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Index

A

Abalone, 28, 112

Accessory gland proteins, 112

Accommodation, 76.

See also Genetic accommodation

Acoustic adaptations, 103, 219-220

Adaptive allelic replacement, 25-26, 35-36

African firefinch, 106

Agriculture, 61, 63-64, 338

Allocentrotus, 146

fragilis, 151

Allochronic speciation, 136, 212

Allopatric speciation, 41, 42.

See also Phylogeographic patterns

Anopheles, 64, 65

avian, 96, 97, 98, 101-102, 103-104, 145

cichlids, 197

fig/fig-wasp mutualism, 136

genetic drift, 25

inter-locus antagonistic coevolution, 26, 27, 28

Mayr’s model, 9-10, 24, 143, 163, 177

neighbor species, 146, 147, 149, 150

process and pace of, 145

reproductive isolation, 5, 9-10, 11, 20, 24, 25, 27, 37-41, 97, 136, 163

Rhagoletis, 92, 165, 175, 178

sea urchins, 145, 146, 147, 148, 147-149, 152, 153, 154-155, 156, 157

Allopolyploidy, 49

Aluja, Martin, 162-181

Amebozoa, 333

Amino acid replacement, 5, 52, 157-158

Angiosperms, 49

Annelida, 336

Anopheles

adaptation to marginal conditions, 63-64

agriculture and, 61, 63-64

allopatric vs. sympatric species, 64, 65

ancestral species, 60, 63

anthropophilic and domestic, 60, 61, 63

arabiensis, 60, 61, 64, 65

bwambae, 61, 63

chromosomal speciation, 6, 51, 60-66

gambiae, 51, 60, 61, 63, 64, 65

geographic distribution, 60, 61, 63

hybrids, 65

introgression in collinear segments, 166

melas, 61, 62, 63

origins, 62

phylogeny, 62

quadriannulatus, 60-62, 63, 64

reproductive isolation, 60, 62, 63, 64-65

subpictus, 60

zoophilic and exophilic, 60, 61

Antbirds (Thamnophilidae), 104

Antisymmetry, 81

Ants, socially parasitic, 84



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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Index A Abalone, 28, 112 Accessory gland proteins, 112 Accommodation, 76. See also Genetic accommodation Acoustic adaptations, 103, 219-220 Adaptive allelic replacement, 25-26, 35-36 African firefinch, 106 Agriculture, 61, 63-64, 338 Allocentrotus, 146 fragilis, 151 Allochronic speciation, 136, 212 Allopatric speciation, 41, 42. See also Phylogeographic patterns Anopheles, 64, 65 avian, 96, 97, 98, 101-102, 103-104, 145 cichlids, 197 fig/fig-wasp mutualism, 136 genetic drift, 25 inter-locus antagonistic coevolution, 26, 27, 28 Mayr’s model, 9-10, 24, 143, 163, 177 neighbor species, 146, 147, 149, 150 process and pace of, 145 reproductive isolation, 5, 9-10, 11, 20, 24, 25, 27, 37-41, 97, 136, 163 Rhagoletis, 92, 165, 175, 178 sea urchins, 145, 146, 147, 148, 147-149, 152, 153, 154-155, 156, 157 Allopolyploidy, 49 Aluja, Martin, 162-181 Amebozoa, 333 Amino acid replacement, 5, 52, 157-158 Angiosperms, 49 Annelida, 336 Anopheles adaptation to marginal conditions, 63-64 agriculture and, 61, 63-64 allopatric vs. sympatric species, 64, 65 ancestral species, 60, 63 anthropophilic and domestic, 60, 61, 63 arabiensis, 60, 61, 64, 65 bwambae, 61, 63 chromosomal speciation, 6, 51, 60-66 gambiae, 51, 60, 61, 63, 64, 65 geographic distribution, 60, 61, 63 hybrids, 65 introgression in collinear segments, 166 melas, 61, 62, 63 origins, 62 phylogeny, 62 quadriannulatus, 60-62, 63, 64 reproductive isolation, 60, 62, 63, 64-65 subpictus, 60 zoophilic and exophilic, 60, 61 Antbirds (Thamnophilidae), 104 Antisymmetry, 81 Ants, socially parasitic, 84

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Aphids, 84 Apple (Malus pumila), 165 Aquifex aeolicus, 233, 273 Arabidopsis lyrata ssp. petraea, 136 Arabidopsis thaliana, 338, 341 Arbacia sp., 146, 147, 151-152 Archaea, 270, 271, 273 Archaeoglobus fulgidus, 271, 272, 273, 278 Arctic charr (Salvelinus), 78 Ardipithecus ramidus, 53 Arms-race evolution, 6 genetic, 20; see also Inter-locus antagonistic coevolution intersexual, 27-28, 29, 41 interspecific antagonistic coevolution, 25, 28 in reproductive proteins, 113 Artificial chromosome libraries, 113 Artificial selection, directional asymmetry, 81 Ascomycota, 337 Aspergillus nidulans, 337 Association mapping, 287, 288, 302 Assortative mating, 156, 311 Australian grassfinches. See Poephilia Australian grasshoppers (Morabinae), 50 Australopithecus afarensis, 53-54 ananmensis, 53 Autopolyploidy, 49 Avian speciation allopatric, 96, 97, 98, 101-102, 103-104, 145 behavioral factors, 96, 102, 103, 106, 157 bottlenecks, 96 chicken genome project, 95, 97, 110, 111, 112, 113 coloration, 157 cryptic mate choice and, 102, 104, 106, 111-113 delimitation, 96, 97-101 developmental recombination, 75 diagnosability, 97-98, 99 divergence, 98, 99, 103 ecological selection, 96, 102, 103, 104 environmental factors, 83 fast-X evolution, 109-110 gene trees, 98-101 genealogical congruence, 99-101 genetic incompatibilities, 95, 96, 97, 107 habitat-dependent selection, 103, 104 Haldane’s rule, 105, 107-109, 110 hierarchy in, 157 hybridization, 102, 104, 105, 107-109, 110-111 internal factors, 96 intraspecific niche polymorphism, 103 large X(Z)-effect, 105, 109 learning, 96, 103, 104-105 mimicry, 105, 106 molecular research, 95, 96 morphological adaptations, 99, 101, 103, 104, 157 parapatric, 102 phylogeographic patterns, 101-103, 105, 113 plumage, 102, 103-104, 109, 111, 157 Poephilia finches, 98-99 reinforcement, 95, 96, 97, 110-111 reproductive character displacement, 103-104 and reproductive isolation, 84, 95, 97, 101-105, 106, 107, 110-111 reproductive proteins and, 111-113 sea urchins compared, 157 sex chromosomes and, 105-111 sexual conflict, 112-113 sexual imprinting, 96, 104-105, 106 sexual selection, 91, 95, 96, 102, 107-109, 111, 157 Solomon Islands, 96 song and, 101-105, 109, 111 species trees, 99-100 sperm competition, 111, 112-113 sympatric, 91, 96-97, 102, 103-105 Ayala, Francisco J., 6, 46-68 B Baboons, 76 Bacillus halodurans, 273 Bacillus subtilis, 272, 273, 336, 342 Bacteria artificial chromosome libraries, 113 barrier to gene exchange, 234-235 base composition analysis, 231-232 clonal evolution, 269, 270, 272 defining species, 236-238 determinants of gene exchange, 234-236 gene replacement, 234

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary genetic distances, 272 genome cohesion, 233-234, 235 genome size, 230 horizontal/lateral gene transfer, 201-202, 229-240, 270-273 ortholog phylogenies, 234, 277 phylogenetic disruption by gene transfer, 231-232, 233-234, 237, 238 speciation attributable to gene acquisition, 238-240 systematic classification, 230 tellurium resistance protein, 237 thermophilic, 271, 272 whole-genome analysis, 277-279 in zebrafish digestive tract, 82 Balakrishnan, Christopher N., 95-119 Balancer chromosomes, 29, 33, 35 Baldwin effect, 7 Basidiomycete, 337 Basidiomycota, 337 Bikonts, 333, 334-335 Bindin evolution, 143, 146-147, 149-152, 153-155, 156, 157-159 Base composition analysis, 231-232, 272 Biodiversity. See also Species, diversity global survey, 3 Internet access to collections, ix, 3 Madagascar, 204-205 Biological networks coexpression, 341 interactions, 344 metabolic, 338-339, 340, 343-344 protein interaction, 340 proteome, 343 regulatory, 338-339, 342-343 scale-free, 340 “small-world” concept, 340 transcriptional, 340-342 Biological species concept, v, vii, 5, 9-10, 20, 47-49, 69, 85, 97, 163, 201, 204, 244-245, 246, 247, 251, 258-261 Biology, future of, 1-4. See also Systems biology Bipedalism, 76-77 Birds. See also Avian speciation fitness, 107 migrant, 84 parental behavior, 75 plumage color, 83 polyspermy, 113 Black-bellied firefinch, 106 Black-bellied seedcracker (Pyrenestes ostrinus), 103 Blastophaga, 124 Bock, Walter J., viii Brain evolution, 56-57, 58 Buchnera, 233 Bush, Guy, 92, 163, 177 Buttercups, 84 Butterflies, 84 C Caenorhabditis elegans, 336, 337, 341, 343 California mice (Peromyscus californicus), 75 Calkins, Jennifer D., 95-119 Catastrophic sexual transmutation hypothesis, 75 Ceratosolen, 123, 125, 126 Chalcid wasps (Agaonidae, Chalcidoidea). See also Fig/fig-wasp mutualism diversity, 123 phylogeny, 135-136 species generalization, 136-137 Charlesworth, Brian, 31 Chicken genome project, 95, 97, 110, 111, 112, 113 Chimpanzees, chromosomal speciation between humans and, 51-58 Chippindale, A., 33 Chitridiomycota, 337 Chlamydomonas reinhardtii, 338 Chlamydophila pneumoniae, 233, 235 Choanoflagellates, 336-337 Chromosomal speciation Anopheles, 51, 60-66 avian, 105-111 colinear regions, 52-57, 59, 166 Drosophila, 58-60 humans and chimpanzees, 51-58 hybrid dysfunction models, 6, 46, 49, 50-51 models, 49-51 polyploidy and, 49-50 rearrangements, 52-57 suppressed-recombination model, 6, 46-47, 50, 51, 53, 54-57, 59-60, 63-65 Cichlid speciation Lake Malawi. See Tropheops speciation Lake Tanganyika, 182, 185, 187-189, 197

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Clonal evolution, 269, 270, 272 Clostridium acetobutylicum, 273 Cnidaria, 336 Cocladogenesis, 122, 124 Coevolution. See also Fig/fig-wasp mutualism; Inter-locus antagonistic coevolution finer-scale, 126-129, 138 Collared flycatchers (Ficedula albicollis), 104, 110 Coluzzi, Mario, 6, 46-68 Complexity hypothesis, 270, 273-274 Conservation of DNA sequences, 112, 294-296, 299-300, 301, 302, 342 of genes, 83 of host associations, 124 of protein interactions, 343 regulatory, 342 of variation, vii, 15 Crenarchaea, 267 Cross-sexual transfer, 74-75 Cryptic variation, 207, 214-216, 219 Cyanobacteria, 267, 270, 273 Cytochrome oxidase genes, 124, 127-129, 135, 146-153, 155 Cytogenetic cloning, 33-35 Cytonuclear conflict, 26 D Dambroski, Hattie, 162-181 Darwin, Charles, v-vi, vii, 30, 41-42, 244, 250, 251, 268, 275 Darwin’s finches, 103, 104, 105 Daubin, Vincent, 201, 229-242 Delimitation, in avian speciation, 96, 97-101 de Queiroz, Kevin, 202, 243-263 Developmental plasticity ancestral, 79 hypothesis, 78 and phenotypic variation, 69-87 Developmental recombination avian, 75 bipedalism as, 76-77 cause and effect, 73 cross-sexual transfer, 74-75 gene expression consequences, 79-80 heterochrony hypothesis, 78 molecular level, 77 and parallel species pairs, 77-79, 83 plasticity hypothesis, 78 and properties of species, 83-85 reexpression of lost phenotypes, 78 reproductive isolation and, 83-85, 86 Developmental switches, 74, 76, 78 Diadema sp., 146, 148, 149-151, 156 Diagnosability, 97-98, 246, 252 Dihydro folate reductase, 333 Divergence. See also Speciation avian, 98, 99, 103 chimpanzees, 53-58 developmental-pathway, 83 Dobzhansky–Muller model, 5, 13 Drosophila, 15, 18, 300 genetic, 6, 14, 15, 17, 20, 24, 25, 28, 42-43, 73, 83-84, 152-155 intraspecific, 84 Malawi cichlid species, 182-197 parallel species pairs, 78 predictions, 152-155 process, 254-256 properties by stage of, 254-256 rapid, 24, 27 rates, 25, 26 recent, 91-93 reproductive isolation and, 70, 83-84, 85 sequence of events, 72-74 Directional asymmetry, 81 DNA, noncoding, 288-289, 293-294 Dobzhansky, Theodosius, vi, vii, 47-49, 85, 87, 163-164, 177, 247 Dobzhansky–Muller incompatibility, 5, 13 Dogs, bipedal, 76 Doolittle, W. Ford, 270, 275 Drosophila. See also Mating behavior, of Drosophila balanced polymorphisms, 297-298 bristle number trait, 290, 303 chromosomal speciation, 6, 58-60 conservation of DNA sequences, 294-296, 299-300 cytogenetic cloning, 33-35 directional asymmetry, 81 divergence, 15, 18, 300 Enhancer-of-split locus, 296, 299, 300, 312 Exelixis collection of mutations, 327 fSNP survey, 286-303

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Gene Disruption Project, 327 gene ontology categories, 318-323 genetic variation, 31, 35-41 genome sequencing, 289-298, 336 hemiclonal analysis, 6, 28-41 Hmr gene, 12, 14, 17 hybrids, 6, 13-17, 59, 107 interactomes, 343 introgression in collinear segments, 166 laboratory island population, 24-25, 27, 28, 30-42 mating behavior, 37-41, 266, 307-327 mauritana, 13-14, 18, 310 melanogaster, 13, 14, 15, 16, 28-43, 286, 287, 288-303, 337, 341, 343 neutral evolution patterns, 296 noncoding DNA, 288, 293-294 Notch signaling, 289-290, 293, 303 nuclear genome, 59 Nup96 gene, 12, 15, 16, 17 OdsH gene, 12, 14, 17 outgroup sequences, 292 peripheral nervous system development, 289-290, 293, 303 persimilis, 51, 58-60, 65, 310 phenotypic variation, 39, 286, 287, 315-317 population genetics analysis, 293 population structure, 298, 301 positive selection events, 296-297 pseudoobscura, 18-19, 51, 58-60, 65, 166, 287, 292, 293-294, 295, 296, 297, 299, 300, 310 quantitative trait loci, 310, 312, 323 regulatory networks, 342, 343 reproductive proteins, 112 reproductive isolation, 9, 11, 12, 13-19, 28-29, 31-32, 37-41, 59-60, 107, 311 sequence traces, 292 sexual isolation, see Sexual isolation in Drosophila simulans, 13-14, 15, 16, 18, 286, 292, 293-294, 297, 298, 310 speciation genes, 13-17, 20, 59 suppressed-recombination model of speciation, 51 tmy gene, 18 Duplicate gene families, 17 Dwarf hamsters (Phodobus sp.), 75 E East Pacific Barrier, 155-156 Echinometra sp., 146, 147, 149-151, 154, 156, 157, 158 Echinothrix, 156 Ecological selection avian, 96, 102, 103, 104 phytophagous insects, 163 sea urchin, 159 Ecological speciation hypothesis, 85 Edwards, Scott V., 95-119 El Niño events, 104 Embryophyta, 338 ENCODE initiative, 344 Endosymbionts, 275-276, 280 Enterobacteriaceae, 233, 235 Environmentally induced change avian speciation, 83 evolutionary potential, 81-83 persistence of traits, 83 Eretmodini, 185 Eretmodus cyanostictus, 185, 187, 189 Escherichia coli, 231-232, 233, 234, 235, 236, 237, 270, 272, 273, 336, 341, 342, 343 Eubacteria, 267, 271, 272 Eucidaris sp., 146, 147, 147-149, 156 Eukaryotes autogenous theories, 279, 280 chimeric theories, 271, 279, 280 collections, 3 compartmentalization, 268 consensus tree, 333, 334-335 diploid cells, 269 genome fusion theories, 265, 267, 268, 270-271, 273, 277-279, 280 genome sequencing, 333, 336-338, 342 horizontal gene transfer and, 268-269, 270-271, 273 nuclear pore complex, 15 nucleus, 268-269, 277 ring of life, 278, 279-281 Eulemur, 218, 219 Evolution. See also Divergence; Human evolution; Speciation arms-race, 6, 20, 25, 27-28, 29, 41 clonal, 269, 270, 272 Darwinian natural selection, v-vi, 14, 70 environmentally induced change, 81-83 extrapolation from laboratory to natural populations, 41-42

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary fast-X(Z), 109-110 faster-male, 107 fig/fig-wasp mutualism, 122, 135 of laboratory-adapted populations, 29-43 laboratory model systems, 24, 27, 30-42; see also Hemiclonal analysis long-tailed shrew tenrecs, 214-217 male-driven, 109 modern theory of, v, vi-vii, 96, 244 multidisciplinary nature of, v neo-Darwinian Synthesis, vi, 5, 70-71 neutral patterns, 296, 300 parallel, 77-78, 83 population variation, vii rapid, 5-6, 15, 26, 32, 42 of similarity, 77 transcriptional, 340-342 Evolutionary significant unit (ESU), 206 Exelixis collection of mutations, 327 F Fast-X evolution, 109-110 Feder, Jeffrey L., 92, 162-181 Fibronectins, 77 Ficus (Moraceae). See also Fig/fig-wasp mutualism African, 126, 130 bullenei, 131, 132-136 C2E19 alleles, 132, 134 citrifolia, 132, 134 colubrinae, 131 diversity, 121 G3pdh gene, 127-129, 132, 135 glabrata, 131 Indo-Australian, 124, 126, 130 lutea, 130 maxima, 131 near-trigonata, 131, 132-136 neotropical (Panamanian), 127, 128, 130, 132-136 obtusifolia, 131 perforata, 131 Pharmacosycea, 123, 127, 131 pollinators associated with, 126, 128 popenoei, 131, 132-136 Tpi gene, 127-129, 132 Urostigma, 124, 126, 127, 131, 132-136 Fig/fig-wasp mutualism allochronic model, 136 allopatric model, 136 cocladogenesis, 122, 124 coevolutionary history, 123-126, 137 conservation of host associations, 124 cytochrome oxidase data, 124, 127-129, 135 description of, 91-92, 121-122 evolutionary dynamics, 122, 135 finer-scale coevolution, 126-129, 138 fitness, 138 gene flows, 133, 135, 136, 138 host colonization, 122 host sharing, 129-131, 136-138 host switching, 124, 125, 131, 137 hybridization, 122, 123, 126, 129, 131, 132-137, 138 introgression in neotropical figs, 122-123, 126, 129, 131, 132-136, 137, 138 isolation models, 132-135 molecular phylogenetic studies, 124, 126-129, 130-131 morphological studies, 122, 123-124, 137 one-to-one rule, 129-130, 136, 137, 138 phylogenies, 122, 124-125, 128, 131, 137 population genetic studies, 132-136, 137 strict-sense cospeciation hypothesis, 120, 122, 123-124, 126-129, 131, 136, 138 sympatric model, 136 Filchak, Kenneth E., 162-181 Fish, migrant, 84 Fisher, R. A., vi, 85 Fitness. See also Reproductive isolation in birds, 107 defined, 70 in fig/fig-wasp mutualism, 138 genetic variation and, 33, 41 in hybrids, 5, 9, 11, 12, 13-17, 50, 51, 107 measuring variation in, 29, 32, 36 phenotypic variation and, 73 and rate of genetic divergence, 25 reproductive behavior and, 9, 11, 12, 13-17, 28-29, 31-32, 37-41 underdominance, 17, 50, 51 Flycatchers (Ficedula sp.), 104, 110 Forbes, Andrew, 162-181 Friberg, Urban, 24-45

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Functional SNPs (fSNPs) identification association mapping, 287, 288, 302 balanced polymorphisms and, 297-298, 300, 301 conserved sequences and, 294-296, 299-300, 301, 302 in Drosophila, 286, 289-303 graphical sliding-window tests, 289, 293, 294, 300 in silico functional annotation, 301-302 neutral evolution patterns and, 296, 300 outgroup sequences, 292 and phenotypic variation, 286, 289 population structure and, 298, 301, 302 positive selection events and, 296-297, 300, 301-302 promoter-reporter assays, 302 G Gamete recognition proteins, 111-112 Gammaproteobacteria, 236, 237, 278 Gene acquisition, 238-240 Gene duplication, 343 Gene expression developmental recombination and, 79-80 divergence, 83-84 profiling, 341 regulation, 342, 343 Gene flows, 6, 164. See also Horizontal/lateral gene transfer cichlids, 182, 183, 191, 193, 197 fig/fig-wasp mutualism and, 133, 135, 136, 138 sea urchin speciation, 149, 156 Gene fusion, 333 Gene ontology categories, 318-323 Gene replacement, 234, 269 Gene transcription, 82 Gene transfer. See also Horizontal/lateral gene transfer Gene trees avian, 98-101 horizontal gene transfer, 269, 275-277 nuclear vs. mitochondrial, 101, 135 Genealogical congruence, 99-100, 252 Genera, defined, 250 Genetic accommodation, 7, 69, 73, 75, 80-81, 83 Genetic assimilation, 80 Genetic clustering, 97, 147, 150, 151-152 Genetic distance, 11, 83, 152, 272 Genetic drift, 10, 20, 25, 50, 133 Genetic hitchhiking, 110 Genetic incompatibilities, 95, 96, 97, 107. See also Reproductive isolation Genetic studies, potential of, 85-87 Genetic variation balancer chromosomes for measuring, 29, 33, 35 Drosophila, 31, 35-41 epistatic interactions, 19, 35, 36, 310, 311 hemiclone analysis of, 6, 24-25, 28, 29-30, 35-36, 37-41 intersexual arms race, 27-28, 29, 37-41 in mating behavior, 266, 309, 311-312, 323, 324-326 for net fitness, 33, 41 future of studies of, 85-87 laboratory model system, 24-25, 27, 28 responsiveness to, 73 Genome ascomycete, 342 chicken genome project, 95, 97, 110, 111, 112, 113 choanoflagellate project, 336-337 cohesion in bacteria, 233-234, 235 comparative sequencing, 299, 303 Drosophila fSNPs, 289-303 eukaryote sequencing, 333, 336-338 functional annotation, 286, 289, 291, 299, 301-303, 340, 341-342, 344 fungi, 337 fusion theories, 265, 267, 268, 270-271, 273, 277-279, 280 human, 3, 287-289, 337, 344 innovation and evolution rates, 274-275 metazoa, 336-337 plantae, 338 prokaryote evolution, 269, 270, 274-275 protistan projects, 333 size, 230 whole-genome analysis, 270, 273-274, 276-279, 333 Genomic imprinting, 26 Genotyping, 287, 288

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Geographic speciation. See also Allopatric speciation; Phylogeographic patterns Malagasy vertebrates, 212-217 Geospiza fortis, 104 Geospiza scandens, 104 Gibbons, 54 Gibson, J., 33 Gilbert, M. Thomas P., 91, 120-142 Glycophorins, 55 Goat, bipedal, 76 Goodman, Steven M., 203-228 Gorillas, 51 Green algae, 338 Greenish warbler (Phylloscopus trochiloides), 102 Ground finches (Geospiza), 104-105 Guppies, 32 Gymnosperms, 49 H Habitat-dependent selection, 103, 104 Haldane, J. B. S., vi, 85 Haldane’s rule, 10, 17, 105, 107-109, 110 Haliotis, 28 Halobacterium sp. NRC-1, 278 Hanley, Carol, 203-228 Haplochromini, 185 HapMap project, 287 HapSTR loci, 93, 184-185, 186, 187, 196-197 Harshman, Larry, 31 Harvard University, viii, 3, 4 Hawthorn (Crataegus spp.), 165, 176 Heckman, Kellie L., 203-228 Heinsohn, Stefanie L., 307-331 Heliocidaris sp., 146, 147, 151-152, 158 Hemicentrotus, 146 Hemiclonal analysis cytogenetic cloning to construct hemiclones, 33-35 Drosophila, 6, 28-41 of inter-locus antagonistic coevolution, 24, 28-29, 37-42 interpretation of results, 41-42 laboratory island population, 24, 30-32 measuring genetic variation, 6, 24-25, 28, 29-30, 35-36, 37-41 measuring net selection gradient on standing phenotypic variation, 6, 25, 29, 36 Herbold, Craig W., 267-285 Hermaphrodites, 49-50 Herre, Edward Allen, 91, 120-142 Heterochrony, 78 Hey, Jody, 92-93, 182-200 Hmr gene, 12, 14, 17 HNTW protein, 111 Homeobox genes, 14 Homo habilis, 57 Homoplasy, 83, 344 Hood, Leroy, 332 Horizontal/lateral gene transfer in bacteria, 201-202, 229-240, 270-273 barrier to, 234-235 base composition analysis, 231-232, 272 complexity hypothesis, 270, 273-274 defining species based on, 236-238 determinants of, 234-236, 274 Drosophila, 6, 13-17, 59, 107 and eukaryote origins, 268-269, 270-271, 273 evidence of, 270-273 exchange-community boundaries, 274 frequency of, 273-274 gene replacement, 234, 269 genome cohesion and, 233-234, 235 incidence among single-copy genes, 238, 238 informational vs. operational genes, 270-272, 273-274, 277, 281 molecular mechanisms, 273 ortholog phylogenies, 234 phylogenetic disruption by, 231-232, 233-234, 237, 238 population size of exchange groups, 274-275 prokaryotic evolution and, 268, 269-275 and rate of genome innovation and evolution, 274-275 and tree-of-life reconstruction, 269, 275-277 speciation attributable to, 238-240 whole-genome analysis, 270, 273-274, 276-279, 333 Host colonization, 122 Host sharing, 129-131, 136-138 Host switching, 124, 125, 131, 137 House finch, 98 Hudson–Kreitman–Aguade tests, 12 Human evolution bipedal locomotion, 76-77 brain, 56-57, 58

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary chimpanzee divergence, 53-58 chromosomal speciation, 51-58 nucleotide differentiation, 52, 54, 55-56 rearranged vs. colinear chromosomes, 52-57 Human genome, 3, 287-289, 337 Hybrids and hybridization Anopheles, 65 avian, 102, 104, 105, 107-109, 110-111 backcrosses, 12-13, 14, 19, 59 chromosomal speciation, 6, 46, 49, 50-51 cichlids, 183 common boundaries, 52 in fig/fig-wasp mutualism, 122, 123, 126, 129, 131, 132-137, 138 fitness, 5, 9, 11, 12, 13-17, 50, 51, 107 4-sim hybrid sterility system, 15-16 Haldane’s rule, 10, 17, 105, 107-109, 110 introgression, 164 inviability, 5, 12, 14, 15, 16, 17, 59, 107 lethal genes, 12-13, 15 male courtship dysfunction, 59 male sterility, 5, 12, 13-20, 27, 49, 59, 107 sea urchins, 158 segregation distortion, 18-20 sex ratio distortion, 18, 19, 20 and species concepts, 246 I Indigobirds (Vidua), 104-105 Informational genes, 270-272, 273-274, 277, 281 Insects. See also Drosophila; Rhagoletis directional asymmetry, 81 preisolation phenotypic divergence, 84 virtual collections, 4 Inter-locus antagonistic coevolution adaptive allelic replacement, 25-26 in allopatry, 26, 27, 28 defined, 25-26 divergence rate, 26 hemiclonal analysis, 24, 28-29, 37-41 intergenomic conflict, 26-28 intragenomic, 26 laboratory model system, 24-25, 27, 28 molecular studies, 24, 27-28 Interactomes, 343 Intergenomic conflict, 26-28 intersexual arms race, 27-28, 29, 37-41 Intragenomic events, 17, 26 Intraspecific niche polymorphisms, 103 Introgression and adaptive divergence, 164 in collinear segments, 166 in hybrids, 164 in neotropical figs, 122-123, 126, 129, 131, 132-136, 137, 138 Island populations, 10, 24-25, 27, 28, 30-42, 83 Isolation-with-migration model, cichlid speciation, 182, 183-193 J Japanese quail (Corturnix japonix), 112, 114 Jennings, W. Bryan, 95-119 K Kalosyce, 124 Kangaroos, 76 Karanth, K. Praveen, 203-228 Kenyanthropus platyops, 53 Kingan, Sarah B., 95-119 Klebsiella pneumonia, 232 L Laboratory island populations, 24-25, 27, 28, 30-42 Lake, James A., 265, 267-285 Lake whitefish (Coregonus), 78 Lampreys (Lampetra), 78 Large X(Z)-effect, 105, 109 Late Cretaceous period, 123 Lateral gene transfer. See Horizontal/lateral gene transfer Learning, avian song, 96, 103, 104-105 Lepilemur, 218 Lerat, Emmanuelle, 201, 229-242 Lessios, H. A., 143-161 Lethal genes, 12-13, 15 Leung, Brian, 162-181 Lew, Timothy A., 24-45 Linder, Jodell E., 24-45 Linkage disequilibrium, 287 Linkage mapping, 288 Linnaeus, Carolus, 244, 258-259

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Little greenbul (Andropodus virens), 103 Long, Anthony D., 265, 286-306 Long-tailed finches (Poephila acuticauda/hecki), 98 Long-tailed shrew tenrecs (Microgale sp.), 214-217 Lycophytes, 338 Lyman, Richard F., 307-331 lysin gene, 28, 112 Lytechnius sp., 146, 147-149, 154-155 M Macaques, 76 Macdonald, Stuart J., 265, 286-306 Machado, Carlos A., 91, 120-142 Mackay, Trudy F. C., 266, 307-331 Madagascar. See also Malagasy vertebrates biodiversity, 204-205 classification problems, 208 conservation priorities, 206 field inventory program, 207-208 Maize evolution, 75 Malagasy vertebrates cryptic variation, 207, 214-216, 219 evolutionary patterns, 214-217 geographic patterns, 212-217 long-tailed shrew tenrecs, 214-217 mouse lemurs, 217-223 plated lizards, 209-211 rate of discovery, 205-206 reciprocal monophyly, 209, 211, 214, 218 species diversity, 207-223 study approach, 207-223 sympatry, 214, 216, 220 taxonomy, 209-211 temporal dimension of diversification, 212, 217-223 trident bats, 212-214 Malaria, 51. See also Anopheles Malignant melanoma, 12-13 Marginal conditions, adaptation to, 63-64 Mating behavior assortative, 156, 311 avian cryptic mate choice, 102, 104, 106, 111-113 copulation latency, 311-327 courtship latency and intensity, 313 diurnal vs. nocturnal species, 219 of Drosophila, 37-41, 266, 307-327 and fitness, 9, 11, 12, 13-17, 28-29, 31-32, 37-41 genes affecting, 266, 309, 311-312, 323, 324-326 male courtship dysfunction, 59 microarray data analysis, 314-315 phenotypic response, 315-317 quantitative genetic analysis, 313 remating, 37-41 and reproductive isolation, 26-27, 38-42 and sexual isolation, 307-327 transcriptional profiling, 313, 317-323, 324-326 Mayr, Ernst allopatric model, 9-10, 24, 143, 163, 177 background, viii biological species concept, 9, 20, 69, 85, 163, 201, 204, 244-245, 246, 247, 251, 258-261 contributions, v, vi, vii-viii, 5, 9-10, 20-21, 24, 49, 87, 91, 96, 261 evolutionary animations, 144 framework for studying speciation, 163, 203-204, 205 sea urchin studies, 92, 143, 145, 155, 156-157, 159 publications, viii on reproductive isolation in allopatry, 9-10 on sexual isolation, 308 McDonald–Kreitman test, 12, 17 Medina, Mónica, 332-349 Meiotic drive, 17-18, 26, 71 Mendel, Gregor, vii Mendelian theory, vi Metabolomes, 343-344 Methanobacterium thermoautotrophicum, 271 Methanococcus janaschii, 270-271, 273 Methanosarcina mazei Goe1, 278 Methanogens, 270, 271, 272 Microarray data analysis, 314-315, 340 Microhabitat partitioning, 220 Migration rates, cichlids, 190-193 Mimicry, 105, 106 Mitochondrial DNA (mtDNA), 65, 98 cytochrome b gene, 209-211, 218 cytochrome oxidase I genes, 146-153, 155 cytochrome oxidase II genes, 218 gene trees, 99-101, 135 ND2 gene, 214

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Modern Evolutionary Synthesis, 244, 247, 250 Moehring, Amanda J., 307-331 Molecular phylogenies applications, 144-145 combinatorial analysis, 279 concatenated gene sequences, 277 conditioned reconstruction, 265, 275-281 distance-based methods, 276 fig/fig-wasp mutualism, 122, 124-125, 126-129, 130-131, 135-136, 137 horizontal gene transfer and, 231-232, 233-234, 237, 238 metazoan, 336-337, 341 molecular clock calibrations, 144, 147 mouse lemurs, 218 ortholog sets, 234, 277, 342 parsimonious analysis, 276-277, 281 plated lizards (Zonosaurus sp.), 209-211 sea urchins, 92, 143, 144, 146, 147-156, 157, 159 whole-genome analysis, 270, 273-274, 276-277 Molecular research avian speciation, 95, 96 inter-locus antagonistic coevolution, 24, 27-28 progress of, 144 Mollusca, 336 Monophyly, 98, 123, 135, 246, 248, 252, 253 Monstera, 74 Morgan, Theodore J., 307-331 Morphological evolution, 343 fig/fig-wasp mutualism, 122, 123-124, 137 songbirds, 99, 101, 103, 104 Morrow, Edward H., 24-45 Mosquitoes. See Anopheles Mouse lemurs (Microcebus) acoustic signaling, 219-220 berthae, 221, 222 hybridization, 220 mate choice mechanisms, 219-220 microhabitat partitioning, 220 molecular phylogeny, 218 morphometric distinctiveness, 221 murinus, 217, 220, 223 myoxinus, 221, 222 number of recognized species, 217-218, 220 olfactory and hormonal signals, 219 ravelobensis, 220, 221, 222, 223 rufus, 217, 218, 222 sympatry, 220 temporal origins, 218-219 torpor patterns, 220, 223-224 mRNA, 268, 343 Mus musculus (mouse), 337 Mutation rates, cichlids, 186-187, 189, 196-197 Mutualisms environmental factors, 82 long-term stability, 121 plant–pollinator, 121; see also Fig/fig-wasp mutualism N Natural selection. See also Fitness to abiotic factors, 17 to biotic factors, 17, 25 cichlids, 183, 197 defining, 70-72 in divergence of speciation genes, 14, 15, 17, 20, 28, 42-43 parallel evolution by, 77 phenotypic vs. genetic definition of, 71-72 phylogeographic breaks in mtDNA, 101 and species concept, 248 Neighbor species, 146, 147, 149, 150 Neurospora crassa, 337 New York Botanical Garden, 3 North Carolina II breeding design, 35 Notch signaling, 289-290, 293, 303 Np96 protein, 17 Nuclear DNA (nDNA), 98 Nuclear gene trees, 101, 135 Nuclear pore complex, 15 Nuclearid amoeba, 337 Nucleoporin genes, 12, 15 Nucleoporin proteins, 15 Nucleotide differentiation, 52, 54, 55-56 Nucleotide substitution, nonsynonymous/synonymous ratios, 14, 52, 54, 56, 65 Nup96 gene, 12, 15, 16, 17

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary O Ochman, Howard, 201, 229-242, 265 OdsH gene, 12, 14, 17 Old World monkeys, 54 Olson, Link E., 203-228 Ontogeny, 74, 78, 86 Operational genes, 270-272, 273-274, 277, 281 Opisthokonta, 333, 337, 342 Orangutans, 51, 54, 57-58, 76 Oreosycea, 124 Orr, Allen, 5, 9-23 Orrorin tugenensis, 53 Ortholog phylogenies, 234 Oryza sativa, 338 P Pacific salmon (Oncorhynchus), 78 Palumbi, Stephen R., 143-161 Parallel evolution, 77-78, 83. See also Coevolution; Mutualism Parallel species pairs, 77-79, 83 Parapatric speciation, 102 Paraphyly, 99, 209, 218 Parental care, 74-75 Parthenogenesis, 50 Partridge, Linda, 31 Pegoscapus sp., 127 Periodical cicadas (Magicicada sp.), 78-79 Phenotypic variation. See also Developmental recombination accommodation, 76 adaptation as, 73-74 arms races and, 27 developmental plasticity and, 69-87 Drosophila, 39, 286, 287, 315-317 fitness effect, 73 fSNPs and, 286, 289 genetic component, 7, 69, 71, 73, 80-81 levels and net selection gradients, 29, 33, 36, 39-41 mating behavior and, 315-317 measuring, 6, 25, 29, 35, 36 and natural selection, 7, 71-72, 286, 289 net selection gradient on, 6, 25, 29, 36 origins of, 70, 289 and reproductive isolation, 83-85, 86 reproductive traits, 26, 27 SNPs, see Functional SNPs Phytogenetic footprinting, 342 Phylogenetic species concept (PSC), 98, 99, 101 Phylogeographic patterns Anopheles, 60, 61, 63 avian, 101-103, 105, 113 cichlids, 193 sea urchins, 143-159 shrew tenrecs, 214-215 Physcomitrella patens, 338 Pied flycatchers (Ficedula hypoleuca), 104, 110 Placozoa, 336 Plants cross-sexual transfer in, 75 genome sequencing, 338 polyploidy, 49 RNA phylogeny, 338 species diversity, 338 virtual collections, 3-4 Plasmodium sp., 51, 336 Plated lizards, 209-211 Platyfish, 12-13 Platyhelmintha, 336 Platyscapa, 124 Poephilia finches, 98-99 Polymorphisms balanced, 297-298, 300, 301 and fSNPs, 297-298, 300, 301 Polyphyly, 99 Polyploidy, 49-50 Polyspermy, 28 Polytypic speciation, 144, 145, 147, 149, 152, 155 Population genetics, vii, 5 Drosophila, 293 fig/fig-wasp mutualism, 132-136, 137 Malawi cichlid species, 182-197 properties emphasized by, 246 Populus tricocarpa, 338 Porifera, 336 Primates, 76, 112, 341 Prokaryotes alkaliphilic, 273 genome evolution, 269, 270, 274-275 genome projects, 333, 336 horizontal gene transfer, 268, 269-275 phylogenetic reconstruction, 267, 269, 273-274 population size, 274-275 tree of life, 275-275

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Prolactin, 75 Promoter-reporter assays, 302 Protamines, 55 Protein–protein interactions, 340, 342, 343 Proteins, developmental recombination, 77 Proteobacterium, 267, 279 Proteomes, 343 Pyrimidine synthesis pathway, 333 Pyrococcus sp., 272 Q Quantitative trait loci, 310, 312, 323 R Rain forests, slash-and-burn agriculture, 61, 63 Ranivo, Julie, 203-228 Raselimanana, Achille P., 203-228 Rasoloarison, Rodin, 203-228 Rattus norvegicus (rat), 337 Receptor tyrosine kinase genes, 12, 13 Reciprocal monophyly, 98, 99, 147, 209, 211, 214, 218 Regulatory networks, 338-339, 342-343 Reinforcement in avian speciation, 95, 96, 97, 110-111 in sea urchin speciation, 158 Reproductive character displacement, 103-104 Reproductive genes, 111-113 Reproductive isolation. See also Fitness; Speciation in allopatric populations, 5, 9-10, 11, 20, 24, 25, 26, 27, 37-41, 97, 136, 163 in Anopheles, 60, 62, 63, 64-65 in avian populations, 84, 95, 97, 101-105, 106, 107, 110-111 chromosomal rearrangements and, 51 developmental recombination and, 83-85, 86 and divergence, 70, 83-84, 85 in Drosophila, 9, 11, 12, 13-20, 28-29, 31-32, 37-41, 59-60, 107, 311 body size and, 84-85 ecological, 11 female resistance to male-induced harm, 27, 37-41 female survival, fecundity, and fertility, 37-41 fig/fig-wasp mutualism, 132-135 gamete reproductive proteins and, 92 genetic basis, 5, 9-21, 85-86; see also Speciation genes genetic distance and, 11 hybrid disfunction models, 13-20, 27, 46, 49, 50-51 intergenomic conflict, 26 inter-locus antagonistic coevolution and, 24-43 intersexual conflict, 27 intragenomic conflicts, 6, 17-20, 26 intrasexual conflict, 26, 28-29 inviability, 12, 14, 15, 16, 17 male sterility, 5, 12, 13-20 mating behavior and, 26-27, 38-42 meiotic drive theory of, 17-18, 20 and parallel species pairs, 77, 78 as pleiotropic product of genetic divergence, 24, 27 postzygotic, 10, 11, 12, 13-18, 20, 27, 107, 110 prezygotic, 12, 27, 50, 102, 103, 110, 111, 311 rate, 10, 11 sea urchins, 150-151, 156-157, 159 sex ratio distortion, 18, 19 and species concepts, 243, 245, 246, 252, 258, 259-260 in sympatry, 10, 11, 204 in Xiphophorus, 10, 12, 13 Reproductive proteins, 28, 111-113 arms-race evolution, 113 bindin evolution, 143, 146-147, 149-152, 153-155, 156, 157-159 Rhagoletis cingulata, 176 Rhagoletis electromorpha, 168-170, 175, 176 Rhagoletis pomonella (apple maggot fly) sibling species complex allochronic isolation, 176 allopatric speciation, 92, 165, 175, 178 apple host, 165 biogeography, 162-179 chromosomal speciation, 162-163, 165, 166-167, 168-176 diapause traits, 162, 165, 166, 176 DNA sequencing, 165, 166-167, 169, 176 ecological adaptation, 164-165, 173, 177

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary gene duplication and deletion hypothesis, 175-176 gene flows, 92, 165, 166-167, 174, 175, 178 gene trees, 162-163, 165, 166-167, 168-176 hawthorn host, 165, 167 host discrimination, 178 host fruiting times, 92 host plant shifting, 162, 164-165, 177, 178 hybridization, 178-179 incomplete-lineage-sorting hypothesis, 174-175 introgression from Altiplano population, 162, 163, 165, 166, 172-174, 175 isolation and introgression, 84, 172-174 Mexican-U.S. haplotype divergence, 165-166, 170, 171, 174, 176 molecular clock, 170, 171 polytene chromosome spreads, 179 relative node depths, 167, 170, 171-173, 175 reproductive isolation, 165, 166, 177-178 secondary contact, 167, 172-174, 175, 177, 178 Sierra Oriental population bridge, 176 sympatric host race formation, 92, 162-179 Rhagoletis suavis, 176 Rhagoletis tabellaria, 169 Rhizobiaceae, 233 Rhizocladus, 124 Rice, William R., 6, 24-45 Ring of life, 278, 279-281 Rivera, Maria C., 267-285 Robbins, Nancy, 91, 120-142 Rollmann, Stephanie M., 307-331 Rose, Michael, 31 rRNA phylogenies, 269, 271, 275-276, 333, 334-335, 337, 338 Rull, Juan, 162-181 Russell, Amy L., 203-228 S Saccharomyces cerevisiae, 270, 278, 336, 337, 341, 342, 343 Sahelanthropus tchadensis, 53 Salmonella sp., 233, 272 enterica, 232, 237 typhimurium, 234, 236 Sandpipers, 75 Schizosaccharomyces pombe, 201-202, 229-240 Sea urchin speciation allopatric (groups 1 and 2), 145, 146, 147-149, 152, 153, 154-155, 156, 157 assortative mating, 156 avian speciation compared, 157 bindin evolution, 143, 146-147, 149-152, 153-155, 156, 157-159 East Pacific Barrier, 155-156 ecological selection, 159 gene flows, 149, 156 genetic clusters, 147, 150, 151-152 genetic distance, 152 hybridization, 158 Mayr’s animation of, 92, 143, 145, 155, 156-157, 159 mitochondrial cytochrome oxidase I genes, 146-153, 155 molecular phylogenies, 92, 143-159 nontropical species, 145 old clades (group 4), 145, 146, 147, 148, 151-152, 153, 154, 155, 156, 157 polytypic species, 145, 147, 149, 152, 155 rate of, 143-144, 150, 152, 153-155, 157, 159 regulatory networks, 342 reproductive isolation, 150-151, 156-157, 159 reinforcement in, 158 sexual arms race, 158 sister species, 146, 147, 152, 155 sympatric overlap (group 3), 143, 145-159 taxonomy, 145 tests of Mayr’s predictions, 146, 152-155 Selaginella moellenforffii, 338 Selection. See Artificial selection; Natural selection; Sexual selection Seminal fluid proteins, 112 Seminogellin II (SEM2), 112 Servin, Jacqueline A., 267-285 Sex chromosomes. See also Chromosomal speciation and avian speciation, 105-111

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary Sex ratio distortion, 18, 19, 20 Sexual conflict avian, 111, 112-113 Drosophila, 309 sea urchins, 158 Sexual imprinting, 96, 104-105, 106 Sexual isolation in Drosophila among species, 309-311 genetic basis, 307, 308-312 incipient, 311-312 mating behavior and, 307-327 quantitative trait loci, 310 Sexual selection avian, 91, 95, 96, 102, 107-109, 111-113 Simonson, Anne B., 267-285 Simpson, George Gaylord, vi, 163, 247, 248, 249 Single nucleotide polymorphisms (SNPs) avian autosomes and sex chromosomes, 95, 97, 110 functional noncoding, see Functional SNPs human genome, 287 Sister species, 146, 147, 152, 155 Sivasundar, Arjun, 92-93, 182-200 Skophammer, Ryan G., 267-285 Slash-and-burn agriculture, 61, 63 Slijper, E. J., bipedal goat, 76 Smelt (Osmerus), 78 Soarimalala, Voahangy, 203-228 Song, and avian speciation, 101-105, 109, 111 Song sparrows (Melospiza melodia), 103 Sorenson, Michael D., 95-119 Speciation. See also Allopatric speciation; Avian speciation; Chromosomal speciation; Divergence; Reproductive isolation; Sympatric speciation defined, 254 diagnosability, 97-98, 99 founder effect models, 10, 20 future of genetic studies, 85-87 gene acquisition and, 238-240 genetic drift in, 10, 20 horizontal gene transfer and, 238-240 island, 10 parapatric, 46, 51, 53, 57-58 problems in, 10 process, 254-255 reinforcement and, 10 stasipatric model, 50 temporal dimension, 217-223 Speciation genes adaptive amino acid replacement, 5 avian, 111 complementation tests, 16, 17 deficiency mapping, 14-15, 16 defined, 11 Dobzhansky–Muller incompatibility, 5, 13 dominance, 14, 17 Drosophila, 13-17, 20, 59 identifying and characterizing, 9, 12, 13-17 intergenomic conflicts, 26, 27-28 intragenomic conflicts, 6, 17-20, 26 methodological dilemma, 11-13 positive Darwinian selection in divergence of, 14, 15, 17, 20, 28, 42-43 prezygotic, 12 postzygotic, 10, 11, 12 rapidly evolving, 5-6, 17, 20, 24, 28, 55 segregation distortion, 18 Species. See also Species problem defined, vii-viii delimitation, 97-111 discovered and named, 3 diversity, 121, 123, 338 as fundamental category of biological organization, 250-253, 256, 257 as taxonomic rank, 244, 251, 253, 257, 260, 261 virtual collections, 3-4 Species problem, 10 asexual organisms, 236-238, 248 biological species concept, vii, 5, 20, 47-49, 243, 245, 246, 252, 258-260 cause of, 254-256 cell analogy, 251, 258 ecological species concept, 245, 246-247, 252-253 evolutionary concept, vii, 245, 248, 251, 252 genotypic cluster species definition, 252 horizontal gene transfer, 236-238 hybrids and, 246 incompatiblitiy of concepts, 245-247 Mayr’s “biological” term and, 244-245, 246, 251, 258-261

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary metapopulation lineage concept, 243, 247-250, 254-261 modern concept, 258-261 nominalistic species concept, 260 nondimensional species concept, 260 organism analogy, 251-252, 257, 258 phenetic concept, 245, 252 phylogenetic species concepts, 245, 246, 248, 252, 253 properties associated with concepts, 202, 243-244, 246-247, 249, 252-257, 258, 258-260 recognition species concept, 252 reproductive isolation and, 243, 245, 246, 252, 258, 259-260 solution to, 256-258 subspecies, 253 unified concept, 257-258 Sperm competition, 111, 112-113 Stebbins, G. Ledyard, vi Staphylococcus aureus, 233, 278 Streptococcus, 233 Strongylocentrotus, 146, 147, 151-152, 154 droebachiensis, 151 franciscanus, 152 nudus, 152 pallidus, 151 purpuratus, 151 Sulfolobus tokodaii, 278 Sunflowers, 51, 166 Superspecies, 144 Swanson, Willie J., 95-119 Swordtail, 12-13 Sycidium, 124, 126 Sycomorus, 126 Symbiotic relationships, 280 Sympatric speciation, 10-11 Anopheles, 64, 65 avian, 91, 96-97, 102, 103-105 by ecological specialization, 164 fig/fig-wasp mutualism, 136 host race formation, 92, 162-179 Malagasy vertebrates, 214, 216, 220 mouse lemurs, 220 partly sympatric, 46 by reinforcement, 164 and reproductive isolation, 10, 11, 204 in Rhagoletis, 162-179 sea urchins, 143, 145-159 secondary, 156 Synechocystis PCC6803, 270, 273 Systematics all-species program, 4 basic tasks of, 163, 203-204, 205, 223 Encyclopedia of Life, 4 and evolutionary biology, 244 and future of biology, 1-4 global initiatives, 4 Internet access to collections, ix, 3-4 Linnean classification, vii, 3, 47, 244 Mayr’s contributions, v, vi, vii-viii species role in, 244 technology, 3 Tree of Life, 4 Systems biology. See also Biological networks comparative studies, 332-333, 336, 339-340, 341, 342, 343, 344 evolutionary, 244, 338-340 genome projects, 333, 336-338 historical perspective, 345 overview, 339 phylogenetically based inference in, 336 research goals, 333 Standing genetic variation, measuring heritable fitness-related traits, 29 Stewart, Andrew D., 24-45 T Taxonomy, Malagasy plated lizards, 209-211 Tellurium resistance protein, 237 Testosterone, 75 Tetrapus, 123, 127 Thermophilic bacteria, 271, 272 Thermotoga maritima, 233 Three-spined stickleback (Gasterosteus aculeatus), 77-78, 86 Thymidine synthase, 333 tmy gene, 18 Tracheloptychus sp., 209 Transcription factor genes, 12, 14, 17 Transcriptional networks, 340-342 Transcriptional profiling, 313, 317-323, 324-326 Tree of life Ecdysozoa vs. Coelomata hypothesis, 336 eukaryote, 333, 334-335, 336

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Systematics and The Origin of Species: On Ernst Mayr’s 100th Anniversary horizontal gene transfer and, 275-277 reconstruction, 275-277 Trident bats (Trianenops sp.), 212-214 Tripneustes, 146, 147, 147-149, 156 depressus, 147 gratilla, 147, 149 ventricosus, 147, 149 Tropheops (Malawi cichlid) speciation allopatric models, 197 amplified fragment-length polymorphism markers, 183 gene exchange, 93, 193, 196 gene flows, 182, 183, 191, 193, 197 HapSTR loci, 184-185, 186, 187, 196-197 hybridization, 183 isolation-with-migration model, 182, 183-193, 196-197 migration rates, 190-193, 194 mutation rates, 186-187, 189, 193, 196-197 natural selection, 183, 197 phylogenetic history, 193 population size, 182, 190-192 rate of, 195-196 reproductive age, 187 shared variation, 183 Tanganyika outgroup divergence, 182, 185, 187-189, 197 time of divergence, 190, 191, 193, 195 Trout (Salmo), 78 Trypanosoma brucei, 63 Tze-tze fly (Glossina), 64 U Unikonts, 333, 334-335 University of Nebraska, 31 V Van Valen, Leigh, 248 Variety, defined, 250 Velez, Sebastian, 162-181 verl gene, 28 Vertebrates, bipedal locomotion, 74-77 Voles (Microtus sp.), 75 W Wallace, Alfred, 30 Wang, Yong, 92-93, 182-200 West-Eberhard, Mary Jane, 6, 69-89 Wiebesia, 123, 124, 125 Wilson, Edward O., ix, 1-4 Won, Yong-Jin, 92-93, 182-200 World Health Organization, 51 Wright, Sewall, vi, 85, 247 X Xie, Xianfa, 162-181 Xiphophorus, 12-13 Xmrk-2 gene, 12, 13, 17 Xylella fastidiosa, 278 Y Yoder, Anne D., 201, 203-228 Z Zea mays, 136, 338 Zebra finches, 113-114 Zebrafish (Danio rerio), 82, 337 Zonosaurus sp., 209-211 ZP3 egg coat protein, 112 Zygomycota, 337

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