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From page 351... ... sympatric species, 64, 65 fragilis, 151 ancestral species, 60, 63 Allochronic speciation, 136, 212 anthropophilic and domestic, 60, 61, 63 Allopatric speciation, 41, 42. See also arabiensis, 60, 61, 64, 65 Phylogeographic patterns bwambae, 61, 63 Anopheles, 64, 65 chromosomal speciation, 6, 51, 60-66 avian, 96, 97, 98, 101-102, 103-104, 145 gambiae, 51, 60, 61, 63, 64, 65 cichlids, 197 geographic distribution, 60, 61, 63 fig/fig-wasp mutualism, 136 hybrids, 65 genetic drift, 25 introgression in collinear segments, 166 inter-locus antagonistic coevolution, melas, 61, 62, 63 26, 27, 28 origins, 62 Mayr's model, 9-10, 24, 143, 163, 177 phylogeny, 62 neighbor species, 146, 147, 149, 150 quadriannulatus, 60-62, 63, 64 process and pace of, 145 reproductive isolation, 60, 62, 63, 64-65 reproductive isolation, 5, 9-10, 11, 20, subpictus, 60 24, 25, 27, 37-41, 97, 136, 163 zoophilic and exophilic, 60, 61 Rhagoletis, 92, 165, 175, 178 Antbirds (Thamnophilidae) Read the entire page →
From page 352... ... , 50 sex chromosomes and, 105-111 Australopithecus sexual conflict, 112-113 afarensis, 53-54 sexual imprinting, 96, 104-105, 106 ananmensis, 53 sexual selection, 91, 95, 96, 102, 107Autopolyploidy, 49 109, 111, 157 Avian speciation Solomon Islands, 96 allopatric, 96, 97, 98, 101-102, 103-104, song and, 101-105, 109, 111 145 species trees, 99-100 behavioral factors, 96, 102, 103, 106, sperm competition, 111, 112-113 157 sympatric, 91, 96-97, 102, 103-105 bottlenecks, 96 Ayala, Francisco J., 6, 46-68 chicken genome project, 95, 97, 110, 111, 112, 113 coloration, 157 B cryptic mate choice and, 102, 104, 106, 111-113 Baboons, 76 delimitation, 96, 97-101 Bacillus halodurans, 273 developmental recombination, 75 Bacillus subtilis, 272, 273, 336, 342 diagnosability, 97-98, 99 Bacteria divergence, 98, 99, 103 artificial chromosome libraries, 113 ecological selection, 96, 102, 103, 104 barrier to gene exchange, 234-235 environmental factors, 83 base composition analysis, 231-232 fast-X evolution, 109-110 clonal evolution, 269, 270, 272 gene trees, 98-101 defining species, 236-238 genealogical congruence, 99-101 determinants of gene exchange, 234 genetic incompatibilities, 95, 96, 97, 107 236 gene replacement, 234 Read the entire page →
From page 353... ... See also Species, diversity species generalization, 136-137 global survey, 3 Charlesworth, Brian, 31 Internet access to collections, ix, 3 Chicken genome project, 95, 97, 110, 111, Madagascar, 204-205 112, 113 Biological networks Chimpanzees, chromosomal speciation coexpression, 341 between humans and, 51-58 interactions, 344 Chippindale, A., 33 metabolic, 338-339, 340, 343-344 Chitridiomycota, 337 protein interaction, 340 Chlamydomonas reinhardtii, 338 proteome, 343 Chlamydophila pneumoniae, 233, 235 regulatory, 338-339, 342-343 Choanoflagellates, 336-337 scale-free, 340 Chromosomal speciation "small-world" concept, 340 Anopheles, 51, 60-66 transcriptional, 340-342 avian, 105-111 Biological species concept, v, vii, 5, 9-10, colinear regions, 52-57, 59, 166 20, 47-49, 69, 85, 97, 163, 201, 204, Drosophila, 58-60 244-245, 246, 247, 251, 258-261 humans and chimpanzees, 51-58 Biology, future of, 1-4. See also Systems hybrid dysfunction models, 6, 46, 49, biology 50-51 Bipedalism, 76-77 models, 49-51 Birds. Read the entire page →
From page 354... ... Ford, 270, 275 Delimitation, in avian speciation, 96, 97- Drosophila. See also Mating behavior, of 101 Drosophila de Queiroz, Kevin, 202, 243-263 balanced polymorphisms, 297-298 Developmental plasticity bristle number trait, 290, 303 ancestral, 79 chromosomal speciation, 6, 58-60 hypothesis, 78 conservation of DNA sequences, 294 and phenotypic variation, 69-87 296, 299-300 Developmental recombination cytogenetic cloning, 33-35 avian, 75 directional asymmetry, 81 bipedalism as, 76-77 divergence, 15, 18, 300 cause and effect, 73 Enhancer-of-split locus, 296, 299, 300, cross-sexual transfer, 74-75 312 gene expression consequences, 79-80 Exelixis collection of mutations, 327 heterochrony hypothesis, 78 fSNP survey, 286-303 Read the entire page →
From page 355... ... , 75 70 environmentally induced change, 81-83 extrapolation from laboratory to natural populations, 41-42 Read the entire page →
From page 356... ... , 127, 128, 107 130, 132-136 measuring variation in, 29, 32, 36 obtusifolia, 131 phenotypic variation and, 73 perforata, 131 and rate of genetic divergence, 25 Pharmacosycea, 123, 127, 131 reproductive behavior and, 9, 11, 12, pollinators associated with, 126, 128 13-17, 28-29, 31-32, 37-41 popenoei, 131, 132-136 underdominance, 17, 50, 51 Tpi gene, 127-129, 132 Flycatchers (Ficedula sp.) , 104, 110 Urostigma, 124, 126, 127, 131, 132-136 Forbes, Andrew, 162-181 Fig/fig-wasp mutualism Friberg, Urban, 24-45 allochronic model, 136 Read the entire page →
From page 357... ... in Drosophila, 286, 289-303 See also Reproductive isolation graphical sliding-window tests, 289, Genetic studies, potential of, 85-87 293, 294, 300 Genetic variation in silico functional annotation, 301-302 balancer chromosomes for measuring, neutral evolution patterns and, 296, 29, 33, 35 300 Drosophila, 31, 35-41 outgroup sequences, 292 epistatic interactions, 19, 35, 36, 310, and phenotypic variation, 286, 289 311 population structure and, 298, 301, 302 hemiclone analysis of, 6, 24-25, 28, 29 positive selection events and, 296-297, 30, 35-36, 37-41 300, 301-302 intersexual arms race, 27-28, 29, 37-41 promoter-reporter assays, 302 in mating behavior, 266, 309, 311-312, 323, 324-326 for net fitness, 33, 41 G future of studies of, 85-87 laboratory model system, 24-25, 27, Gamete recognition proteins, 111-112 28 Gammaproteobacteria, 236, 237, 278 responsiveness to, 73 Gene acquisition, 238-240 Genome Gene duplication, 343 ascomycete, 342 Gene expression chicken genome project, 95, 97, 110, developmental recombination and, 79- 111, 112, 113 80 choanoflagellate project, 336-337 divergence, 83-84 cohesion in bacteria, 233-234, 235 profiling, 341 comparative sequencing, 299, 303 regulation, 342, 343 Drosophila fSNPs, 289-303 Gene flows, 6, 164. See also Horizontal/ eukaryote sequencing, 333, 336-338 lateral gene transfer functional annotation, 286, 289, 291, cichlids, 182, 183, 191, 193, 197 299, 301-303, 340, 341-342, 344 fig/fig-wasp mutualism and, 133, 135, fungi, 337 136, 138 fusion theories, 265, 267, 268, 270-271, sea urchin speciation, 149, 156 273, 277-279, 280 Gene fusion, 333 human, 3, 287-289, 337, 344 Gene ontology categories, 318-323 innovation and evolution rates, 274Gene replacement, 234, 269 275 Gene transcription, 82 metazoa, 336-337 Gene transfer. Read the entire page →
From page 358... ... , 165, 176 population size of exchange groups, Heckman, Kellie L., 203-228 274-275 Heinsohn, Stefanie L., 307-331 prokaryotic evolution and, 268, 269-275 Heliocidaris sp., 146, 147, 151-152, 158 and rate of genome innovation and Hemicentrotus, 146 evolution, 274-275 Hemiclonal analysis and tree-of-life reconstruction, 269, cytogenetic cloning to construct 275-277 hemiclones, 33-35 speciation attributable to, 238-240 Drosophila, 6, 28-41 whole-genome analysis, 270, 273-274, of inter-locus antagonistic coevolution, 276-279, 333 24, 28-29, 37-42 Host colonization, 122 interpretation of results, 41-42 Host sharing, 129-131, 136-138 laboratory island population, 24, 30-32 Host switching, 124, 125, 131, 137 measuring genetic variation, 6, 24-25, House finch, 98 28, 29-30, 35-36, 37-41 Hudson�Kreitman�Aguade tests, 12 measuring net selection gradient on Human evolution standing phenotypic variation, 6, bipedal locomotion, 76-77 25, 29, 36 brain, 56-57, 58 Read the entire page →
From page 359... ... See Horizontal/ Inter-locus antagonistic coevolution lateral gene transfer adaptive allelic replacement, 25-26 Learning, avian song, 96, 103, 104-105 in allopatry, 26, 27, 28 Lepilemur, 218 defined, 25-26 Lerat, Emmanuelle, 201, 229-242 divergence rate, 26 Lessios, H A., 143-161 hemiclonal analysis, 24, 28-29, 37-41 Lethal genes, 12-13, 15 intergenomic conflict, 26-28 Leung, Brian, 162-181 intragenomic, 26 Lew, Timothy A., 24-45 laboratory model system, 24-25, 27, 28 Linder, Jodell E., 24-45 molecular studies, 24, 27-28 Linkage disequilibrium, 287 Interactomes, 343 Linkage mapping, 288 Intergenomic conflict, 26-28 Linnaeus, Carolus, 244, 258-259 Read the entire page →
From page 360... ... C., 266, 307-331 163, 201, 204, 244-245, 246, 247, 251, Madagascar. See also Malagasy vertebrates 258-261 biodiversity, 204-205 contributions, v, vi, vii-viii, 5, 9-10, 20 classification problems, 208 21, 24, 49, 87, 91, 96, 261 conservation priorities, 206 evolutionary animations, 144 field inventory program, 207-208 framework for studying speciation, Maize evolution, 75 163, 203-204, 205 Malagasy vertebrates sea urchin studies, 92, 143, 145, 155, cryptic variation, 207, 214-216, 219 156-157, 159 evolutionary patterns, 214-217 publications, viii geographic patterns, 212-217 on reproductive isolation in allopatry, long-tailed shrew tenrecs, 214-217 9-10 mouse lemurs, 217-223 on sexual isolation, 308 plated lizards, 209-211 McDonald�Kreitman test, 12, 17 rate of discovery, 205-206 Medina, M�nica, 332-349 reciprocal monophyly, 209, 211, 214, Meiotic drive, 17-18, 26, 71 218 Mendel, Gregor, vii species diversity, 207-223 Mendelian theory, vi study approach, 207-223 Metabolomes, 343-344 sympatry, 214, 216, 220 Methanobacterium thermoautotrophicum, 271 taxonomy, 209-211 Methanococcus janaschii, 270-271, 273 temporal dimension of diversification, Methanosarcina mazei Goe1, 278 212, 217-223 Methanogens, 270, 271, 272 trident bats, 212-214 Microarray data analysis, 314-315, 340 Malaria, 51. Read the entire page →
From page 361... ... , 209-211 Natural selection. See also Fitness sea urchins, 92, 143, 144, 146, 147-156, to abiotic factors, 17 157, 159 to biotic factors, 17, 25 whole-genome analysis, 270, 273-274, cichlids, 183, 197 276-277 defining, 70-72 Molecular research in divergence of speciation genes, 14, avian speciation, 95, 96 15, 17, 20, 28, 42-43 inter-locus antagonistic coevolution, parallel evolution by, 77 24, 27-28 phenotypic vs. Read the entire page →
From page 362... ... See also Polyspermy, 28 Developmental recombination Polytypic speciation, 144, 145, 147, 149, accommodation, 76 152, 155 adaptation as, 73-74 Population genetics, vii, 5 arms races and, 27 Drosophila, 293 developmental plasticity and, 69-87 fig/fig-wasp mutualism, 132-136, 137 Drosophila, 39, 286, 287, 315-317 Malawi cichlid species, 182-197 fitness effect, 73 properties emphasized by, 246 fSNPs and, 286, 289 Populus tricocarpa, 338 genetic component, 7, 69, 71, 73, 80-81 Porifera, 336 levels and net selection gradients, 29, Primates, 76, 112, 341 33, 36, 39-41 Prokaryotes mating behavior and, 315-317 alkaliphilic, 273 measuring, 6, 25, 29, 35, 36 genome evolution, 269, 270, 274-275 and natural selection, 7, 71-72, 286, 289 genome projects, 333, 336 net selection gradient on, 6, 25, 29, 36 horizontal gene transfer, 268, 269-275 origins of, 70, 289 phylogenetic reconstruction, 267, 269, and reproductive isolation, 83-85, 86 273-274 reproductive traits, 26, 27 population size, 274-275 SNPs, see Functional SNPs tree of life, 275-275 Read the entire page →
From page 363... ... See also Fitness; Reproductive proteins, 28, 111-113 Speciation arms-race evolution, 113 in allopatric populations, 5, 9-10, 11, bindin evolution, 143, 146-147, 149-152, 20, 24, 25, 26, 27, 37-41, 97, 136, 163 153-155, 156, 157-159 in Anopheles, 60, 62, 63, 64-65 Rhagoletis cingulata, 176 in avian populations, 84, 95, 97, 101- Rhagoletis electromorpha, 168-170, 175, 176 105, 106, 107, 110-111 Rhagoletis pomonella (apple maggot fly) chromosomal rearrangements and, 51 sibling species complex developmental recombination and, 83- allochronic isolation, 176 85, 86 allopatric speciation, 92, 165, 175, 178 and divergence, 70, 83-84, 85 apple host, 165 in Drosophila, 9, 11, 12, 13-20, 28-29, 31- biogeography, 162-179 32, 37-41, 59-60, 107, 311 chromosomal speciation, 162-163, 165, body size and, 84-85 166-167, 168-176 ecological, 11 diapause traits, 162, 165, 166, 176 female resistance to male-induced DNA sequencing, 165, 166-167, 169, harm, 27, 37-41 176 ecological adaptation, 164-165, 173, 177 Read the entire page →
From page 364... ... haplotype divergence, hybridization, 158 165-166, 170, 171, 174, 176 Mayr's animation of, 92, 143, 145, 155, molecular clock, 170, 171 156-157, 159 polytene chromosome spreads, 179 mitochondrial cytochrome oxidase I relative node depths, 167, 170, 171-173, genes, 146-153, 155 175 molecular phylogenies, 92, 143-159 reproductive isolation, 165, 166, 177- nontropical species, 145 178 old clades (group 4) , 145, 146, 147, 148, secondary contact, 167, 172-174, 175, 151-152, 153, 154, 155, 156, 157 177, 178 polytypic species, 145, 147, 149, 152, Sierra Oriental population bridge, 176 155 sympatric host race formation, 92, 162- rate of, 143-144, 150, 152, 153-155, 157, 179 159 Rhagoletis suavis, 176 regulatory networks, 342 Rhagoletis tabellaria, 169 reproductive isolation, 150-151, 156Rhizobiaceae, 233 157, 159 Rhizocladus, 124 reinforcement in, 158 Rice, William R., 6, 24-45 sexual arms race, 158 Ring of life, 278, 279-281 sister species, 146, 147, 152, 155 Rivera, Maria C., 267-285 sympatric overlap (group 3) Read the entire page →
From page 365... ... See also Allopatric speciation; Species problem, 10 Avian speciation; Chromosomal asexual organisms, 236-238, 248 speciation; Divergence; biological species concept, vii, 5, 20, 47 Reproductive isolation; Sympatric 49, 243, 245, 246, 252, 258-260 speciation cause of, 254-256 defined, 254 cell analogy, 251, 258 diagnosability, 97-98, 99 ecological species concept, 245, 246 founder effect models, 10, 20 247, 252-253 future of genetic studies, 85-87 evolutionary concept, vii, 245, 248, 251, gene acquisition and, 238-240 252 genetic drift in, 10, 20 genotypic cluster species definition, horizontal gene transfer and, 238-240 252 island, 10 horizontal gene transfer, 236-238 parapatric, 46, 51, 53, 57-58 hybrids and, 246 problems in, 10 incompatiblitiy of concepts, 245-247 process, 254-255 Mayr's "biological" term and, 244-245, reinforcement and, 10 246, 251, 258-261 Read the entire page →
From page 366... ... Ledyard, vi historical perspective, 345 Staphylococcus aureus, 233, 278 overview, 339 Streptococcus, 233 phylogenetically based inference in, Strongylocentrotus, 146, 147, 151-152, 154 336 droebachiensis, 151 research goals, 333 franciscanus, 152 Standing genetic variation, measuring nudus, 152 heritable fitness-related traits, 29 pallidus, 151 Stewart, Andrew D., 24-45 purpuratus, 151 Sulfolobus tokodaii, 278 Sunflowers, 51, 166 T Superspecies, 144 Swanson, Willie J., 95-119 Taxonomy, Malagasy plated lizards, 209 Swordtail, 12-13 211 Sycidium, 124, 126 Tellurium resistance protein, 237 Sycomorus, 126 Testosterone, 75 Symbiotic relationships, 280 Tetrapus, 123, 127 Sympatric speciation, 10-11 Thermophilic bacteria, 271, 272 Anopheles, 64, 65 Thermotoga maritima, 233 avian, 91, 96-97, 102, 103-105 Three-spined stickleback (Gasterosteus by ecological specialization, 164 aculeatus) , 77-78, 86 fig/fig-wasp mutualism, 136 Thymidine synthase, 333 host race formation, 92, 162-179 tmy gene, 18 Malagasy vertebrates, 214, 216, 220 Tracheloptychus sp., 209 mouse lemurs, 220 Transcription factor genes, 12, 14, 17 partly sympatric, 46 Transcriptional networks, 340-342 by reinforcement, 164 Transcriptional profiling, 313, 317-323, and reproductive isolation, 10, 11, 204 324-326 in Rhagoletis, 162-179 Tree of life sea urchins, 143, 145-159 Ecdysozoa vs. Read the entire page →
From page 367... ... speciation Voles (Microtus sp.) , 75 allopatric models, 197 amplified fragment-length polymorphism markers, 183 W gene exchange, 93, 193, 196 Wallace, Alfred, 30 gene flows, 182, 183, 191, 193, 197 Wang, Yong, 92-93, 182-200 HapSTR loci, 184-185, 186, 187, 196-197 West-Eberhard, Mary Jane, 6, 69-89 hybridization, 183 Wiebesia, 123, 124, 125 isolation-with-migration model, 182, Wilson, Edward O., ix, 1-4 183-193, 196-197 Won, Yong-Jin, 92-93, 182-200 migration rates, 190-193, 194 World Health Organization, 51 mutation rates, 186-187, 189, 193, 196- Wright, Sewall, vi, 85, 247 197 natural selection, 183, 197 phylogenetic history, 193 X population size, 182, 190-192 rate of, 195-196 Xie, Xianfa, 162-181 reproductive age, 187 Xiphophorus, 12-13 shared variation, 183 Xmrk-2 gene, 12, 13, 17 Tanganyika outgroup divergence, 182, Xylella fastidiosa, 278 185, 187-189, 197 time of divergence, 190, 191, 193, 195 Trout (Salmo) Read the entire page →

From page 351...

... sympatric species, 64, 65 fragilis, 151 ancestral species, 60, 63 Allochronic speciation, 136, 212 anthropophilic and domestic, 60, 61, 63 Allopatric speciation, 41, 42. See also arabiensis, 60, 61, 64, 65 Phylogeographic patterns bwambae, 61, 63 Anopheles, 64, 65 chromosomal speciation, 6, 51, 60-66 avian, 96, 97, 98, 101-102, 103-104, 145 gambiae, 51, 60, 61, 63, 64, 65 cichlids, 197 geographic distribution, 60, 61, 63 fig/fig-wasp mutualism, 136 hybrids, 65 genetic drift, 25 introgression in collinear segments, 166 inter-locus antagonistic coevolution, melas, 61, 62, 63 26, 27, 28 origins, 62 Mayr's model, 9-10, 24, 143, 163, 177 phylogeny, 62 neighbor species, 146, 147, 149, 150 quadriannulatus, 60-62, 63, 64 process and pace of, 145 reproductive isolation, 60, 62, 63, 64-65 reproductive isolation, 5, 9-10, 11, 20, subpictus, 60 24, 25, 27, 37-41, 97, 136, 163 zoophilic and exophilic, 60, 61 Rhagoletis, 92, 165, 175, 178 Antbirds (Thamnophilidae)

Index Pages 351-368

Index
Pages 351-368