ichthyosaurs, 179
inbreeding, 336, 340–341; effect of on genetic recombination, 343; effect of on genotype and allele frequencies, 343; identity by descent in an inbreeding pedigree, 341; inbreeding depression and heterosis, 344; long- and short-term consequences of, 343; measuring the degree of, 341–342; measuring inbreeding coefficients and rates of self-fertilization, 342–343, 343; models and evidence of inbreeding depression, 344–345; purging and, 345–346. See also inbreeding, consequences for molecular evolution and genome evolution; inbreeding depression
inbreeding, consequences for molecular evolution and genome evolution, 344; chromosome evolution, 344; Haldane’s sieve, 344; long-term consequence (hitchhiking), 344; sex allocation, 344
inbreeding depression, 306, 340, 356, 360
inclusive fitness, 663, 671, 677, 679; virulence and, 744–745
individuals, 204
Industrial Melanism, 37
infanticide: offspring killing (filial infanticide), 712
influenza, 7; Haemophilus influenzae, 363; vaccines for, 735–736
inheritance: blending of, 18; Lamarckian inheritance, 19; Mendelian inheritance, 306, 425; multiplicity of forms of, 46; non-Mendelian inheritance, 347; soft inheritance, 420, 426
insects, 167, 477, 508, 605, 667, 697; comparative evidence for kin selection in, 217; cooperation as a key to the success of, 672; evolution of Arthropoda, 94; of the Mesozoic era, 149; mutualism and, 672
Institute for Creation Research (ICR), 827
integrative conjugative elements (ICEs), 132
intelligent design (ID), 817, 819, 829–830; legal decisions concerning, 829
International Code of Zoological Nomenclature, 489
International Human Haplotype Map (HapMap) project, 462
intervention studies, 683
introgression, 460, 491, 495, 529, 555, 563
inversion types: Chiricahua inversion type (CH), 207; Standard inversion type (ST), 207–208
isolation/isolating mechanisms, 492, 514; behavioral isolation, 515; ecological isolation, 544; extrinsic postzygotic isolation, 515, 543, 546; genetic isolation, 545, 803; genetics of postzygotic isolation, 545–547; genetics of prezygotic isolation, 543–544; habitat (resource) isolation, 493, 514–515; intrinsic postzygotic isolation, 515–516, 543, 546–547; isolation by adaptation (IBA), 549, 555; isolation by distance, 801, 805; mechanical isolation, 493; natural selection and reproductive isolation, 513–514, 516; pollinator isolation, 515; postmating isolation, 527–528; postzygotic isolation, 497–498, 531; prezygotic isolating mechanism, 243, 531; reproductive isolation (reproductive isolating barriers), 496, 498, 512, 514–516, 518, 521, 523, 524, 529, 591, 594; sexual isolation, 544–545; temporal isolation, 493, 515. See also reinforcement
jellyfish, 160, 164; Aurelia, 164; box jellyfish, 164
Jurassic era, 149, 179, 582; Early Jurassic era, 178; Late Jurassic era, 30
katydid (Pterophylla camellifolia), 279
Kenyanthropus platyops, 185
Kepler, Johannes, 11
key innovations, 486, 563, 592; in evolutionary biology, 592–593; evolutionary diversity and, 593–595; examples of, 594–595, 597; key evolutionary innovation hypothesis, 592; origins of, 593; problems concerning, 596–598; testing hypotheses of, 595–596
Kimura, Motoo, 26, 68, 369, 453, 467
kin recognition, 215, 218; challenges to, 218–219
kin selection, 193, 200, 672, 679, 697, 741; comparative evidence for in social insects, 217; eusociality and, 698–699; experimental evidence of in microbes, 217–218; fraternal cooperation and, 672–673; inclusive fitness and, 196, 202–203, 215, 216, 219, 656, 698
King, Jack Lester, 68, 369, 432
knapweed: spotted knapweed (Centaurea maculosa), 296
Koarchaeota, 129
Koshima Island, 798
Kropotkin, Peter, 19
Kuhn, Thomas, 17
Lamarck, Jean-Baptiste, 14
Lamarckism/Neo-Lamarckism, 20, 425–426; Lamarckian inheritance, 19
land, colonization of, 171
language. See linguistics, and the evolution of human
language Leakey, Richard, 581, 833
lecithin, 123
Leclerq, Georges Louis (Comte de Buffon), 14, 76
Lederberg, Joshua, 421
lepidosaurs, and their relatives, 178–179
lichens, evolution of, 157
life: biochemistry of, 283; conditions required for life’s origin, 122; definition of life in evolutionary terms, 121–122; growth of, 270; hierarchical organization of, 5; key features of life’s functional systems, 278–279; maintenance of, 270; origin of, 120–121; possible sites for the origin of life, 122; prebiotic polymerization reactions and, 123–124; primary monomers of life, 122; relationships between three domains of life, 131; self-assembly of boundary membranes and, 123; synthetic artificial life, 122; terrestrial life, 121. See also life histories
life histories, 268, 325–326, 685, 687; aspects of life history evolution, 272–273; definition of, 269; demographic theory and, 271–272; empirical research concerning, 273–274; future research concerning, 274–275; life history diversity, 269–270; life history factors favoring the evolution of eusociality, 699; life history specializations of arthropods, 172–173; life history traits, 193, 195; life span/senescence and, 272–273; of organisms, 191; theory of, 269; theory of the evolution of, 270–272; variation in species life histories, 666
likelihood, 100, 102, 105. See also maximum likelihood (ML) estimation procedures
lineage, 567, 594–595, 801; lineage diversification, 104–105; lineage sorting, 82; lineage sorting and the coalescent, 85–86
linguistics, and the evolution of human language, 786, 788–793; cognates and, 786; definition of language, 786; distance methods and, 791–792; future of language evolution, 793–794; Germanic languages, 790; Indo-European language family tree, 791; language adaptation to speakers, 793; language density and, 789; likelihood methods and, 792; linguistic half-life and, 792–793; number of spoken languages in the world, 788–789; parsimony methods and, 791; rates of lexical replacement, 792; regular sound correspondences and, 786, 790–791; relationships between language and species, 789; Sanskrit language, 789; when did language evolve, 786–787; why did language evolve, 787–788
linkage, 328; generation of linkage disequilibria, 332; linkage disequilibrium (LD), 40, 44–45, 228, 307, 328, 331–332, 458, 462, 549, 554; linkage equilibrium, 44
Linnaeus, Carolus, 12, 14, 107, 138, 152; classification of plants and animals by, 12; critique of his taxonomic system, 108
lipase, 774
liposomes, 123
liquid crystal, 120
lizards, 61, 179, 442; horns of flat-tailed lizards, 227; lizards of the Middle and Late Jurassic eras, 179; New World lizards, 509; number of digits in the hand of a lizard, 263; western fence lizard (Sceloporus occidentalis), 766. See also Anolis
lizards load. See genetic load
lock-and-key hypothesis, 493
Locke, John, 611
locus, 40; autosomal locus, 44; sex-linked locus, 40
logistic (density-dependent) growth, 117
Lophotrochozoa, 162
Lord Howe Island, 509
lungfish: Australian lungfish (Neoceratodus), 34, 36
lycophytes, 146
Lyell, Charles, 8, 13, 17, 116
Lynch, Michael, 318, 319, 407, 432, 571
Lysenko, Trofim D., 20, 425–426
MacArthur, Robert, 270, 271, 508, 509
macroevolution, 25, 89, 118–119, 573, 579; autonomy of, 203; cospeciation and, 535; Court Jester model of, 579, 584–585; drivers of and extinction, 584–585; effect macroevolution, 588; hormones and, 621–622; Red Queen model of, 579, 584–585. See also evolution, key innovations of; macroevolutionary rates; macroevolutionary trends
macroevolutionary rates, 567; how “fast” is evolution, 567–568; rates of speciation and extinction, 568–570; rates of trait evolution, 570–572; relationships between rates of trait evolution and diversification, 572
macroevolutionary trends, 486–487, 573; directionality in evolution, 573–574; examples of trend hypotheses, 576–577; trends as accumulated microevolution, 575; trends from species selection, 575–576; trends within groups of species, 574–575; trends within species, 574
major histocompatibility complex (MHC), 679, 772
Malacostraca, 170
maladaptation, 193
malaria, Plasmodium falciparum, 735
Malaysia, agriculture in, 810–811, 812
male-male competition, 641; adaptations to sperm competition and, 644; alternative mating strategies and, 643–644; example of, 642; in large and small animals, 642; in plants, 644–645; reasons for, 641–642; sperm competition, 641, 644, 647; weapon evolution and, 642–643, 643
Malthus, Thomas Robert, 16–17, 19
mammals, 9, 36, 409, 506, 605; Cope’s rule and, 576; evolutionary rate of, 579; Morganucodon, 31; senescence and sex difference in, 720
Mandibulata, 170
manikins: wire-tailed manikins (Pipra filicauda), 711
mapping: between genotype and phenotype, 190; genetic mapping of model organisms, 329; QTL mapping, 345
Margulis, Lynn, 137
Marine Protected Areas (MPAs), 770
Marjum Formation, 160
Markov chain Monte Carlo (MCMC) algorithms, 71, 72
Markov models: of correlated evolution, 104; of discrete characters, 102
marmots: yellow-bellied marmots, 245
Martin, John, 15
mate choice, 647; appeal of to evolutionary biologists, 647–648; benefits of male choice, 652–653; breeding rates and, 650–651; cryptic female choice, 644, 648–649; cryptic male choice, 649; direct benefit and, 647; genetic benefit and, 647; male versus female cryptic choice, 649–650; prudent choice, 650; rewards of, 651–653; what constitutes mate choice, 648–649
mating systems, 356; alternative male mating strategies, 629–630; classes of (monogamy, polygyny, and polyandry), 357, 636, 641; continuous mating systems and the evolution of behavior, 637–638; definition and importance of, 632–633; dynamic nature of, 637; E and O model of, 633–634; environmental potential for polygamy (EPP) and, 634; evolutionary history of, 361–362; evolutionary potential and, 638–639; indirect genetic effects (IGEs) and, 638; mate choice/preference, 521, 629; mating trait, 521; measurement of, 357–358; 633–634, 636; mixed mating, 358; outcrossing rates and, 359, 359; polygyny and “mating niche,” 644; postmating isolation, 527–528; preference for mating, 813; and the problem of mixed mating, 361; relevance of the study of, 639–640; and the reproductive assurance hypothesis, 361; regression of fitness on mating success, 636; sib-mating, 340; unconventional mating behavior, 644; variation in mating patterns, 358–359
Matthew, Patrick, 17
maximum likelihood (ML) estimation procedures, 63–64, 70–71, 79
Maynard Smith, John, 201, 204, 470, 625, 672, 711, 783
Mayr, Ernst, 16, 90, 491, 497, 507, 543; on “beanbag thinking,” 550; on the biological species concept, 24–25, 512, 520
McDonald-Kreitman (MK) test, 468–470; bias in, 469–470
Medicago truncatula, 321
medicine, 8; medical intervention studies, 687. See also evolutionary medicine
meiotic drive, 201, 203, 347; female meiotic drivers, 350–351
meiotic nonreduction, 556
Melanesia, 807
melanocortin 1 receptor (Mc1r), 41, 45
Mendel, Gregor, 7, 18, 21, 341, 363, 425
Mendelism, 21
menopause, 685, 718, 722–723; the grandmother hypothesis and, 723, 724; menopause as modern artifact argument, 723; the mother hypothesis and, 723–724; reproductive competition and, 724
mesocosm, 298
mesoderm, 164
mesosuchians, 180
Mesozoic era, 30, 116. 117, 146, 172, 179, 575; Mesozoic radiations, 177, 181; plants of, 150
Messel Oil Shale, 114
messenger RNA (mRNA), 26, 40, 41, 374, 378, 398, 409, 414, 421, 609, 774; process of translation and, 774; rates of mRNA production and degradation, 433
metamorphosis, 167; complete metamorphosis, 172
metapopulations, 321, 325, 346, 489, 536, 604
meteorites: carbonaceous meteorites, 123; Murchison meteorites, 123, 123
mice, 6, 348; allelic killers and, 351; color variations in beach mice, 43; color variations in deer mice (Peromyscus polionotus), 40–41, 44; house mice (Mus musculus and Mus domesticus), 532, 712; shortening of mice tails, 425; tailless mice, 96; “Tokyo” mice, 712
microbes, 38, 117, 148, 149, 230, 299, 319, 320, 371–372, 383, 431, 464, 565, 756, 764; antibiotic resistance in, 247; eukaryotic microbes, 231; experimental evidence for kin selection in, 217–218; fast-evolving microbes, 728; motile microbes, 138; parasitic microbes, 733; pathogenic microbes, 737; social microbes, 672; symbiotic microbes, 539; unicellular microbes, 136, 231, 318
microbial forensics, 754; the Ames strain and the 2001 anthrax letters, 757–759; development of, 754–755; DNA fingerprints and, 754, 755; genetic technology and the significance of a “match,” 756; the Kameido Aum Shinrikyo anthrax release and, 756–757; molecular epidemiology and, 755, 759; uses of DNA in human and microbial forensics, 755–756
microevolution, 25, 238, 483, 683; “autonomy” of, 203; hormones and, 620–621; in natural populations, 241
Microsporidia, 155
Middle East, 761
migration, 305, 332, 514; gene flow and, 212; migration load, 321, 324, 337
Miller, Stanley, 122
Milton, John, 15
mimicry. See Müllerian mimicry
Mimulus: pink monkeyflowers (M. lewisii), 455, 516; red monkeyflowers (M. cardinalis), 455, 516; yellow monkeyflowers (M. guttatus), 353, 454, 555
mineralocorticoid receptor (MR), 621
mites (Acari), 169
mitochondria, 131, 137, 674; ancient mitochondrial genomes, 478; mitochondrial DNA (mtDNA), 475, 478, 480; “mitochondrial Eve” data, 84; remnant mitochondria (hydrogenosomes and mitosomes), 137
mitochondrial genes, 85
Modern Synthesis, 507, 543, 545, 833. See also evolutionary synthesis (1930–1940)
modernism/modernity, 21; mismatches to modernity, 733, 738–739
modifier genes, 253, 254, 254–255
mold, 152; Trichoderma reesei, 156
molecular biology, 6; evolutionary theory and, 26
molecular clock, 67–68, 307, 312, 367, 368, 369; Bayesian estimation of divergence times, 71–72; dating of, 68–69; fossil/node calibrations and, 72, 73, 73; maximum likelihood (ML) estimation of divergence times, 70–71; perspectives on, 73–74; relaxed clocks and the prior model of rate drift, 72–73; statistical methods for divergence time estimation, 70; testing of, 69–70
molecular evolution, 56, 367, 373; biological insights derived from the study of, 371–372; definition of, 367–368; evolution of novel traits and their underlying gene regulatory networks, 448–450, 448; goals of studies in evolutionary development biology, 445; impact of natural selection on, 370–371; mapping genotype to phenotype during development, 445–446; mapping genotype to phenotype during evolution, 446–448; origins of, 368–370; rates of change and, 381. See also molecular networks, evolution of
molecular networks, evolution of, 428, 430; evolution of global network organization, 431–433; evolution of local network organization, 434; future of, 435; local organization and the dynamics of biological networks, 433–434; network representations of biological data and, 430; organization of global biological networks and, 430–431
molecular toolkit, 159
monkeyflowers. See Mimulus
monkeys: macaques, 414–415, 798
monoandry, 700
monomorphism, 206
monophyletic groups. See clades (evolutionary lineages)
monophyly, reciprocal, 82
Morgan, Thomas Hunt, 23, 363, 612
morphospace, 276, 436–437; evolution in, 438–439
Morris, Desmond, 692
Morris, Henry M., 827
mortality, 271; adult mortality, 271
mosquitoes: Anopheles mosquitoes, 555, 556; dengue mosquitoes (Aedes aegypti), 287
moths: Biston betularia, 37; courtship pheromones in arctiine moths (Utetheisa ornatrix), 659–660; interactions between yuccas and yucca moths, 538
motif enrichment, and identification, 384
Muller, H. J., 23, 361, 362, 546
Müllerian mimicry, 407, 538; in Heliconius butterflies, 453
multicellularity, 673; origin of sponges and, 163; origins of, 142
multilameller matrix, 120
multilocus nested-clade phylogeographic analysis (ML-NCPA), 805, 806; inferences about human evolution from, 806
“multiple hits” problem, 64
multiple-locus variable analysis (MLVA), 754, 756, 757–758
multiplex automated genome engineering (MAGE), 778, plate 7
mutation(s), 4, 211–212, 248, 305, 315, 367, 368, 371, 426, 454, 466, 473, 600, 609, 809, 810; beneficial mutation, 230; causes of, 316; deleterious mutation rates, 336–337, 339, 463, 468–469, 470; in DNA, 444; error threshold and, 319; evolution and, 316–317, 320; evolution of mutation rate, 257–258; extinction and, 320; genome size and, 319–320; genomic complexity and, 319–320; heritable mutations, 316; indels and, 316; loss-of-function mutations, 233; in the Mc1r gene, 455, 456; meaning of, 315–316; mutation accumulation (MA), 403, 718; mutation bias, 374; mutation load theory, 334–337; mutation-selection balance, 317; mutational decay, 247; mutational variance, 419; natural variations versus mutations, 612–613; nonadaptive mutations, 318; randomness of, 317–318, 712–713; recessive mutations, 344, 345; selective sweeps and, 471–473, 471; transcription-induced mutation (TIM), 319; variation in mutation rate within the genome, 318–319; variation in mutation rate among taxa, 318. See also causative mutations, phenotypic effects of
mutual benefit, 216
mutualism(s), 19, 219, 671, 672, 760; agriculture as a mutualism, 763; forms of mutualism that favor population divergence, 538–539; mutualistic networks and speciation, 538–539; symbiotic mutualisms, 538
mycelium, 152
mycology, 152
mycorrhizae, 152; ectomycorrhizae (ECM), 157; evolution of, 157; mycorrhizae root associations, 48. See also fungus/fungi
myxozoans, 165
Naked Ape, The (Morris), 692
Nash equilibrium condition, 627–628, 629, 630
National Aeronautics and Space Administration (NASA), 784; Evolvable Systems Group of, 784–785
National Science Foundation (NSF), 781
natural history, 10, 11, 14, 15, 19, 24, 268, 291, 645, 767; field-based, 766; revolution in, 107, 832; rise of, 12
natural populations: measuring selection in, 238–239; microevolution in, 241
natural selection, 3, 5, 7, 9, 17, 24, 91, 125, 189–191, 238, 276, 318, 467, 574, 588, 606, 630, 694, 817; accidental selection, 222; agents of divergent selection, 241–243; basic principles of, 213–214; components of, 210; conflicting selection, 298; connection of to fitness in hierarchies, 197–198; considerations when studying natural selection and speciation, 516–517; as the core of evolutionary theory, 19; correlated response to, 221, 228; correlational selection, 227, 616, 619, 663, plate 3; cost of, 338; definition of, 194; density-dependent selection, 193; direct selection, 647; direct versus indirect selection, 256–257; directional selection, 206, 208, 225, 239, 240, 512, 513–514; disruptive selection, 206, 208–209, 225, 239, 240, 244, 245, 506, 512, 513; divergent selection, 238, 241, 242, 535, 549; epistatic selection, 332; evolutionary change and, 4; example of, 207–208, 209; fertility selection, 206, 210; field studies of, 8; Fisher’s fundamental theorem of, 22, 208; forms of selection in a geographic context, 514; frequency-dependent selection, 193, 211; gametic selection, 210; “gene’s-eye view” of, 796; genetic consequences of, 213–214; genetic response to, 223–225; genetic theory of, 191; genic selection, 200, 201; genome size and, 319; how selection works, 222–223; impact on molecular variation, 370–371; indirect selection, 221, 227, 647; individual selection, 193; levels of, 200; limits to, 245; lineage-level selection, 203; main tenets of, 363; maintenance of diversity and, 235; modes of, 206, 226, 240; multifarious selection, 551; multilevel selection, 200, 202; negative selection, 380; and the neutral theory, 26, 68; opportunity for, 688; origins of the theory of, 17; overdominance and, 206; patterns of, 208–210, 209; phenotypic selection, 222–223, 225, 238, 239; positive selection, 367, 380, 469, 473; power of, 198; as the primary driver of adaptive evolution, 221; process of, 512; psychology and, 691; purifying selection, 367, 380; r and K selection, 270–271; recognition of, 198–199; related processes and, 211–213; selection experiment, 230; selection mosaic, 535, 536; as a statistical process, 223; strong selection, 249; studies of natural selection acting on variation within a population, 277; in sub-Saharan Africa, 811; trait combinations and, 281; truncation selection, 223, 225; types of natural selection contributing to reproductive isolation, 513–514; types of social selection, 216–217; uniform directional selection, 514; unit of selection, 200, 201; viability selection, 207, 210–211, 240. See also group selection; heritability; kin selection; natural populations; selection gradient; sexual selection; species selection; stabilizing (optimizing) selection
Natural Theology (Paley), 15, 817, 818, 829
Neanderthals, and the origin of modern humans, 186–187, 480
nematocysts, 162
Nematoda, 170
Neocallimastigomycota, 153
neofunctionalization, 397, 401, 406
Netherlands, the, 245
network organization, 430; evolution of global network organization, 431–433; evolution of local network organization, 434; global network organization, 428, 430–431; local network organization, 428; network motifs and, 428, 434. See also regulatory
networks neurotransmitters, 617
neutral theory, 68, 307, 308, 312–313, 367, 370, 467–468, 469, 502; predictions of the neutral theory for variation within and between species, 370
New Zealand, 80, 179, 766, 769
Newell, Norman D., 25
Newton, Isaac, 11
nicotinamide adenine dinucleotide phosphate (NADP), 134
nomenclature: future of phylogenetic nomenclature, 110; misunderstanding of phylogenetic nomenclature, 110; primary goal of biological nomenclature, 108
nonadaptive behavior, 9, 710, 712; apparently nonadaptive behavior, 710; cannibalism, 712–713; definition of, 710–711; insights from nonadaptive behavior, 716–717; manipulation, 713–714; same-sex behavior (SSB), 715–716; sexual cannibalism, 714–715
nongovernmental organizations (NGOs), 766, 768
nonparametric rate-smoothing (NPRS), 71
North America, 79, 80, 146, 241, 360, 506, 507, 510, 530; Appalachian Mountains of, 769; Gulf Coast of, 589; predator types in the lakes of, 604
North Atlantic Land Bridge, 79
Northern Range Mountains (Trinidad), 273–274
nucleocytoplasm, 131
nucleoskeletal hypothesis, 374
Occam’s razor. See parsimony
oceanic islands. See islands
Oligocene era, 79
On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (C. Darwin), 4, 18, 24, 29, 47, 107, 138, 183, 318, 483, 605; biogeography chapters of, 76; components of, 17–18; evolutionary psychology and, 691–692; genesis of, 16–17; main thesis of, 512; parasites described in, 733; publication of, 17; religious reaction to, 19; scientific and public reception of, 18–19
ontogeny, 19
Onychophora, 170
Oomycetes, 153
operational sex ratio (OSR), 634, 637, 647, 653
orchids: Dactylorhiza sambucina, 225
Ordovician era, 117; end-Ordovician, 581, 582; Late Ordovician era, 29; Middle Ordovician era, 145
organisms, 489, 671, 675–676; complex design of, 820; detection of environmental variation and, 714; evolution and development of, 436; evolutionary constraints and patterns of allometry in, 437–438, 440; form and function in organismal design, 276–277, 437; future research concerning, 443; organismal complexity, 576–577; patterns of parallel evolution and, 440–442
orthograde posture, 183
Orsten Formation, 114
Osborn, Henry Fairfield, 20
ostrich (Struthio camelus), 108
outcrossing, 587; outcrossing rates, 359, 359
oviparity, 101
Paleocene era, 79
paleontology, 5, 21, 22; biology and, 25
Paleoproterozoic era, 137
Paleozoic era, 117, 150, 175, 176
Paley, William, 15, 817, 820, 829; writings of, 818
palms: Howea palms, 509
pangolins, 592
panmictic populations, 22
Paradise Lost (Milton), 15
paramutation, 420
parapatric speciation, 504, 509
paraphyletic groups, 107
parasites, 139, 152, 153, 727, 733, 741; cell parasites, 348, 350; diversification and, 537–538; genome parasites, 348, 350; infectious transmission and, 736; parasite manipulation, 710; reproductive parasites, 347, 348, 350–353; somatic parasites, 347, 348, 350. See also parasite virulence
parasite virulence, 741; basic reproductive number Ro and, 741; definition of, 741–742; examples of accidental infections, 742; horizontal transmission and, 741; host genetic variation and, 745; multiple infections, inclusive fitness, and virulence, 744–745; phase model of (Phase 1): accidental infections, 742–743; phase model of (Phase 2): evolution of virulence following successful invasion, 743; phase model of (Phase 3): evolution of optimal virulence, 743; reproductive parasites and, 741; success of optimality models in predicting virulence, 746; tradeoff model and, 743–744; vertical transmission and, 741, 745
parental care: diversity in the forms of parental care, 664; evolution of, 663, 664–666; evolutionary maintenance of parental care, 666–668; genetics and epigenetics of, 668–669; parental effect, 663; parental effort, 663; parental expenditure, 663; parental investment, 663; parent-offspring coadaptation, 663; parent-offspring conflict, 663, 667–668; sex differences (sex roles) in the provision of parental care, 667; sociality and, 669–670
Pasteur, Louis, 733
Patau syndrome, 398
pathogens, 152, 734–736, 749; emerging pathogens, 735; evolution of animal pathogens, 157–158; garden pathogen Escovopsis, 764; Neisseria, 130; Olpidium brassicae, 155; Phytophthora infestans, 152
Pavlov, Ivan, 609
Paxton Lake, 546
payoff matrix, 624
Peacocke, Arthur, 822
pearl-bordered fritillary (Boloria selene), 289
Pearson, Karl, 21
“Pedigree of Man” (Haeckel), 54
Pennsylvanian era, 30, 146, 149
performance, 276
peripatric speciation, 504, 507
Permian era, 146, 581, 584; end-Permian, 582; Late Permian era, 146; Permian-Triassic boundary, 150
permineralization, 114
pesticides, 37; evolution of pesticide resistance, 7, 247
petrification, 114
Pezizomycotina, 157
phage, 127, 133, 317, 777; phage display, 776; phage display experiment, plate 6; phage T4, 234
Phanerozoic eon, marine diversity in, 117–119
pharyngognathy, 278
phenotypes, 5–6, 40, 193, 221, 363–365, 815; definition of, 298; disparity and, 559; features of the genotype-phenotype map, 261; function of phenotypic traits, 191; mapping between genotypes and phenotypes, 190, 215; multidimensional phenotypes, 225, 227; in natural populations, 464; phenotypic clusters, 499–500; phenotypic selection, 222–223, 225, 238, 239; phenotypic variation, 4; reaction norm and, 191; relative viability and, 207; selection coefficient and, 207; sex-ratio phenotype, 348; strength and patterns of phenotypic selection, 239–241; variation in (phenotypic effect size), 452. See also phenotypic engineering; phenotypic evolution, genetics of; phenotypic integration; phenotypic plasticity
phenotypic engineering, 616, 620
phenotypic evolution, genetics of, 452; architecture of, 452–454; future research concerning, 456–457; genetic basis of repeated phenotypic evolution, 455–456; molecular basis of, 454; mutations responsible for phenotypic evolution, 459–460; testing whether phenotypes are adaptive, 454–455
phenotypic integration, 616; hormone pleiotropy and, 618–619
phenotypic plasticity, 5, 6, 9, 45, 191, 245, 261, 298, 444, 450, 618, 710, 714; assimilation and, 426–427; canalization and, 262–263; costs of, 263–264; evolutionary significance of, 266; is plasticity adaptive, 264; prediction of, 264; selection on plasticity, 263
pheromones, 543, 655; courtship pheromones in Lepidoptera, 659–660; oviposition marker pheromones, 658–659; role of in sexual isolation, 544
philopatry, 697; benefits of, 678
Philosophie zoologique (Zoological Philosophy [Lamarck]), 14
phlox: Linanthus parryae, 269, 271; Phlox cuspidate, 41, 518; Phlox drummondii, 41, 45, 518
photosynthesis, 134; distribution of in eukaryotes, 139–141; photosynthetic bacteria, 29
PhyloCode (ICPN: International Code of Phylogenetic Nomenclature), 106, 108–110
phylogenetic diversity (PD), 769
phylogenetic inference, 57; Hennig’s rule and, 61; impact of Bayesian statistics on, 65–66; logical and statistical inference, 60–62; phylogenetic analysis and, 65, 84, 95, 164, 491, 655, 704; statistical support for clades and, 65
phylogenetic tree(s), 28, 47, 51, 53, 60, 92, 93, 590, 790; ancestral state reconstruction and, 51, 57–58; branch length, 569; branch rotation, 54; computational aspects of tree estimation, 64–65; distance-based approaches to tree estimation, 64; “good species” and, 570; internal nodes of, 101; internodes of, 101; introduction to, 52; lack of trunks in evolutionary trees, 52, 54; long branches of, 767; maximum likelihood (ML) tree estimation procedure, 63–64, 70–71; misreading trees as ladders of progress, 54, 56; misreading of trees with species-poor lineages, 54; monophyletic group of, 101; role of in the study of evolutionary key innovations, 595–596; rooted trees, 128, 130–131; single-gene phylogenetic trees, 131–132; species trees, 51–52; stepwise addition and tree estimation, 64; taxon sampling and, 57; terminal nodes of, 101; tree balance, 567, 569; tree topology and, 52, 64; use of the parsimony procedure for estimating trees, 62–63. See also clades (evolutionary lineages); phylogenetic inference
phylogenetics, 5, 736, 766, 767; and the history of life, 47–49; molecular phylogenetics, 595; phylogenetic diversity (PD), 766; phylogenetic regression, 103–104; phylogenetic relationships, 5; phylogenetic shadowing, 380, 383–384; phylogenetic signals, 103; species in a phylogenetic framework, 108–110. See also phylogenetic tree(s)
phylogeny, 6, 19, 51, 54, 65, 68, 75, 100, 564, 590, 767, 786; comparative method and, 100–101, 105; “molecular phylogenies,” 26; phylogenies and indications of “ancestral” or “older” in extant species, 56–57. See also phylogenetic tree(s)
phylogeography, 48, 76, 82–83; ancient population genetics and, 477–479; comparative phylogeography, 85, 277–278; definition of, 82; direct interpretation of single-locus gene genealogies and, 83–85; lineage sorting and, 82, 85–86; mismatch distribution and, 82, 84; mtDNA phylogeography, 83–84, 86; multilocus gene genealogies and, 86; testing models of population history and, 86–87
phyloinformatics, 110
phytochemicals, 298
Phytophthora infestans, 152
pines: lodgepole pine (Pinus contorta), 293, 300–301; Pinus sylvestris, 323, 324
placozoans, 165; Trichoplax, 165
Planctomycetes, 130
planktotrophs, 589
plants, 469; Cardamine hirsuta, 323; coevolution of land plants with animals, 149–150; Crepis sancta, 323; evolution of, 143; examples of transgenerational epigenetic effects in plants, 424; innovation in land plant bodies, 148; innovation in land plant reproduction, 148–149; interactions with pollinators, 591; male-male competition in, 644–645; modern ferns, 144; origin and diversification of angiosperms, 147–148; origin and diversification of early land plants, 145; origin and diversification of seed plants, 147; origin and diversification of vascular plants, 145–147; phylogenetic framework of, 144, 144–145; seed plant reproductive evolution, 149; Silene latifolia, 228
plasmids, 128, 500, 747, 749; plasmid persistence, 751
Plasmodium falciparum, 735
plasticity. See phenotypic plasticity
plastid genes, 140
plastids, 136, 140; kleptoplastids, 141
Plato, 11
Platonic philosophy, as “idealist,” 11
Platyhelminthes, 164
pleiotropy, 195, 247, 413, 442, 453, 610; antagonistic pleiotropy (AP), 268, 272–273, 273, 718, 721; constraints on evolution and, 250–251; genetic pleiotropy, 619; hormone pleiotropy, 616, 618–619; pleiotropic effects of genes, 249
Pleistocene era, 115, 683, 686, 805, 806
plesiosaurs, 179
ploidy level, 253
pollen/pollination, 348, 506, 518, 538; abiotic pollination, 358; biotic pollination, 358; interaction of globeflower plants with pollinating flies, 538; passive pollination, 675; plant interaction with pollinators, 591; pollen discounting, 360; pollen limitation, 357; sperm and pollen competition, 493–494. See also self-pollination
polyandry, 647
polymerase chain reaction (PCR), 475, 476, 479–480, 774, 775
polymorphism, 419, 466, 468–469, 470; amplified fragment length polymorphisms (AFLPs), 552; DNA polymorphisms, 610; expected patterns of, 468; maintenance of, 210–211; protein polymorphism, 368; single nucleotide polymorphisms (SNPs), 458, 459, 461, 462, 464, 466, 471–472, 552; synonymous polymorphism, 468
polypeptides, 41
polyphyletic groups, 107
polyploidy, 21, 561, 603; allopolyploid speciation, 533, 556; allopolyploidy, 556, 561; autopolyploidy, 556
polyspermy, 556
polysporangiophytes, 145
population genetics, 4, 5, 10, 385, 729, 768; ancient population genetics, 477–479; population genetic models/theories, 462–463, 499
populations, 221–222, 231, 371, 661; changes within, 36–38; clonal populations, 754; crosses between, 326; demographic history of, 322; effective population size (Ne), 307, 310–311, 466, 472–473, 771–772; evolution in spatially structured populations, 325–326; exponential population growth, 813; intrinsic growth rates and, 288, 289; local adaptation and population divergence, 241–245, 242; local populations, 801; monomorphic populations, 624; polymorphic populations, 624; population bottlenecks, 771–772; population changes, 36–38; population divergence in hormone-mediated suites, 621; population fitness and evolutionary stability, 628; population isolation, 771–772; population trees, 803–804; population viscosity, 679; reproductive isolation and, 443; of selfing species, 359–360; studies of natural selection acting on variation within a population, 277; sympatric populations, 514; testing models of population history, 85–86; total human population size, 812. See also natural populations
Porifera, 162
porins, 749
posttranscriptional regulation, 380
Precambrian era, 29
predation, 300–301, 601, 602, 604; high-predation (HP) environments, 274; low-predation (LP) environments, 274; predators and diversification, 537–538
Price, George, 223, 590, 606, 625, 711
Price equation, 223
primates. See bonobos; chimpanzees; gorillas; macaques; orangutans
Principles of Geology, The (Lyell), 13, 15, 116
progymnosperms, 146
prokaryotes, 48, 127, 496; definition of, 128–129; deletion pressure in prokaryote genomes, 133; gene transfer in, 133; restriction endonucleases and, 133; role of horizontal gene transfer (HGT) in the evolution of, 131–132; symbioses and, 131
pronograde posture, 183
prosauropods, 181
proteins, 40, 41, 449–450, 729, 776, 778; central dogma of cellular proteins, 609, 610; directed evolution of, 776–777; DNA-binding proteins, 547; eosinophil cationic proteins (ECPs), 401; master regulatory proteins, 418; modification of DNA-associated proteins, 422; protease (protein capable of breaking peptide bonds), 774; protein essentiality, 429; protein polymorphism, 368; protein sequencing, 370; protein shuffling, 778; protein synthesis, 371; receptor proteins, 616; replacement and the protein-coding sequence, 466; synonymous and the protein-coding sequence, 466; transcription factor protein, 413. See also tumor necrosis factor-α (TNF-α)
Proterospongia, 163
Protista/protists, 136, 138, 350; Plasmodium falciparum, 735
Protostomia, 162
pseudocongruence, 76
Pseudomonas aeruginosa, 218
Pseudomonas fluorescens, 235, 565
Psisotales, 144
psychology, 609
pterosaurs, 180
pulsed-field gel electrophoresis (PFGE), 755
“Punctuated Equilibria: An Alternative to Phyletic Gradualism” (Gould and Eldredge), 25
punctuated equilibrium, 25, 25, 91
python (Python regius), external hand limb of, 35
quantitative genetics, 21, 219, 458; quantitative genetic variation, 45
quantitative trait locus (QTL), 413, 458, 459, 459–460, 610; QTL mapping, 444, 446, 452, 453, 460, 463, 464
race, 801; adaptive traits and the definition of human races, 807; biological meaning of, 801–802; biological races in chimpanzees, 803–804; biological races in humans, 804–806; lineage definition and, 804–805
rates. See macroevolutionary rates
Raven, Peter, 77
Ray, John, 817
recombinant inbred lines (RILs), 460
recombination, 128, 132–133, 195, 328, 375–376, 458, 496, 549, 556, 809, 810; definition of, 328, 329; ectopic recombination, 315; evolution of, 258–259; facilitation of selection and, 332–333; meiotic recombination, 459; molecular recombination, 329, 330; rates of, 329, 331; recombination load, 337–338; reinforcement and, 517–518; selection-recombination antagonism, 549–550, 551; sexual antagonism and, 389; V(D)J recombination mechanism, 353
reduction principle, 257
regulatory networks, 718; evolution of novel traits and their underlying gene regulatory networks, 448–450, 448; modular gene regulatory network, 444; testing of the same gene regulatory network, 448
reinforcement, 485, 498, 512, 513; definition of, 517; geographic patterns of, 518; one-allele mechanism and, 517–518; recombination and, 517–518; two-allele mechanism and, 517
relatedness, 215
religion, and evolution, 817–818, 823–824; the Bible and evolution, 11, 820–821; the Bridgewater treatises and, 818–819; the Christian Research Society’s “Statement of Belief” concerning the Bible and evolution, 821; effect of Darwin’s revolution on religion, 819–820; Jewish view of evolution, 821; Lutheran view of evolution, 821; Natural Theology and, 818; Pope John Paul II’s view of evolution, 821; Presbyterian view of evolution, 820–821; the problem of evil and, 821–822; the question of imperfect design (dysfunction) and, 822–823. See also creationism; intelligent design (ID)
Religious Philosopher, The (Nieuwentijdt), 818
Remipedia, 170
reproduction, 270; asexual reproduction, 288; costs of, 685; differential reproduction, 222; reproductive assurance hypothesis, 357, 361; reproductive competition and menopause, 724; reproductive conflict, 681–682; reproductive division of labor, 677; reproductive fitness, 710; reproductive isolation (reproductive isolating barriers), 496, 498, 512, 514–516, 518, 521, 523, 524, 529, 591, 594; reproductive skew, 677, 681. See also iteroparity; semelparity
reproductive biology, 357
reptiles, 30; jaws and dentary of, 31
rhynchocephalia, 179; Gephyrosaurus bridensis, 179. See also tuataras
Rhynie Chert, 114; Devonian Rhynie Chert, 158; plants of, 145–146
Rift Valley, 505
RNA, 40, 41, 83, 124, 125, 367–368, 376, 377, 414, 729; alternative splicing and, 374, 380, 397; amino tRNA synthetases, 127; genomic regions and, 385; micro RNAs, 168; noncoding RNA, 372; retroposition and, 397; ribosomal RNA (rRNA), 130, 132, 138, 173, 400, 404; RNA interference (RNAi), 413, 418; RNA polymerase, 128, 382, 384, 415; RNA-seq method, 414, 415; RNA viruses, 319; RNA World Hypothesis, 120; transfer RNA (tRNA), 404, 749, 774, 777. See also messenger RNA (mRNA)
roaches: Nauphoeta cinerea, 645
Roman Catholic Church, 11
rotifers: bdelloid rotifers, 132, 500
Sacred Theory of the Earth (Burnet), 818
Sagan, Carl, 833
Saguenay-Lac-Saint-Jean, recessive genetic disorders in the population of, 326
Saint-Hilaire, Étienne Geoffroy, 15
salamanders: Ambystoma mexicanum, 97, 98, 99; barred tiger salamanders (Ambystoma tigerinum mavortium), 770; Hemidactylium scutatum, 97, 98, 99; Plethodon salamanders, 561; Proteus anguinus, 97, 98, 99; tiger salamanders (Ambystoma californiense), 768, 770
salmon, Atlantic and Pacific, 272
Salmonella enterica, 674
saprotroph, 152
scala naturae (“ladder of nature”), 12
Schmalhausen, I. I., 256
scientific revolution, the, 11
sclerotization, 167
Scopes, John T., 21
Scyphozoa, 164
sea scorpions (Eurypterida), 169
sea slugs (Elysia), 141
sea spiders (Pycnogonida), 168–169
sea urchins (Diadema antillarum), 84
seals, elephant, 308
Sedgwick, Adam, 15
seeds: dispersal of in the common dandelion (Taraxacum officinale), 530; as a form of heterospory, 143; seed discounting, 360
segregation: Mendelian segregation, 348; segregation load, 337–338
Seilacher, Adolf, 160
selection. See natural selection
selection gradient, 238
selective sweeps, 471, 471; common statistics for the detection of sweeps, 471–472; single- and multiple-origin soft sweeps, 472–473
selector genes, 444
self-compatibility (SC), 362
self-fertilization, 340, 346, 357, 358, 590–591; evolution of, 359–360; measuring rates of, 342–343
self-incompatibility (SI), 341, 362, 590
selfish gene, 203
Selfish Gene, The (Dawkins), 203, 833
selfish genetic element (SGE), 347; applied uses of, 354; definition of, 347–348; diversity of, 348, 349, 350–352; genome evolution and, 352–353; population variation and, 353–354; research concerning, 348; speciation and, 254
self-organization, 697
self-pollination, 357; geitonogamy self-pollination, 360, 361; models of, 356–357
senescence, 718, 719; demographic senescence, 719; disposable soma theory and, 718, 721–722; origin of, 721; physiological senescence, 719; programmed death theory and, 718, 721. See also aging
sensory bias, 655
Sepkoski, J. Jack, Jr., 117, 582
Sepkoski diversity curve, 117–118
severe acute respiratory syndrome (SARS), 735
sex, 195, 328, 329; evolution of, 258–259; heterogametic sex, 387; homogametic sex, 387; same-sex sexual behavior (SSB), 710, 715–716; sex allocation and inbreeding, 344; sex-biased expression, 387; sex determination, 387; sexual antagonism, 710, 716. See also sex chromosomes, evolution of; sexual selection
sex chromosomes, evolution of, 387, 638–639; association of sex-specific expression with the trafficking of new genes, 409–410; gene content evolution of sex chromosomes, 392–393, 393; gene dose deficiency in heterogametic sex and, 391–392; gene trafficking and, 409–410; models of Y chromosome degeneration, 391; origin of sex chromosomes, 388–390, 389; origin of sex chromosomes from autosomes, 388–389; sex determination of chromosomes (genetic sex determination [GSD] and environmental sex determination [ESD]), 395–396
sexual propagation. See parthenogenesis
sexual selection, 210, 222, 225, 238, 387, 520, 521, 605, 606, 667, 695; definition of, 521; direct selection for genetic benefits, 651; diversity and, 521–522; ecological context of, 645–646; environmental sex determination (ESD), 387; Fisherian runaway sexual selection, 520, 523, 525–526; genetic incompatibility and, 527–528; “good genes” sexual selection, 520–521, 524–525; indirect selection for genetic benefits, 651–652; intersexual selection, 641; intrasexual selection, 641; mechanisms of sexual selection that cause speciation, 523–527; opportunity for, 634, 636; postmating isolation and, 527–528; prevention of extinction and, 639; processes of, 642; sensory drive and, 521, 523–524; sexual conflict and, 521, 526–527; sexual selection against hybrids, 527; total sexual selection, 645. See also male-male competition; mate choice; mating systems
shifting balance theory, 23
short tandem repeats (STRs), 316
signals: cues and, 657; signal intensity, 655; signal-to-noise ratio, 655
Silene latifolia, 228
Silurian era, 145; Late Silurian era, 30
simian immunodeficiency viruses (SIVs), 735
Simpson, George Gaylord, 25, 77, 491, 560, 561, 567, 579
single nucleotide polymorphisms (SNPs), 458, 459, 461, 462, 464, 468, 471–472, 552; microbial forensics and, 754, 756, 758
sink populations, evolutionary stasis in, 295–296
slime molds, 136, 153; Dictyostelium discoideum, 153, 218; Fonticula, 139; Physarum polycephalum, 153
snails, 165, 262, 325, 493, 509; Cepea nemoralis, 325; hermaphroditic snails, 360; zombie snails, 713–714
snakes, 61, 179, 227; ball python (Python regius), 35; correlation selection in garter snakes, plate 3; external hand limb of Python regius, 35; Lampropeltine snakes, 564; Najash rionegrina, 179; northwestern garter snake, 227
social exchange, 690
social parasitism, 668
Sociobiology (E. O. Wilson), 684, 692, 833
Solomon Island flycatchers, 545
somatic doubling, 556
source-sink dynamics, 288
South America, 36, 79, 80, 241, 301, 507, 510, 539; mammals of, 36
sparrows: house sparrow (Passer domesticus), 37
Spartina: S. anglica, 38; S. alterniflora, 38; S. maritima, 38
specialist organism, 282
specialization, limiting factors of, 235–236
speciation, 28, 38, 496, 521, 531, 561, 586, 599; chromosomal rearrangements and, 555–556; cladogenetic speciation, 508; coevolved symbionts and, 539; considerations when studying natural selection and speciation, 516–517; cospeciation, 535, 540–541, 541; definition of, 550; diversification and, 565–565; drivers of (antagonistic trophic interactions and competition), 537–538; as the evolution of intrinsic barriers to gene exchange, 492, 512–513; genome evolution and, 549–558; genomic architecture and, 557; geography of speciation and extinction, 603–604; macroevolution and, 483–484; mechanisms of, 485–486; modes of, 603; mutation-order speciation, 485; mutualistic networks and, 538–539; parallel speciation, 512; rates of, 568–570; reciprocal speciation, 538; selfish genetic elements (SGEs) and, 354; sex chromosomes and, 556–557; species interaction, 599; species richness, 599; studies of, 494–495; symbiont-induced speciation, 535; vicariant speciation, 504, 506–507. See also coevolution, and speciation; speciation, genetics of; speciation, and geography; speciation patterns
speciation, genetics of, 543; ecological isolation and, 544; genetics of prezygotic isolation, 543–544; sexual isolation and, 544–545
speciation, and geography, 504, 506–508, 514, 550–551; challenges concerning, 510; geographic and geological triggers of speciation, 510; geographic patterns of species and speciation, 505–506; islands and their implications, 508–509; islands as “natural laboratories,” 508; speciation and area, 509–510. See also allo-parapatric speciation; allopatric speciation; parapatric speciation; peripatric speciation; sympatric speciation
speciation patterns, 496–497; in asexuals, 498–500; global diversity patterns, 501–502; linking of patterns with process, 502–503; in sexual eukaryotes, 497–498
species, 203, 321, 483; anagenetic species, 508; asexual species, 295; coexistence of, 602; in the context of gene flow, 533; diversity patterns of, 484; as the fundamental units of biodiversity, 489; morphospecies, 579; “primitive” or “older” distinctions for, 57; quasispecies, 774; sexual species, 295; sister species, 504, 505, 507; species-area relationships and, 509; species drift, 588; species richness, 504; testing the nature of, 496–497; transmutation of, 13–14, 17. See also species, concepts and definitions of; species selection
species, concepts and definitions of, 489–490; biological species concept (BSC), 24–25, 491, 492, 512, 520; character-based concepts, 490–491; cohesion and recognition as the basis for species definition, 492; evolutionary species concept, 491; “good species,” 570; phylogenetic concepts, 491
species selection, 200, 203, 575–576, 586; concepts of, 586–587; consequences of, 587–588; fossil-based tests and, 589–590; history and controversies concerning, 588–589; phylogeny-based tests and, 590–591; species sorting, 588
Spencer, Herbert, 19
sperm competition, 641, 644, 647
spiders, 167, 172, 262, 560, 677; diversity of, 169; fangs of, 168; jumping spiders, 169, 522; redback spiders (Latrodectus hasselti), 714–715, 715; social spiders, 302, 341; wolf spiders, 169
spiral cleavage, 162
sponges, 83, 114, 138, 159, 161, 164, 165, 576–577; intertidal sponges, 644; multicellularity and, 163; origins of, 163; sponge-specific sterane biomarkers, 115
squamates, 33, 178, 179. See also lizards; snakes
squid: same-sex behavior in, 716; use of luminescent bacteria by, 131
stabilizing (optimizing) selection, 207, 209, 225, 239, 240
Staphylococcus aureus (MRSA), 7, 735
stasis, 5, 25, 225, 247, 293, 486, 567, 571–572, 589, 812, 833; behavioral stasis, 704; the paradox of morphological stasis, 442–443
Stebbins, G. Ledyard, 362
stratigraphy, 112; geologic timescale of the International Commission on Stratigraphy, plates 1 and 2
subfunctionalization, 397, 401
substrates, extension of, 235
Summa Theologiae (Aquinas), 817
Sumner, William Graham, 19
symbiosis, 19, 131; extant symbioses, 141
sympatric speciation, 20, 21, 489, 496, 504, 507, 509, 510
synapomorphy, 51
syntrophy, 131
SYR genes, 389
Systema Naturae (Linnaeus), 12
Systematic Theology (Strong), 820
Systematics and the Origin of Species (Mayr), 24–25
tagma, 167
taphonomy, 112, 576; fossilization and, 113–115
Taphrinomycotina, 156
Tardigrada, 170
Tasmanian devils, 772
taxa/taxon, 106–107, 497, 602–603; definition of, 579; taxon sampling, 57
taxonomy, 21, 496; codes used for taxonomic naming bacteria, plants, and animals, 107; evolutionary taxonomy, 107–108; in historical context, 106–107; least inclusive taxonomic unit (LITU), 109; prokaryote taxonomy, 500. See also nomenclature
teleology: Aristotelian teleology, 20; teleological (goal-oriented, purposeful) thinking, 11, 19
teleosts, 597
tempeh (Rhisopus oryzae), 154
Tempo and Mode in Evolution (G. G. Simpson), 25, 567
termites, 141, 155, 172, 216, 539, 669, 697, 699; colony structure of, 698, 700; defenses of, 215; farming of fungus by, 760; towers of, 215
Testimony of the Rocks, The (H. Miller), 819
Tetrahymena, 421
tetrapods, 28, 30, 165; Acanthostega, 30, 32, 176; ancestry of, 174–175; Elpistostege, 175–176; Ichthyostega, 30, 32, 176; overview of tetrapod evolution, 175; Panderichthys, 32, 176; pattern of tetrapod limbs, 32; shared characteristics of with fishes, 33–34; Tiktaalik, 32, 176; transition of lobe-finned fish to tetrapods, 31–32, 32
thermoacidophiles, 128
thermophiles, 128
Thiry, Paul-Henri (Baron d’Holbach), 12
Thompson, William (Lord Kelvin), 18–19
thrifty genotype hypothesis, 811
ticks, 169
Tinamou (Tinamus major), 108
Tinbergen, Nikolaas, 609
tits: blue tits, 799; great tits (Parus major), 323, 669
toads. See frogs
tolerance, 282; adaptive variation in, 284–285; physiological tolerance, 283
tool usage, 186–187, 694; in chimpanzees, 6, 708, 709; Oldowan tool industry, 183; tool manufacture, 183; use of stone tools, 186
tortoises, 309
total daily energy expenditure (TDEE), 739
tradeoffs, 193, 195, 240, 268, 270, 271, 616, 722, 733; elusiveness of, 274; genetic correlation and, 250; genetically-based tradeoffs as a limit and constraint to evolution, 249–251; quality-quantity tradeoff in sexual selection, 651–652; study of, 250; tradeoffs in human traits, 737–738
trait(s), 100, 101, 195, 589; adaptive traits and the definition of human races, 807; aggregate species traits, 586, 587; analysis of multiple traits, 103–104; analysis of single traits, 102–103; chromosomal linkage and, 250; complex traits, 365, 458; effect of genes on, 248; emergent traits, 586, 587; fitness measure and, 195; genetic variation in complex traits, 458–459; homologous traits, 444; individual traits, 203; interactions among, 442–443; life history traits, 193, 195; optimality models and, 683, 684; performance traits, 280; phylogenetic signals and, 103; quantitative traits, 611; “racial” traits, 807; rates of trait evolution, 570–572; robust traits, 262; serial homologous traits, 444; signals (traits modified by selection), 521; species-level traits, 586–588; trait disparity, 571; trait evolution and lineage diversification, 104–105
transcription, 774
transcription factors (TFs), 429, 444, 445–446, 449, 774, 778; evolution of TFs, 418; evolution of TF factor binding, 418; feedforward loops and, 428, 434
transcription-coupled repair (TCR), 319
transgenic organisms, 444–445, 447
transitions. See fossils/fossil record, transitions in
transmutation, of species, 13–14, 17
transposable elements (TEs), 315, 316, 348, 350, 352, 353, 372, 375, 308, 406, 420; DNAX TEs, 407; as “domesticated,” 407; Pack-Mule TEs, 407
tree of life, the, 5, 6, 9, 138; fungi in, 152–153. See also phylogenetic tree(s)
trends. See macroevolutionary trends
Triassic era, 36; Early Triassic era, 180; end-Triassic, 581; Late Triassic era, 180
Trivers, Robert, 674
tuataras, 178, 179, 769; Sphenodon guntheri, 767; Sphenodon punctatus, 766
tumor necrosis factor-α (TNF-α), 774, 776
ultraconserved elements, 380, 381, 385–386
unicoloniality, 219
uniformitarianism, 10, 13, 112, 116
Unikonta (“unikonts”), 153
unity of type, 28, 29, 30, 32–33
Ustilaginomycotina, 155
variation, 222; adaptive variation in regulation, 285; adaptive variation in tolerance, 284–285; among species, 17–18; impact of natural selection on molecular variation, 370–371; molecular basis for, 26; in natural populations, 23; natural variations and fitness in the wild, 620; natural variations versus mutations, 612–613; physiological variation, 283; predictions of the neutral theory for variation within and between species, 370; spatial variation, 211; studies of natural selection acting on variation within a population, 277; temporal variation, 211. See also genetic variation
vascular tissue, composition of, 143
Vendian era, 160
Verrucomicrobia, 130
vertebrates, 34, 35; comparison of hand appendages in, 13; early vertebrates, 29–30; Haikouichthys, 29; Myllokunmingia, 29. See also tetrapods
vesicles, 120; lipid vesicles, 124; phospholipid vesicles, 124
Vestiges of the Natural History of Creation, The (Chambers), 14
viability, absolute, 206
vicariance/vicariance event, 76; vicariance biogeography, 77
virulence, 741. See also parasite virulence
vitamin C, synthesis of, 34
Voltaire, 818
von Frisch, Karl, 609
von Humboldt, Alexander, 76
von Linné, Karl. See Linnaeus, Carolus
Waddington, Conrad H., 93–94, 96, 267, 420, 421
walkingsticks (Timema cristinae), 324, 516, 601–602; coloration in, 322
Wallace, Alfred Russel, 17, 76–77, 222, 506, 725; as the “father of zoogeography,” 76; principal works of, 76
wasps: paper wasps (Polistes dominulus wasps), 674, 680
waterfalls, effect of on species diversity, 273–274
Weismann, August, 19, 20, 201, 231, 333, 425; germ plasm theory of, 720
Wells, William Charles, 17
Whewell, William, 29
whooping cranes, 308
Williams, George C., 201–202, 203, 272–273, 587–588, 589, 733–734, 833; on antagonistic pleiotropy, 721
Wilson, Edward O., 270, 271, 508, 509, 684, 692, 833
Wisdom of God Manifested in the Works of Creation, The (Ray), 817–818
Wolbachia, 306, 352, 354, 407, 539, 675, 745
wolves: Mexican wolves, 309
Wonderful Life (Gould), 834
worms, 160, 165, 358; echiuran worm (Bonellia virdis), 395; fall army worm (Spodoptera frugiperda), 556–557
Wright, Sewall, 22–23, 255, 307, 561, 610; on genetic drift, 23, 26; measurement of gene flow and, 771; “shifting balance” theory of, 23, 201
Wynne-Edwards, V. C., 588
xenology, 90
X-inactivation, 420
yeast, 152, 230, 382–383, 403; Caenorhabditis elegans, 351, 378, 403; prudent yeast strains, 325; Saccharomyces cerevisiae, 325, 382–383, 403, 404, 407, 431; yeast duplicate genes, 402
yuccas/yucca moths, interactions between, 538
Zoonomia; or the Laws of Organic Life (E. Darwin), 12, 15