cooperation and true altruism, 673; problem of, 215–216, 788; reciprocal altruism, 219; reproductive altruism, 697; spread of, 204
Alvarez, Luis, 582
Ambulacraria, 162
amide utilization, experimental evolution of, 233
amniotes, 33, 174; origins of, 176–177; representative skulls of, 177
amoebae, 136, 138, 218; farming amoebae, 141; Paulinella amoeba and photosynthesis, 141; Radiolaria, 141
amphiphile, 120
amplified fragment length polymorphisms (AFLPs), 552
anagenesis, 564
analysis of variance (ANOVA), 460, 461
analysis of molecular variance (AMOVA), 802, 803, 804
anamolocaridids, 168
anapsids, 174
ancestral areas, 75; inferring ancestral areas, 78–79, 105
ancestral state, 100; ancestral state reconstruction, 51, 57–58, 101–102
ancestry: common/shared ancestry, 33–34, 107; least universal common ancestor (LUCA), 128; most recent common ancestor (MRCA), 128, 130, 132; traces of in fetal mammals, 34
ancient DNA, 475; ancient genomes, 479–480; ancient population genetics, 477–479; beginnings of, 475–476; future of, 480; importance of being clean and, 476–477; molecular phylogenies and, 477
aneuploidy, 397
angiosperms, origin and diversification of, 147–148
animals: animal diversity, 165; animal personalities, 302; animal phylogeny, 160–163; bilaterian animals, 160, 162; coevolution of land plants with animals, 149–150; complexity of, 576–577; divergence in animal courtship songs, 545; elements of animal communication, 655–657; evolutionary relationships of major animal phyla, 161; examples of commonality among, 610; examples of transgenerational epigenetic effects in, 424–425; hermaphroditic organisms/animals, 340, 341, 360; invertebrate animals, 464; origin of animal phyla and the Cambrian explosion, 159–160; reliability of animal communication, 660–661; SYR genes in, 389
Annelida, 170
Anolis lizards, 61, 179, 442; leg lengths of, 225; radiation of Anolis lizards in the Lesser Antilles, 537, 560, 602; speciation of Anolis lizards in the Greater Antilles, 509; toepads of, 33–34, 33
antibiotics, 727–728, 734, 777; antibiotic production, 735; definition of, 747; development of tylosin, 778; future of, 752–753; importance of, 747–748. See also antibiotics, resistance to
antibiotics, resistance to, 7, 37, 728, 747–748; compensatory evolution and, 751; coselection of resistance genes, 750; cost-free resistance, 750–751; dissemination of resistant bacteria, 749–750; fitness-enhancing resistance, 751; minimum inhibitory concentration (MIC) and, 747, 750; origins of antibiotic-resistance mechanisms, 748–749; persistence and reversibility of resistance, 750–751; plasmid persistence and, 751; slowing or stopping resistance evolution to antibiotics, 751–752
ants, 171, 172, 216, 217, 219, 395, 531, 669, 698, 702, 729; agriculture in ants, 763–764; army ants, 215, 671; communication in, 656; cultivation of fungus for food by, 541, 671, 672, 729; defenses of, 701; division of labor in ant colonies, 697, 699, 700–701; intergroup conflict among, 701–702; leaf-cutter ants, 152, 157–158, 215, 539; tunnel systems of, 215
Apoprotein-E (ApoE), coronary artery disease and, 815
aptamers, 774, 775, 776; aptamer selection experiment, plate 5
Aquinas, Thomas, 817
Arabidopsis: A. lyrata, 352; A. thaliana, 326, 346, 352, 407, 423
Archaea, 127, 129, 130, 137, 138, 350, 380; halophilic Archaea, 129, 132–133; Igniococcus, 129; mesophilic Thaumarchaeota, 129; Methanococcus paludis, 131; Methanosarcina, 134; Nanoarchaea, 129; paraphyletic Archaea, 131
Archaeopteryx, 31
archegonium, 145
Ardipithecus, 56; A. kadabba, 184; A. ramidus, 184
Aristotle, 11
Arnold, Steve, 227
Arthopoda/arthropods, 3, 165, 563; evolution of, 167–168, 169; life history specializations of, 172–173; phylogenetic framework of, 168–171; protoarthropods, 168; shared features of, 168
artificial selection, 8, 22, 230, 436, 440, 610, 618, 620–621, 760, 761, 764; agriculture and, 222, 247; ancient artificial selection, 46; in fruit flies, 718; process of, 762; rapid responses to, 442
Ascomycota, 155, 156, 157, 158
Ashfall Fossil Beds, 115
Asia: East Asia, 186; Southeast Asia, 761, 788, 810; West Asia, 187, 324
assortative mating, 512, 520, 522
ATPase/ATPsynthase, 127, 130, 132
Augustine, 817
Australasia, 187
Australia, 80, 301, 788; mammals (marsupials) of, 36
Australopithecines, 183, 184–185; Australopithecus afarensis, 185; Australopithecus africanus, 185; Australopithecus bahrelghazali, 185; Australopithecus robustus, 185; Australopithecus sediba, 186
autosomes, 40, 311, 348, 388, 389, 390, 394, 544, 556, 638–639; gene trafficking of sex chromosomes and, 409–410; ratio of sex chromosomes to (X:A ratio), 395–396
Avise, John, 56
bacteria, 127, 129–131, 137, 138, 230, 380, 749, 797; Actinobacteria, 130; Agrobacterium, 130; Alphaproteobacteria, 130, 131, 137; bacterial lineages, 129–130; Betaproteobacteria, 130; Bifidobacterium, 130; Buchnera, 675; Campylobacter jejuni, 751; Chlamydiae, 130; Clostridia, 130; Cyanobacteria, 130, 134, 140–141; dangerous strains of (Mycobacterium tuberculosis and Staphylococcus aureus), 728, 749; Deltaproteobacteria, 130; Desulfovibrio vulgaris, 131; dissemination of resistant bacteria, 749–750; Epsilonproteobacteria, 130; Firmicutes, 130; Haemophilus influenzae, 363; heterotrophic Bacteroidetes, 130; importation of DNA and, 133; Lactobacillus, 130; Mycobacterium, 130; Mycobacterium tuberculosis, 728, 749; Myxobacteria, 130; Nitrospirae, 130; phototrophic bacteria, 130; Planctomycetes, 130; Propionibacterium, 130; Pseudomonas aeruginosa, 218; relationships among bacterial isolates (membership), 754; Rickettsia, 130; secretions of, 217; spirochetes, 130; Staphylococcus aureus (MRSA), 7, 735; Streptococcus, 501; transfer of genetic material between bacterial cells (conjugation), 747; Verrucomicrobia, 130
bacteriophage, 774, 776; Qbeta bacteriophage, 775
Baker, Herbert G., 359
Baker’s law, 359
balanced polymorphism, 24
barnacles, 262
Bateman’s principle, 206
Bayesian statistics, 65–66, 70–71, 72, 73, 79; approximate Bayesian computation (ABC), 87
bees: dance language of Western honey bees (Apis mellifera), 659; sweat bees (Halictus rubicundus), 673, 677
beetles: Ambrosia beetles, 760; burying beetles (Nicrophorus vespilloides), 669, 712; European corn borer (Ostrinia nubilalis), 544; leaf beetles, 515, 552; relationship between Camellia fruits and Japanese weevils, 223–224; same-sex behavior (SSB) in flour beetles (Tribolium castaneum), 716; seed beetles (Stator limbatus), 640; Tribolium beetles, 351, 450
behavior, 6, 610, 695; analysis of (natural variations versus mutations), 612–613; comparative studies of behavior and hormones, 621–622; continuous mating systems and the evolution of behavior, 637–638; definition of, 609; future of behavioral genetics, 614–615; game theory and, 624–630; genes and, 610–611; learned behavior, 6; nature versus nurture theory and, 611; as transaction, 711–712. See also human behavioral ecology
Bell, Charles, 818
Belyaev, Dmitri, 707
Bennettitales, 149
Bergey’s Manual of Systematic Bacteriology (Garrity), 129
Bering Land Bridge, 79
Beringia, 79
Bermuda, 35; examples of native and introduced species in, 37
Bicyclus anynana, 440
bilateria, 159, 162; origins of, 164–165
biodiversity, 138, 191, 489, 559–560; and conservation, 251–252; distribution of, 504
biogeography, 21, 34–35, 48, 75; cladistic biogeography, 76, 77–78; controversy concerning, 80; development of, 76–77; Gondwanan connections and, 79–80; historical biogeography, 75, 76; integrative biogeography, 75; Laurasian connection and, 79; New World connections and, 80; panbiogeography, 77; progress in understanding classical biogeographic patterns, 79–80; vicariance biogeography, 77
Biological and Computing Shared Principles (BCSP), 781
biological species concept (BCS), 24–25, 491, 492, 512, 520
biological systems, 191, 253–255
biometry, 21
biostratinomy, 113; biostratinomic processes, 113
biotic environment, adaptation to: abundance of species and, 302–303; in complex natural communities, 300–301; conflicting selection and community complexity complicating detection of biotic adaptation, 299–301; definition of, 298–299; definition of the biotic community, 298; differences between adaptation to biotic versus abiotic environments, 299; factors influencing, 299; lessons learned from introduced species, 301–302; in simple communities, 300
biotrophs, 152
bioturbation, 115
bipedalism, 278
birds, 107, 323, 494, 505, 563, 569, 594–595, 605, 667; bill shapes and feeding in, 225; brood parasites and, 710; egg dumping of, 668; imposter birds, 713–714; passerine evolution, 597; relationship of Deinonychosauria to, 181; same-sex behavior (SSB) in, 716; sexual isolation and coloration in, 545; utility of feathers for flight and, 96. See also avian (bird) flu; Galápagos Islands, finches of (“Darwin’s finches”)
birth-death model, 567
BLAST (Basic Local Alignment Search Tool), 381
blenny: roughhead blenny (Acanthemblemaria aspera), 86
Blind Watchmaker, The (Dawkins), 833
Blyth, Edward, 17
bootstrapping, 65
bottlenecks. See populations, population bottlenecks
Boyd, Robert, 705, 797, 798, 799
Branchiopoda, 170
breeding, 22–23; breeder’s equation, 224–225; dog breeds and breeding, 7, 18, 37; inbreeding depression, 694; outbreeding depression, 321; selective breeding, 7, 37. See also cooperative breeding; inbreeding
Bridgewater treatises, 818–819
bristletails: tree-dwelling bristletails, 171
Brittan, Roy J., 414
Brook’s parsimony analysis (BPA), 77
Brosius model of retroposition, 407
Brothers Island, 767
Brown, Robert, 102
brown bear (Ursus arctos), right manus of, 36
Brownian motion, 102, 103; Brownian motion process, 72; geometric Brownian motion process, 72, 73
Bryan, William Jennings, 21
bryophytes, 145
Buckland, William, 819
bug: soapberry bug (Jadera haematoloma), 241
butterflies, 531, 533; Canadian tiger swallowtail (Papilio canadensis), 292–293; Heliconius butterflies, 563; Müllerian mimicry in Heliconius butterflies, 453
Caenorhabditis: C. briggsae, 447; C. elegans, 351, 378, 403, 404, 447, 704
Cain, 77
Cambrian era, 29, 68, 117, 168, 170, 577, 584; Late Cambrian era, 581; Middle Cambrian era, 114. See also Cambrian explosion
Cambrian explosion, 117, 167, 564, 829; and the origin of animal phyla, 159–160
Camellia fruits, relationship with Japanese weevils, 223–224
Campylobacter jejuni, 751
Candida albicans, 384
canalization, 261; evidence for, 266; evolutionary significance of, 266; examples of, 262; phenotypic plasticity and, 262–265; selection for, 265–266
canaries (Serinus canaria), 669
cannibalism, 666, 712–713; filial cannibalism, 710; sexual cannibalism, 710, 714–715
Carboniferous era, 148, 171; Late Carboniferous era, 177
Carus, Titus Lucretius. See Lucretius
cats (family Felidae), 14; domestic cats, 93; Florida panther (Puma concolor coryi), 770
causative mutations, phenotypic effects of, 461–462; additive effect, 461; dominant effect, 461; frequency of causative and marker mutations, 462–463; homogeneity of population sample, 443; linkage disequilibrium, 462; multiple testing, 463
Cavalli-Sforza, Luigi Luca, 797
Caytonia, 150
Cech, Tom, 775
Cenozoic era, 79, 116, 117, 148, 172, 575; Cenozoic radiations, 177
centimorgan (cM), 328
centipedes, 94
Central America, 539
Cepea nemoralis, 325
Cephalocarida, 170
Chambers, Robert, 14; as a materialist, 14
character adaptation, 89–90; character evolvability and, 89, 96–97, 97, 99; character similarity test and, 92–93; character variation and Darwinism, 90–91; congruence test and, 92, 93; conjunction test and, 92; evolutionary analysis (testing principles) of character homology and, 91–95; testing hypotheses of, 95–96
character displacement, 242–243, 535
character states, 51, 60; ancestral state reconstruction, 57–58; homologous character states, 61; shared derived character state (synapomorphy), 51; shared derived character state (synapomorphy) versus shared ancestral traits (symplesiomorphy), 58
cheilostomes, 442
Chelicerata, 168
chimpanzees, 58, 184, 331, 414, 704, 812; biological races, 803–804; tool use among, 6, 708, 709
Chlamydiae, 130
choanoflagellates, 138, 159, 161
chromatin, 319, 413, 420; chromatin immunoprecipitation, 413
chromosomes, 91–92, 638–639; chromosomal duplication, 398; chromosomal inversion, 549; chromosomal linkage, 250; chromosomal rearrangement, 353, 555–556; evolution of, 344; ploidy level and, 253; sex chromosomes and speciation, 556–557; trisomy and, 398; unequal crossing-over and, 397. See also sex chromosomes, evolution of
Chytridiomycota/chytrids, 153, 155, 158
cis-regulatory element, 413, 444; cis-regulatory changes, 416; cis-regulatory divergence, 415; divergent expression and, 417
City of God, The (Augustine), 817
clades (evolutionary lineages), 49, 60, 75, 496, 567, 573, 586, 589; apomorphy-based definitions of, 108; bootstrapping and, 65; example of variation within an asexual clade and a sexual clade, 499; examples of, 78; monophyletic group, 51; naming of, 104; node-based definitions of, 108; paraphyletic group, 51; phylogenetic clades, 290; sampling error and, 65; sister clades, 101, 104, 569, 590, 595; statistical support for, 65; stem-based definitions of, 108; trait evolution and lineage diversification in, 104–105, 595–596
cladogenesis, 564
cladograms, 51, 52, 55, 75, 93; area cladogram, 75; general area cladogram, 75
cnidarians, 162; evolution of sensory structures in, 163–164
coalescence, 307, 313–314; analysis of, 85–86
coevolution, 299, 520, 535, 760; antagonistic coevolution, 520; coevolution hot spots, 535; coevolutionary arms race, 733, 736; coevolutionary dynamics, 526–527; escape-and-radiate coevolution, 539–540; examples of, 172–173; geographic mosaic of, 535, 536. See also coevolution, and speciation
coevolution, and speciation, 535; divergence of species and coevolution, 535–536; speciation with character displacement, 536–537
cognition, 703–704, 709; abstract thoughts and, 703, 708; cognitive complexity of human beings, 787; cognitive decomposition, 703, 705; cognitive promiscuity, 703, 708; combinatorial operations and, 703, 708; domestication and, 707; measurement of, 704–706; possibilities and, 706–707; recursive operations and, 703, 708; symbolic expression and, 703
colonization, 294, 352; character displacement during sequential colonization of a habitat, 537
columbines (genus Aquilegia), nectar spur of, 594, 596, 601
combinatorial chemistry, 120, 125
communication, evolution of, 655; acoustic communication in the Lepidoptera, 660; communication systems and adaptation, 524; dance language of Western honey bees (Apis mellifera), 659; definition of communication, 657–658; elements of animal communication, 655–657; examples of evolutionary trajectories, 658–660; origins of communication, 658; oviposition marker pheromones and, 658–659; private channels and, 656; reliability of animal communication, 660–661. See also linguistics, and the evolution of human language
communities, evolution of, 599; definition of communities, 599–600; evolutionary change and, 600–601; functional group of species within a community, 599; neutral community dynamics and, 603
comparative biology, 32–34, 101, 104
compensatory evolution, 747, 751
competition, 16–17, 19, 559, 650; between populations adapting to different environments, 536–537; between siblings, 667; as a driver of speciation, 537–538; reproductive competition and menopause, 724. See also male-male competition; sperm competition
“Concluding Remarks” (Hutchinson), 289, 690
condors: Andean condors (Vultur gryphus), 108; California condors, 309
conflict: conflict and conflict control in fraternal cooperative systems, 674–675; conflict and conflict control in egalitarian cooperative systems, 675; conflict suppression/policing mechanisms, 204; genetic conflict, 347; intergenomic conflict, 485; intergroup conflict and its resolution, 701–702; interlocus sexual conflict, 638; intragenomic conflict, 201, 485; parent-offspring conflict, 663, 667–668; reproductive conflict, 681–682; sexual conflict, 638, 647
conifers, 145, 147, 149, 323, 537–538, 594
conjugation, 127, 132–133, 747
conservation, 326; biodiversity and, 251–252; conservation triage, 766–767; conserving evolutionary history, 768–769; conserving potential for future evolutionary change, 769–770; deep conservation, 434; evolution, genetics, and conservation, 766–768; genomics and, 772; hybridization as a threat to, 770–771; niche conservation, 75–76, 289, 296; population bottlenecks and isolation as a threat to, 771–772
constraint, 247–248, 436, 437–438, 440; constraint due to pleiotropy, 250–251; developmental constraint, 89, 91, 95; evolutionary constraints and patterns of allometry in organisms, 437–438, 440; importance of evolutionary constraint, 252; lack of genetic variation as a constraint, 248–249; tradeoffs and, 249–251
convergent evolution, 455
cooperation, 671, 677, 697; cheating and, 671; conflict and conflict control in fraternal cooperative systems, 674–675; conflict and conflict control in egalitarian cooperative systems, 675; cooperative societies, 678; definition and importance of, 671–672; direct benefits and egalitarian cooperation, 673–674; egalitarian cooperation, 671, 672; evolution of, 630; fraternal cooperation, 671, 672; fraternal cooperation as explained by kin selection, 672–673; fraternal cooperation and true altruism, 673; group enforcement of the common good (policing), 674–675; organismality and, 675–676. See also cooperative breeding
cooperative breeding, 677; direct fitness benefits and, 680; discriminate helping and, 679–680; ecology and evolution of, 677–678; enforced fitness benefits and, 680; evolution of helping, 678–679; harming and, 677; helping and, 677; indiscriminate helping and, 679; individual differences in helping behavior, 680–681; reproductive conflict and, 681–682
Copernicus, Nicolaus, 11; the Copernican revolution and, 819–820
coprolites, 114
copy-number variants (CNVs), 316, 384
cospeciation, 535
covariance, 221, 223; environmental factors and, 227–228
creationism, 825; belief in evolution and, 825; the creation-evolution continuum, 826–829, 826; the dangers of false balance and, 833–834; day-age creationists, 827–828; flat-earthism and, 826; future of, 830; gap creationism, 827; geocentrism and, 826; materialism and, 828–829; old-earth creationists (OECs), 827–828, 829, 830; theistic evolution (TE) and, 828; types of creationists (including non-Christians), 825–826; young-earth creationists (YECs), 826–827, 828, 829, 830
Crenarchaeota, 129;
Cretaceous era, 149; Cretaceous-Paleogene boundary, 150; Cretaceous-Tertiary (KT) boundary, 582; Early Cretaceous era, 148, 178; end-Cretaceous, 581, 582, 833; Late Cretaceous era, 148, 179, 576; mid-Cretaceous flowers, 149–150
Crick, Francis, 609
criminal forensics, 8
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), 127, 133
Croizat, Leon, 77
Cronkite, Walter, 833
crossbills, geographic divergence in, 538
crossopterygians, 175
Crozier’s paradox, 218
crustaceans, 160, 170; decapods, 280
Cuba, 537
cuckoos: feeding behavior of cuckoos (Cuculus canorus), 713
cultural evolution, 795, 797–798; conformist bias and, 798; definition of, 795; definitions of culture, 799–800; memetics and, 796–797; nonhuman cultural evolution, 798–799; prestige bias and, 798; use of information and, 799; what cultural evolution is not, 795–796
cynodonts, 178; Cynognathus, 36; Probainognathus, 31; therapsids, 178
cytoplasmic distorters, 351–352
cytoplasmic male sterility (CMS), 351–352, 352, 354
damselflies: Enallagama damselflies, 602, 603, 604; Lestes damselflies, 602
Daphnia magna, 292; ecological niche of, 290, 291
Darlington, Phillip, 77
Darrow, Clarence, 21
Darwin, Charles, 4, 7–8, 28, 29, 35, 38, 76, 107, 132, 317, 361, 725, 780, 819–820; on animal mating systems, 358, 633; on artificial selection, 761, 762; on the concept of species, 483; discoveries on Tristan da Cunha, 15; discovery of the fossil of extinct ground sloth (Megatherium), 15; education of, 14–15; on eusocial insects, 698; examples of observed evolution by, 37; fossils found by in South America, 36; genesis of publication of On the Origin of Species, 16–17; on the imperfection of the fossil order, 116; influences on, 15; on natural selection, 200, 201, 222, 238, 512, 574, 586, 606, 817; on the organs of extreme perfection and complication, 783; on the principle of inheritance, 782; privately circulated essays of, 17; the problem of heredity and, 17–18; sexual selection theory of, 605, 606, 644, 711; on the struggle for existence, 292; study of finches (Geospiza) by, 38; Voyage of the Beagle and, 15–16, 16, 47. See also Galápagos Islands, finches of (“Darwin’s finches”)
Darwin, Robert, 15
Darwin on Trial (P. Johnson), 829–830
Darwinism, alternatives to, 19, 21–22; evangelical opposition to evolution, 21; isolation and the role of geographic barriers, 20–21; mutationism, 20; neo-Lamarckian view of evolution, 20, 21; orthogenesis, 20, 21
Darwinism, and character variation, 90–91
data patterns, 60
Davidson, Eric H., 414, 434, 435
Dawkins, Richard, 201, 203, 713, 796, 797, 833
De Genesi ad litteram (On the Literal Meaning of Genesis [Augustine]), 821
de Monet, Jean-Baptiste Pierre Antoine (Chevalier de Lamarck). See Lamarck, Jean-Baptiste
De rerum naturae (On the Nature of Things [Lucretius]), 10
De revolutionibus orbium celestium (Copernicus), 819
de Waal, Frans, 708
degeneration, theory of, 14
demographic transition, 683, 688
Descent of Man and Selection in Relation to Sex, The (C. Darwin), 183, 257, 605, 607, 642, 691–692, 789
descent with modification, 19, 29, 33, 36, 38, 100–101, 222, 371, 372
deuterostomes, 34, 162, 164–165
developmental bias, 436
developmental biology, and evolutionary theory, 25–26
developmental constraint, 89, 91, 95
developmental drive, 436
Devonian era: Devonian ecosystems, 149; fossil record of the Late and Middle Devonian eras, 146; global cooling in the Late Devonian era, 148; Late Devonian era, 171, 581; Late Devonian Fram Formation, 176
diagenesis, 113
Dictyostelium discoideum, 153, 218
Diderot, Denis, 12
Die Mutationstheorie (The Mutation Theory [de Vries]), 20
dinosaurs, 9, 107, 477; Deinonychosauria, 181; Ornithischian dinosaurs, 180–181; theropods, 181
diploid, definition of, 340
directed evolution, 774–775; of cells, 777–779; future of, 779; of nucleic acids, 775–776; of proteins, 776–777
directional selection, 206, 208, 225, 239, 240, 512, 513–514
disaptation, 89
disease, 734; Alzheimer’s disease, 813; autoimmune diseases, 736; coronary artery disease, 815; Crohn’s disease, 737; defense mechanisms against, 736–737; diseases caused by mismatches to modernity, 738–739; evolution and, 727–728; germ theory of, 733; Haemophilus influenzae, 363; incidence of infectious diseases, 737; Lyme disease, 130; Mycobacterium tuberculosis, 728, 749; nosocomial infection, 747; Parkinson’s disease, 6–7; pathogens and, 734–736; schizophrenia, 813; Staphylococcus aureus (MRSA), 7, 735; Streptococcus, 501; syphilis, 130; use of penicillin in the treatment of, 752; yaws, 130
dispersal, 75, 288, 509; dispersal kernel, 321; heterogeneity in, 323
disruptive selection, 206, 208–209, 225, 239, 240, 244, 245, 506, 512, 513; negative frequency-disruptive selection, 225
divergence, 470; Bayesian estimation of divergence times, 71–72; cis-regulatory divergence, 415; direction of, 526; divergence in animal courtship songs, 545; divergence hitchhiking, 549, 554; divergence of species interactions, 535–536; divergence time estimation, 70; evolutionary divergence, 7; evolutionary forces responsible for expression divergence, 418–419; genomic island divergence, 549; geographic divergence in crossbills, 538; heterogeneous genomic divergence, 549; local adaptation and population divergence, 241–245; maximum likelihood (ML) estimation of divergence times, 70–71; population divergence, 621; statistical methods for divergence time estimation, 70; synonymous divergence, 468
diversity/diversification, 535, 567, 572, 586; diversification rate hypothesis, 505–506; effect of waterfalls on species diversity, 273–274; influence of genetics on, 606; latitudinal diversity gradient, 505; physiological diversity, 282–283; physiological tolerance and diversity, 283; rates of, 567, 569; timing of diversification, 564–565; trait diversity within a clade, 595–596; variation in diversification rates, 568. See also biodiversity
DNA, 5, 7, 26, 40, 63, 91, 134, 318, 367–368, 382, 609, 775; alignment (aligned data matrix) and, 60; alignment of two DNA double-helices, 328; central dogma of molecular biology and, 42; complementary DNA (cDNA), 398; contaminating DNA, 475; crossover events and, 376; DNA barcoding, 497; DNA-binding proteins, 547; DNA decay, 247, 248, 249, 475; DNA exchange, 506; DNA fingerprint, 754, 755; DNA fragility, 456; DNA libraries, 480; DNA polymorphisms, 610; DNA sequence comparison and the similarity test, 93; DNA sequences, 312, 315, 321, 324, 354, 370, 400, 414, 445, 475–476, 502, 547, 609, 802, 813 (see also quantitative trait locus [QTL]); DNA shuffling, 777; DNA substitutions, 69, 385; DNA synthesis, 319; DNA transfer (conjugation), 127, 132–133, 329; DNA variants, 461, 462; enhancer DNA sequence, 452; in fossil material, 114–115; FOXP2 segment of, 787; genome size and, 375; genomic DNA, 415; inversion and, 452; loss and gain of intronic DNA, 377–378; methylated DNA, 133, 422–423, 425; mitochondrial DNA (mtDNA), 475, 478, 480; mobile DNA elements, 376; mutations in, 444; noncoding DNA, 364, 374, 375, 377–378, 379; nonfunctioning stretches of, 6, 416; nucleotides of, 41; repair of, 316, 319, 329; repair of double-stranded breaks (DSBs), 375–376; repetitive DNA (knobs), 350; replication of, 257, 316, 460, 748; the replicator and, 193; selfish DNA, 96, 374, 378; TE DNA, 350; structure of, 363; transduction of, 747; uptake of free DNA (transformation), 128, 747; uses of in human and microbial forensics, 755–756; variation in the sequence of, 42, 43, 44, 46, 313, 371. See also ancient DNA; cis-regulatory element; plasmids; recombination; transposable elements (TEs)
Dobzhansky, Theodosius, 6, 7, 24, 120–121, 483, 491, 512, 546, 610, 828
Dobzhansky-Muller model (Dobzhansky-Muller incompatibilities), 543, 546–547
dogs: dog breeds/breeding, 7, 18, 37; evolution and domestication of, 706
dolphins, same-sex behavior (SSB) in, 716
domestication, and the evolution of agriculture, 760–761, 764, 811; agriculture as a mutualism, 763; animal domestication, 762; definition of domestication, 761–762; domestication syndrome, 760, 763; evolution and domestication of dogs, 706; evolution under domestication, 762–763; plant domestication, 761–762
dominance, 253; evolution of, 255–256, 256; overdominance, 206, 710; pseudo-overdominance, 345
dosage compensation, 387
Doushantuo Formation, 114, 160
Down syndrome, 398
Drosophila, 172, 245, 251, 265, 293, 329, 348, 353, 377, 409, 494, 545, 550, 555, 556, 704; Drosophila enhancers, 416; D. eyeless, 418; D. mauritiana, 544; D. persimilis, 518; D. pseudoobscura, 24, 207–208, 409, 416, 515, 518; D. sechellia, 446, 544; D. simulans, 544; D. subobscura, 241, 322; D. teissieri, 407; D. yakuba, 407; gene content of, 392–394; genetic studies of, 547; Jingwei gene of, 406, 407; rates of adaptation and, 469; seminal products of, 644; sexual isolation and, 544; sympatric Drosophila, 498; trichomes and, 446. See also Drosophila melanogaster
Drosophila Genome Reference Panel (DGRP), 614
Drosophila melanogaster, 23, 26, 93–94, 210, 285, 319, 337, 351, 353, 416, 418; behavioral genetics of, 612–613; chromosomes of, 329; development of, 411; evolution of senescence in, 273; genetic diversity in, 331; genomic sequence of, 409; organ development in, 440; population size of, 462, 468, 472
Dunnock (Prunella modularis), 323
early diverging animals, 159
Ebola virus, 7
Ecdysezoa, 162
ecological niches, 288–289; complexities of, 291–292; definition of, 289–291; demographic constraints on niche evolution, 293–296, 294; genetic variation in, 292–293; microniches, 23; niche conservation, 75–76, 289, 296; niche response surface, 289, 290; niches evolving in communities, 296. See also Hutchinson niche
ecological opportunity, 561–562, 563, 567, 594
ecological speciation, 105, 243, 485, 535, 599, 601, 602
ecology: ecological theory, 560–561; interactions of with evolution, 274–275. See also human behavioral
ecospace, 579
ecotypes, 512, 514, 516; interbreeding between, 517
Ediacaran fossils, 160
Edwards syndrome, 398
effective population size (Ne), 307, 310–311, 466, 472–473, 771–772
efficient causes, 11
Egerton, Francis Henry, 818
egrets: sibling competition among cattle egrets (Bubulcus ibis), 667
Eichhornia paniculata, 359
Eisner, Thomas, 659
Eldredge, Niles, 116, 203, 589
embryonic development, 14
embryophytes, 145
Endangered Species Act (ESA [1973]), 766, 768
endemism, area of, 75
Endogonales, 155
endophytes, evolution of, 157
endoplasmic reticulum, 137
endosymbiosis, 136, 137; secondary endosymbiosis, 141
Enos Lake, 517
Entomophthoromycotina, 154–155
environment of evolutionary adaptedness (EEA), 690, 694
environmental sex determination (ESD), 387
enzyme electrophoresis, 5
Eocene era, 79
epialleles, 420
Epicurus/Epicureans, 10; legacy of, 11; materialism of, 11
epigenetics, 420, 427, 609, 615; behavioral epigenetics, 614; concept of, 421; epigenetic processes, 423; evolution and, 426; gene regulation and, 421–422; history of, 421; molecular epigenetics, 422–423; transgenerational epigenetic effects (in plants, animals, and humans), 424–425
epinucleic information, 421
epistasis, 195, 227, 328, 473, 543; epistatic selection, 332; negative epistasis, 336; positive epistasis, 336
equilibrium, 206, 208–209; genetic equilibrium, 317; monomorphic equilibrium, 206; Nash equilibrium condition, 627–628; polymorphic equilibrium, 206, 208; punctuated equilibrium, 486, 571, 589
escalation hypothesis, 577
escape from adaptive conflict (EAC) model, 401–402, 403, 405
Escherichia coli, 130, 232, 234, 235–236, 250, 565, 601, 674, 776, 778; lactose metabolism in, 233; mutation rate in, 318; trimethoprim resistance in, 750
Essay on the Principle of Population, An (Malthus), 16–17
ethology, 609
eugenics, 609, 809; genetic engineering and, 814–815
eukaryotes, 29, 34, 48, 69, 144, 152–153, 336, 352, 379, 496, 500, 556; amitochondriate eukaryote lineages, 137; cartoon tree of eukaryote lineages, 140; cytoskeleton of, 136, 137; distribution of photosynthesis in, 139–141; diversity of, 136; eukaryotic genomes composed of mobile DNA elements, 376; eukaryotic microbes, 231; formation of, 674; fossils of, 138; genome diversity in microbial eukaryotes, 141–142; the history of eukaryotic classification, 138; marine eukaryotes, 502; multicellular eukaryotes, 415; origins of, 131, 137; and the origins of multicellularity, 142; parasitic eukaryotes, 352; phylogenetic relationships among, 138; radiation of eukaryote lineages, 138; sexual eukaryotes, 133–134, 497–498, 501; timing of the origin and diversification of, 137–138. See also eukaryotes, major clades of; fungus/fungi, evolution of
eukaryotes, major clades of, 138; Amoebozoa, 138, 139; Excavata, 138, 139; Opisthokonta, 138–139; SAR (Stramenopiles + Alveolates + Rhizaria), 138, 139
euphorbs: Dalechampia vine, 601
Euryarchaeota, 129; thermophilic Euryarchaeota (Archaeoglobi, Thermococci, Thermoplasmata), 129
eusociality/eusocial societies, 215, 669–670, 697–698; caste differentiation and, 700; division of labor and, 700–701; drivers of, 698–700; ecological and life history factors favoring the evolution of, 699; intergroup conflicts and, 701–702; kin selection and, 698–699; role of family structure in, 699
evening primrose (Oenothera lamarckiana), 20
evil, problem of, 817, 821–822
evolution, 3, 817; in action, 36–38; beginnings of, 124–125; combinational chemistry and, 120, 125; contributions of human behavioral ecology to the study of, 688–689; definition of, 4; disbelief of in the United States, 7; evangelical opposition to, 21; evidence for, 28–38; as fact and theory, 38; flexibility of, 440; gene’s eye view of, 202–203; haploidy versus diploidy evolution, 259; human evolution in modern societies, 687–688; interactions between evolution and ecology, 274–275; in the laboratory, 125–126; major evolutionary transitions, 203–204; modern society and, 727–731; mutation and, 316–317, 320, 467; neo-Lamarckian view of, 20, 21; neutral evolution, 374, 378–379; optimization and, 259–260; as a paradigm, 17; parallel evolution, 90, 93, 94, 105, 436, 437, 440–442, 455, 516, 763; as a process (evolutionary process), 3, 7, 8, 9, 57, 58–59, 305–306, 769; punctuated phyletic evolution, 91; rapid evolution, 8, 241, 547; rates of, 486; regulatory evolution, 413–414, 415–416; repeated evolution, 452, 455–456; in response to natural environmental changes, 37–38; social consequences of, 7; in spatially structured populations, 325–326; technology and, 728–729; wet-dry cycles and, 124–125
evolution, as a composite of five different theories, 17, 90; Common Descent, 17, 89, 91; Evolution as Such, 17, 90; Gradualism, 17, 90–91; Multiplication of Species, 17, 90; Natural Selection, 17, 91
evolution, and computing, 780–781; commonalities between evolution and computing evolution, 781; digital evolution, 780; digital evolution in the Avida-ED system, plate 8; digital organisms, 780; evolutionary computation, 780; evolutionary engineering (robotics), 780; experimental evolution and, 780; future of, 785; genetic algorithm form of, 780; growth of, 784–785; how evolutionary biology joined with computer science, 781–783
evolution, future of, 8, 809; future adaptive evolution, 814; future nonadaptive evolution, 811–814; genetic engineering and, 814–815; has human evolution stopped, 810–811; predictions of human evolution, 809–810
evolution, and the media, 832; the Darwinius affair and, 835; evolution and the birth of modern science communication, 832–833; media personalities associated with science, 833; science magazines, 832
evolutionary developmental (evo-devo) biology, 364, 414, 437, 442, 444; future areas of research in, 450; goals of studies in, 445
evolutionary medicine, 733–734; flu vaccines, 735–736; goals of, 736; implications of, 739–740; pathogens and, 734–736
evolutionary psychology (EP), 9, 690–691; application of evolutionary models in, 693–694; Darwinian background of, 691–692; evolutionary alternatives and, 694–695; models of, 691; modern-day program of, 692–693; psychological evidence and, 693
evolutionary stable strategy (ESS), 624, 628, 629
evolutionary synthesis (1930–1940), 4–5, 10, 19, 21–22; first phase, 22–23; second phase, 23–24; third phase, 24–26
evolutionary theory, in the age of molecular biology, 26
exaptation-deregulation-amplification-modification (EDAM) process, 233
experimental evolution, 230, 250
extended spectrum beta-lactamase (ESBL), 748
extinction(s), 3, 288, 586, 599; adaptation to species’ interactions and, 301; background extinction, 580; declining extinction risk, 583–584; definition of, 579; of dinosaurs, 580; drivers of macroevolution and, 584–585; extinction events, 580–581; extinction styles and magnitudes, 580–581; geography of speciation and extinction, 603–604; insertion of extinct species into molecular phylogenies, 477; mass extinctions (“big five” mass extinctions), 118–119, 579, 581–583; mutation and, 320; and orthogenesis, 20; prevalence of, 580; pseudoextinction, 579, 580; rates of, 568–570, 602; recovery of life after extinction, 583; species extinction, 579–580
fecundity, 263, 590; reduction of, 679, 722
felsen measurement, 103
Felsenstein, Joseph, 63, 517, 551
ferns, evolutionary history of, 146
ferrets, 309
figs/fig wasps, interactions between, 538
final causes, 11
finches: Galapagos Island finches (“Darwin’s finches”), 8, 225, 442, 446, 506, 560, 546, 567, 571; Gouldian finches, 649
fish, 280, 300, 605; algal grazing in, 594; bony fish (Osteichthyes), 29–30, 34, 174, 569; cichlid fishes, 441–442, 507, 508–508, 516–517, 545, 560, 561, 563; coelacanths, 567; Devonian fish fauna, 174–175; divergence due to hybridization and, 532; diversification of cichlids, 563; effects of cooling on tropical fish, 283; evolution of antifreeze glycoproteins in, 563; evolutionary success of, 597; fish-tetrapod transition, 175–176; founder effect in lake trout, 308, 310; guppies, 8, 274, 600–601, 603; hybridization and, 531, 533; impact of alewife (Alosa pseudoharengus) on zooplankton assemblages, 601; independent evolution of pharyngognathy in, 278; jawed fish, 30; jawless fish, 29; regulation of osmotic pressure in, 284; stickleback development, 515; threespine sticklebacks (Gasterosteus aculeatus), 243, 524, 537, 546, 553, 557, 601; transition of lobe-finned osteolepiforms to tetrapods, 31–32, 32; visual communication in, 658; Xiphophorus fishes, 95
Fisher, Ronald A., 22, 23, 201, 255, 307, 348, 453, 520, 525–526, 610; fundamental theorem of natural selection, 22, 208
Fisher’s fundamental theorem of natural selection, 22, 208
Fitch, Tecumseh, 705
Fitch, Walter, 736
fitness, 203, 206, 221, 228, 258, 268, 276, 306, 403, 586–588, 627, 687; age-, stage-, and site-specific complications of, 195–196; benefits of direct fitness, 680; condition-dependent fitness, 274; connection of to selection in hierarchies, 197–198; definition of, 194; direct fitness, 677; emergent fitness, 586; enforced fitness benefits, 680; estimation of, 239; fitness-enhancing behavior, 798; of genotypes, 212; heritable variance of, 231; of heterozygous hybrids, 326; indirect fitness, 677; kin selection and inclusive fitness, 196, 202–203, 215, 216, 219, 656, 698; mean fitness, 206, 208, 334; natural variation and fitness in the wild, 620; population fitness and evolutionary stability, 628; reduction in, 720, 751; in relation to load, 339; reproductive fitness, 710, 720; tradeoffs and, 193, 195; units of selection and, 197. See also epistasis; fitness, hypotheses concerning; Hamilton’s rule; inclusive fitness
fitness, hypotheses concerning: group augmentation hypothesis, 680; pay-to-stay hypothesis, 680; prestige hypothesis, 680; skills hypothesis, 680
FitzRoy, Robert, 15
fixation, 206, 367, 368, 369, 371, 466, 492; evolutionary forces acting on the fixation of new genes, 410–410; in a lineage, 406; rapid fixation, 370; of a retrogene, 409
flagellins, 127
flies: abdomens of, 449; African fruit flies, 407; apple maggot fly (Rhagoletis pomonella), 508, 553, 554, 555, 556, 601, 603–604; artificial selection in fruit flies, 719; fruit flies, 6, 7, 724–725; gall midges (Diptera/Heteropeza), 395, 396; interaction of globeflower plants with pollinating flies, 538; stalk-eyed flies (Cyrtodiopsis), 354; wingless fly groups, 172. See also Drosophila
flight, evolution of, 171–172; development of feathers and, 181
floral design, 356
floral display, 356
fluorescence-activated cell sorting (FACS), 774, 776, 777
flycatchers, 545. See Solomon Island
flycatchers Fontaneto, Diego, 500
form and function, evolution of: functional duplication and, 279–280; general principles of, 279–281; key features of life’s functional systems, 278–279; many-to-one mapping of form to function, 280–281; measurement of, 277–278; in organismal design, 276–277
fossils/fossil record, 7, 14, 25, 28, 29–30, 105, 506, 564, 604; appearance of chordates in, 160; body fossils, 112, 114; DNA in fossil material, 114–115; fidelity of and live-dead comparisons, 115; fossil/node calibrations, 67, 72, 73; fossil/sequence information plot, 67; importance of rapid burial for fossils, 113; incompleteness of, 68–69; lagerstätten (fossil deposits with well-preserved soft tissue), 114; living fossils, 567; microfossils, 145; nature of the fossil record, 115–117; stasis and, 437, 442–443; trace fossils, 112, 114; transitions in, 30–32; value of the fossil record, 112–113, 119. See also Phanerozoic eon, marine diversity in; progression; taphonomy
founder effect, 307, 507; examples of in various species, 308–309, 310
French Revolution, the, 11–12, 13, 17, 672
frequency dependence, 196–197, 624–625; negative frequency dependence, 196, 225
frequency-dependent selection, 193, 211; negative frequency-dependent selection, 225
frequency distribution, 221, 223
frogs: cane toads, 301–302; same-sex behavior (SSB) in male toads (Bufo bufo), 716
fruiting body, 152; evolution of the Dikaryon and multicellular fruiting bodies, 155–156
functional morphology, 276
fungus/fungi, 350, 382, 748; age of, 158; Amanita muscaria (fly garlic), 156; barberry wheat rust (Puccinia graminis), 156; Candida albicans, 384; chestnut blight fungus (Cryphonectria parasitica), 156; Chytridiomycota/chytrids, 153, 155, 158; corn smut fungus (Ustilago maydis), 156; cultivation of by ants and termites, 541, 671, 672, 729, 760; diversity of basal fungi lineages, 153–155; ergot fungus, 156; evolution of, 152; evolution of animal pathogens and mutualists, 157–158; evolution of decayers and plant pathogens, 156; evolution of mycorrhizae, lichens, and endophytes, 157; flax rust (Melampsora lini), 156; fungal effectors, 156; fungi in the tree of life, 152–153; fungus gnat (Sciara), 395; gigantic bracket fungus, 155–156; gongylidia of, 764; heterokaryons, 500; Hyaloraphidium curvatum, 155; hypogeous fungi, 156; Neurospora, 382; Olpidium brassicae, 155; Penicillium notatum, 777–778; Phycomyces, 407; phylogenetic relationships of, 154; rice blast fungus (Magnaporthe grisea), 156; slime molds, 153
G protein-coupled receptors (GPCRs), 164
Galápagos Islands: finches of (“Darwin’s finches”), 8, 225, 442, 446, 506, 560, 546, 567, 571; tortoises of, 309
Galilei, Galileo, 11
Galton, Francis, 21
game theory, 624; adaptive dynamics and, 628; applications of, 629–630; convergent stability and, 628; economic roots of, 625; examples of (Hawk-Dove and sex-ratio games), 625–626, 628; fitness and, 627; frequency dependence and, 624–625; future of, 630; importance of process to, 628–629; Nash equilibrium condition and, 627–628, 629, 630; payoffs and, 627; Prisoner’s Dilemma game, 630; role asymmetries and, 628; strategies concerning, 626–627
gastropods, 114
gastrulation, 163
gel electrophoresis, 125
gene duplication, 41, 127, 130, 280, 364, 397, 408; determinants of, 403–404; divergent resolution of duplicate genes, 401; fixation of duplicate genes, 398, 400; functional diversity of duplicate genes, 404–405; functional redundancy and, 397, 404; future directions for the study of, 405; mechanisms of, 398, 399; neofunctionalization and, 397, 401, 402; rate of, 403; retroduplicates, 398; stable retention of duplicate genes, 400–403, 402; subfunctionalization and, 397, 401; whole genome duplication (WGD), 403; yeast duplicate genes, 402
gene exchange, types of barriers to, 492; postmating (prezygotic) barriers, 493–494; postzygotic barriers, 494; premating barriers, 492–493
gene expression, evolution of, 413; ectopic expression, 413; enhancer evolution and, 416, 418; evolution of transcription factors and, 418; evolutionary forces responsible for expression divergence, 418–419; finding expression differences within and between species, 414–415; genomic sources of regulatory evolution, 415–416; microarrays and, 414
gene flow, 212, 243, 247, 251, 286–287, 321, 338, 484–485, 489, 506, 520, 600, 801, 809; adaptation and, 325; balance alteration of genetic drift to gene flow, 813; between putative species, 497; complex patterns of, 323–324; continual gene flow, 814; Dobzhansky-Muller incompatibility and, 528; gene flow at range margins, 324; genetic diversity and, 325; genetic pattern variation and, 324; geography and, 550; heterogeneity in, 323; measurement of, 771; the origin of species and, 530–531; pseudogenization after duplication, 400; reason for the occurrence of, 813; species cohesion and, 529–530; species in the context of gene flow, 533
generalist organisms, 282
generalized least squares (GLS), 103
gene transfer: biased gene transfer, 132; gene trafficking, 406; gene transfer agents (GTAs), 127, 133; lateral gene transfer (LGT), 48, 79, 127, 136, 138, 407, 747, 797; transfer of genes within and between groups, 133–134. See also horizontal gene transfer (HGT)
genes, 40, 138, 195, 363–365, 529; behavior and, 610–611; candidate genes, 444; chimeric genes, 406, 408–409, plate 4; definition of, 41, 611–612; distal-less (Dll) gene, 448–449; effect of on traits, 248; evolution of gene number, 382–383; foraging gene, 613; gene clusters (operons), 380; gene conversion, 315, 328, 397; gene frequencies, 4; gene sampling, 324; gene swamping, 321, 324; “good genes,” 520–521, 524–525, 652; homologous genes, 428; introgression and, 328; lineage-specific genes, 382; locating genes, 6; multilocus gene genealogies, 86; odorant receptor (OR) genes, 404; orthologous versus coregulated genes, 383; orthologue genes, 380, 406, 413; Overdrive and, 515–516; paralogous genes, 397, 406; pleiotropic effects of genes, 249, 279; posttranscriptional gene regulation, 428; posttranslational gene regulation, 428; pseudogenes, 371, 380, 400; resistance genes (resistomes), 747, 749; shared gene order (synteny), 380, 382; shared patterns of gene comparison, 94–95; similarity between genes and cultural variants, 799; speciation genes, 485, 549; supergene complexes, 453; transplantation experiments and, 447–448; types of gene classification, 611. See also gene duplication; gene exchange; gene expression, evolution of; gene flow; gene transfer; genes, evolution of
genes, evolution of, 406; de novo origination of new genes, 407, 408, 418, 449; decay-accelerating factor (DAF) and, 407; evolutionary forces acting on new genes (fixation), 410; functions and phenotypic effects of new genes, 411; molecular mechanisms of, 408; mutational mechanisms generating new genes, 407; patterns of new gene evolution, 409; preferential location of new genes, 410; rates of new gene origination, 407–409; targets of selection and, 411; tracking of new genes between sex chromosomes and autosomes, 409. See also gene expression, evolution of
genetic assimilation, 89–90, 261, 420, 426; the Baldwin effect and, 266–267
genetic code, 6, 42; amino acids and, 33, 41; universality of, 33
genetic correlations, 228, 245, 718; tradeoffs and, 250
genetic differentiation, 801, 804–805; isolation and, 803
genetic diversity, 346, 600; genetic drift and, 322; habitat choice and, 322–323; selection and, 322
genetic drift, 23, 26, 189, 212–213, 249, 305, 307–310, 321, 600, 771, 809, 810; balance alteration of genetic drift to gene flow, 813; genetic diversity and, 322; random genetic drift, 332; role of in Wright’s shifting balance theory, 368
genetic engineering, 809; eugenics and, 814–815
genetic load: drift load, 337; gender load, 338; load consequences, 338–339; recombination load, 337, 338; segregation load, 337–338; substitution load, 338
genetic transmission, 253; evolution of, 257
genetic variation, 5, 40, 202, 245, 247, 258, 317, 458, 718, 809; additive genetic variance, 45; aging and, 722; clonal genetic variation, 294; descriptions of, 44–45; in ecological niches, 292–293, 294; environmental genetic variance, 45; host genetic variation, 745; lack of as a limit and constraint to evolution, 248–249
Genetical Theory of Natural Selection, The (Fisher), 22
genetics, 28, 38; behavioral genetics, 610–611, 614–615; classical genetics, 331; comparative genetics, 6, 380; forward genetics, 610; genetic bottlenecks, 307, 308; genetic clusters, 499–500; genetic coupling, 658; genetic covariance, 436, 442; genetic degradation, 346; genetic imprinting, 420; genetic load, 326, 334; genetic rescue, 321, 326; landscape genetics, 766, 769; mathematical population genetics, 22–23; Mendelian genetics, 21, 22, 611; of natural populations, 23–24; reverse genetics, 610; systems genetics, 610, 613–614. See also phenotypic evolution, genetics of; population genetics; quantitative genetics; speciation, genetics of
Genetics and the Origin of Species (Dobzhansky), 24, 25, 512
genomes, 3, 248, 363–365, 372, 375, 425, 529; adaptation in, 466–473; analysis of the human genome, 686; draft genome, 475; genome duplication (polyploidization), 398; genome evolution, 344; genome hitchhiking, 549, 554–555; genome parasites, 347; genome scans, 552–554, 555; genome sequencing, 6, 364–365; genomic architecture and speciation, 557; genomic imprinting, 423; genomic islands, 551, 552; noncoding DNA in, 5; pairs of chromosomes in the great apes, 32; pairs of chromosomes in the human genome, 32; retrogenes and the human genome, 408–409; systems genetics and, 613–614. See also genomes, evolution of; genomics
genomes, evolution of, 374, 407; comparative genomics and, 381–382; drivers of (adaptive evolution and neutral evolution), 378–379; evolution of genome architecture, 375; evolution of untranslated regions (UTRs) and introns, 377–378, 379, 408; genome expansion and restructuring, 375–378; speciation and, 549–558. See also genomics
genome-wide association testing, 458, 461, 463–464; future research concerning, 464
genomics, 610; future of, 386; gene content comparison, 381–382; genome evolution and, 381–382; genomic imprinting, 669; identification of regulatory regions and, 383–384; landscape genomics, 769; rates of change across genomic regions, 384–385. See also genomes
genotypes, 40, 193, 243, 262–263, 334, 336, 461; changes in, 363; features of the genotype-phenotype map, 261; fitness of, 212; genotype frequencies, 44, 340, 342; high-sinigrin phenotypes, 302; mapping between genotypes and phenotypes, 190; spatial variation and, 211. See also Hardy-Weinberg genotype frequencies; reaction norms
genotypic sex determination (GSD), 387
geographic information system (GIS), 769
geology, 11, 22; development of (eighteenth and nineteenth centuries), 12–13; geologic time scale, plates 1 and 2. See also speciation, and geography
Geology and Mineralogy (Buckland), 819
geotaxis, 610
germ line, 420
Gilbert model of exon/domain shuffling, 407
globeflower plants, interactions with pollinating flies, 538
glucocorticoid receptor (GR), 621
God, 7, 11, 12, 19, 817; argument from design and, 817–818; divine intervention and, 828; the problem of evil and, 817, 821–822. See also evolution, and religion
Goodson, J. L., 622
Gora Island, distinct languages of, 789
gorillas, 57, 58, 184, 186, 704, 811, 812
Gould, Stephen J., 25, 95–96, 116, 203, 589, 784, 833; on the lack of biological change in humans, 810; objection of to gradualism, 571
Grant, Peter, 8
grasses: Anthoxanthum oderatum, 507; Spartina anglica, 38
grasshoppers, 87
Great American Interchange, 510
group selection, 193, 200, 204, 219, 588–589; group selection controversy, 201–202
Gulick, Thomas, 20
gymnosperms, 145; progymnosperms, 146
habitat: habitat choice, 322–323; habitat selection, 321
Haeckel, Ernst, 19, 54; biogenetic law of, 19; depiction of the “Tree of Life,” by, 138
Haldane, John Burdon Sanderson, 22, 23, 201, 255, 307, 335, 336, 610, 721; appending of kin selection theory by, 699; on the cost of natural selection, 338; pollen example of, 348
Haldane’s rule, 494
halophile, 127
Hamilton, William D., 202–203, 625, 679, 724, 833; kin selection theory of, 672, 679, 697, 698
Hamilton’s rule, 202, 215, 216, 219, 671, 698
Hand, Its Mechanisms and Vital Endowments as Evincing Design, The (C. Bell), 818–819
haplodiploidy, 387, 697; haplodiploid hypothesis, 215; haplodiploids, 217; haploidy versus diploidy evolution, 259
haplotype, 82, 458, 462, 471–472, 801; extended haplotype homozygosity (EHH), 471; haplotype networks, 84; haplotype trees, 805; mismatch distributions and, 84
Hardy-Weinberg equilibrium (Hwe), 40, 44
Hardy-Weinberg genotype frequencies, 341
Heliconius butterflies, 563; Müllerian mimicry in, 453
hemizygosity, 387
Hennig, Willi, 61, 77, 107, 108
Henslow, John Stevens, 15
heredity, 7, 611; lack of a hereditary mechanism in Darwin’s theory of evolution, 21; problem of the origin of variations and, 17–18
heritability, 40, 221, 222, 247, 282, 458; heritability plot and response to natural selection, 224; of life history and health traits, 687; missing heritability, 458, 464; species heritability, 586–588; variation in a trait and, 248–249
hermaphroditic organisms/animals, 340, 341, 360
herons: grey heron (Ardea cinerea), 323
heterogamety: female, 387; male, 387; male versus female, 388, 388
heterosis, 321
heterospory, 143
heterozygosity, 44, 313, 647, 809; increase of heterozygosity levels in humans, 813–814
heterozygotes, 40, 44, 46, 342, 345; expected heterozygosity and, 44
Hispaniola, 537
Histoire naturelle (Natural History [Leclerq]), 14
histones, 130, 368, 371, 381, 404, 420, 421, 422; chromatin and, 415
history: historical population records, 683, 687; markers of history, 34; rough history, 198; understanding of evolution and, 5. See also life
histories hitchhiking, 328, 344, 466, 467; adaptive hitchhiking, 470–471; divergence hitchhiking, 549; genetic hitchhiking, 747; genome hitchhiking, 549, 554–555
HIV, 37, 324, 735, 752. See also AIDS
Holocene era, 117
homeobox genes, 26
Homo erectus, 185–186, 787; spread of from Africa into Eurasia, 805–806
Homo floresiensis, 186
Homo habilis, 185
Homo heidelbergensis, 186
Homo sapiens. See humans (Homo sapiens)
homology, 28, 48, 90, 786; congruence test of as applied to morphological characters, 93; deep homology, 89, 94, 97; evolutionary analysis of character homology, 91–95; of jaw bones, 31; of morphological structures, 94–95; serial homology, 90
homozygotes/homozygosity, 342, 346, 359, 461, 647; excess of, 336; extended haplotype homozygosity (EHH), 471
Hooke, Robert, 818
Hooker, Joseph Dalton, 17, 18, 77
horizontal gene transfer (HGT), 127, 747, 749, 750, 755, 795; biochemical innovation as a result of, 134; role of in the evolution of prokaryotes, 131–132
hormones, 616, 622; activational effect and, 616, 617; behavioral effects on (the challenge hypothesis), 616, 618; comparative studies of, 621–622; correlated evolution and, 619–620; definition of, 617; evolution of hormones and their receptors, 621; hormonal cascades, 617–618; hormone-mediated suites, 616, 621; hormone-mediated trait, 616; macroevolution and, 621–622; microevolution and, 620–621; organization effect and, 616, 617; sites and modes of hormone action, 617; sources of variation in hormone-mediated phenotypes, 618; steroid hormones, 617
horns: parietal horns, 227; squamosal horns, 227
horses: Przewalski’s horses, 309
human accelerated region (HAR), 385
human behavioral ecology, 683–684; contributions of to the study of evolution, 688–689; development of, 684–685; focus of on evolution in modern societies, 687–688; menopause and, 685; optimality models and, 683, 684; problems and criticism concerning, 685–687
Humani generis (Of the Human Race [Pope Pius XII]), 820
humans (Homo sapiens), 56, 57, 414, 694, 704; cognitive complexity of, 787; cooperation among, 218–219; early humans (Homo erectus), 185–185; examples of transgenerational epigenetic effects in, 425; incest taboos among, 690; limits to the human life span, 724–725; neural development in, 186; posture of (orthograde and pronograde posture), 183, 184. See also humans, evolution of; linguistics, and the evolution of
human language humans, evolution of, 183–184, 605–607; evolution and what it means to be human, 729–730; Kenyanthropus platyops, 185; Neanderthals and the origin of modern humans, 186–187, 480; origins of modern humans (hominins), 184; Orrorin tugenesis, 184; recent human evolution, 187–188; Sahelanthropus tchadensis, 184
Hume, David, 821
hunter-gatherers, 683
Huntington’s disease (HD), 721
Hutchinson, G. Evelyn, 289, 497
Hutchinson niche, 288, 289, 292
Huxley, Thomas Henry, 17, 18, 31, 560; as Darwin’s bulldog, 19
Hyatt, Alpheus, 20
hybrid speciation, 529, 532–533
hybridization, 343, 529, 539, 563–564, 603, 770–771; between divergent lineages, 532; as a common phenomenon, 531; evolutionary outcomes of, 531–533; examples of (sunflowers, fish, butterflies, oaks), 531, 533; formation of hybrid zones and, 529, 532, 537; introgressive hybridization, 559, 563
hydrogenosomes, 137
Hydrozoa, 164
Hymenoptera, 217
hyphae, 152
hypothalamic-pituitary-gonadal (HPG) endocrine, 618