Index
A
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
Allocentrotus, 146
fragilis, 151
Allochronic speciation, 136, 212
Allopatric speciation, 41, 42.
See also Phylogeographic patterns
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
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
allopatric vs. sympatric species, 64, 65
anthropophilic and domestic, 60, 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
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
Aphids, 84
Apple (Malus pumila), 165
Arabidopsis lyrata ssp. petraea, 136
Arabidopsis thaliana, 338, 341
Arbacia sp., 146, 147, 151-152
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
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
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
developmental recombination, 75
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
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
species trees, 99-100
sperm competition, 111, 112-113
sympatric, 91, 96-97, 102, 103-105
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
genetic distances, 272
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
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
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
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
Buchnera, 233
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
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
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
Clonal evolution, 269, 270, 272
Clostridium acetobutylicum, 273
Cnidaria, 336
Coevolution.
See also Fig/fig-wasp mutualism;
Inter-locus antagonistic coevolution
Collared flycatchers (Ficedula albicollis), 104, 110
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
Crenarchaea, 267
Cross-sexual transfer, 74-75
Cryptic variation, 207, 214-216, 219
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
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
chimpanzees, 53-58
developmental-pathway, 83
Dobzhansky–Muller model, 5, 13
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
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
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
Enhancer-of-split locus, 296, 299, 300, 312
Exelixis collection of mutations, 327
fSNP survey, 286-303
Gene Disruption Project, 327
gene ontology categories, 318-323
genome sequencing, 289-298, 336
interactomes, 343
introgression in collinear segments, 166
laboratory island population, 24-25, 27, 28, 30-42
mating behavior, 37-41, 266, 307-327
melanogaster, 13, 14, 15, 16, 28-43, 286, 287, 288-303, 337, 341, 343
neutral evolution patterns, 296
Notch signaling, 289-290, 293, 303
nuclear genome, 59
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
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
phytophagous insects, 163
sea urchin, 159
Ecological speciation hypothesis, 85
Edwards, Scott V., 95-119
El Niño events, 104
Embryophyta, 338
ENCODE initiative, 344
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
Eucidaris sp., 146, 147, 147-149, 156
Eukaryotes
chimeric theories, 271, 279, 280
collections, 3
compartmentalization, 268
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
Evolution.
See also Divergence;
Human evolution;
Speciation
arms-race, 6, 20, 25, 27-28, 29, 41
Darwinian natural selection, v-vi, 14, 70
environmentally induced change, 81-83
extrapolation from laboratory to natural populations, 41-42
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
population variation, vii
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
colubrinae, 131
diversity, 121
glabrata, 131
Indo-Australian, 124, 126, 130
lutea, 130
maxima, 131
neotropical (Panamanian), 127, 128, 130, 132-136
obtusifolia, 131
perforata, 131
pollinators associated with, 126, 128
Urostigma, 124, 126, 127, 131, 132-136
Fig/fig-wasp mutualism
allochronic model, 136
allopatric model, 136
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
Fitness.
See also Reproductive isolation
in birds, 107
defined, 70
in fig/fig-wasp mutualism, 138
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
Flycatchers (Ficedula sp.), 104, 110
Forbes, Andrew, 162-181
Friberg, Urban, 24-45
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
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
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 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
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
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
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
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’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
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
HNTW protein, 111
Homeobox genes, 14
Homo habilis, 57
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
and eukaryote origins, 268-269, 270-271, 273
evidence of, 270-273
exchange-community boundaries, 274
frequency of, 273-274
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
chimpanzee divergence, 53-58
chromosomal speciation, 51-58
nucleotide differentiation, 52, 54, 55-56
rearranged vs. colinear chromosomes, 52-57
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
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
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
Interactomes, 343
Intergenomic conflict, 26-28
intersexual arms race, 27-28, 29, 37-41
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 whitefish (Coregonus), 78
Lampreys (Lampetra), 78
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
Leung, Brian, 162-181
Lew, Timothy A., 24-45
Linder, Jodell E., 24-45
Linkage disequilibrium, 287
Linkage mapping, 288
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
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
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
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
Mendel, Gregor, vii
Mendelian theory, vi
Metabolomes, 343-344
Methanobacterium thermoautotrophicum, 271
Methanococcus janaschii, 270-271, 273
Methanosarcina mazei Goe1, 278
Microarray data analysis, 314-315, 340
Microhabitat partitioning, 220
Migration rates, cichlids, 190-193
Mitochondrial DNA (mtDNA), 65, 98
cytochrome b gene, 209-211, 218
cytochrome oxidase I genes, 146-153, 155
cytochrome oxidase II genes, 218
ND2 gene, 214
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
molecular clock calibrations, 144, 147
mouse lemurs, 218
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
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
Morrow, Edward H., 24-45
Mosquitoes. See Anopheles
Mouse lemurs (Microcebus)
acoustic signaling, 219-220
hybridization, 220
mate choice mechanisms, 219-220
microhabitat partitioning, 220
molecular phylogeny, 218
morphometric distinctiveness, 221
number of recognized species, 217-218, 220
olfactory and hormonal signals, 219
ravelobensis, 220, 221, 222, 223
sympatry, 220
temporal origins, 218-219
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
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 pore complex, 15
Nuclearid amoeba, 337
Nucleoporin proteins, 15
Nucleotide differentiation, 52, 54, 55-56
Nucleotide substitution, nonsynonymous/synonymous ratios, 14, 52, 54, 56, 65
O
Ochman, Howard, 201, 229-242, 265
Old World monkeys, 54
Olson, Link E., 203-228
Operational genes, 270-272, 273-274, 277, 281
Oreosycea, 124
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
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
genetic component, 7, 69, 71, 73, 80-81
levels and net selection gradients, 29, 33, 36, 39-41
mating behavior and, 315-317
and natural selection, 7, 71-72, 286, 289
net selection gradient on, 6, 25, 29, 36
and reproductive isolation, 83-85, 86
SNPs, see Functional SNPs
Phytogenetic footprinting, 342
Phylogenetic species concept (PSC), 98, 99, 101
Phylogeographic patterns
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
Plated lizards, 209-211
Platyfish, 12-13
Platyhelmintha, 336
Platyscapa, 124
Poephilia finches, 98-99
Polymorphisms
Polyphyly, 99
Polyploidy, 49-50
Polyspermy, 28
Polytypic speciation, 144, 145, 147, 149, 152, 155
Drosophila, 293
fig/fig-wasp mutualism, 132-136, 137
Malawi cichlid species, 182-197
properties emphasized by, 246
Populus tricocarpa, 338
Porifera, 336
Prokaryotes
alkaliphilic, 273
genome evolution, 269, 270, 274-275
horizontal gene transfer, 268, 269-275
phylogenetic reconstruction, 267, 269, 273-274
population size, 274-275
tree of life, 275-275
Prolactin, 75
Promoter-reporter assays, 302
Protamines, 55
Protein–protein interactions, 340, 342, 343
Proteins, developmental recombination, 77
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
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
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
sea urchins, 150-151, 156-157, 159
and species concepts, 243, 245, 246, 252, 258, 259-260
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
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
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
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
Rivera, Maria C., 267-285
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
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
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
Sex ratio distortion, 18, 19, 20
Sexual conflict
Drosophila, 309
sea urchins, 158
Sexual imprinting, 96, 104-105, 106
Sexual isolation in Drosophila
among species, 309-311
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
future of genetic studies, 85-87
gene acquisition and, 238-240
horizontal gene transfer and, 238-240
island, 10
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
defined, 11
Dobzhansky–Muller incompatibility, 5, 13
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
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
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
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
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
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
Superspecies, 144
Swanson, Willie J., 95-119
Swordtail, 12-13
Sycomorus, 126
Symbiotic relationships, 280
Sympatric speciation, 10-11
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
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
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
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
horizontal gene transfer and, 275-277
reconstruction, 275-277
Trident bats (Trianenops sp.), 212-214
Tripneustes, 146, 147, 147-149, 156
depressus, 147
Tropheops (Malawi cichlid) speciation
allopatric models, 197
amplified fragment-length polymorphism markers, 183
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
mutation rates, 186-187, 189, 193, 196-197
phylogenetic history, 193
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
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
West-Eberhard, Mary Jane, 6, 69-89
World Health Organization, 51
X
Xie, Xianfa, 162-181
Xiphophorus, 12-13
Xylella fastidiosa, 278
Y
Z
Zebra finches, 113-114
Zebrafish (Danio rerio), 82, 337
Zonosaurus sp., 209-211
ZP3 egg coat protein, 112
Zygomycota, 337