Index
1000 Genomes Project, 108
A
Aegean archipelago, 220
Africa, 295, 296-298 (see also Southern Africa dispersals)
Aggregate site frequency spectrum (aSFS), 51-52, 57, 58, 59-60
Agulhas Current, 12
Alaska, 30, 258, 260, 263, 267, 268, 269, 287, 289, 302, 303, 304
Albacore tuna, 18
Aleutian Archipelago, 13
Allopatric speciation, 1, 15, 18, 19, 20-21, 32, 180, 216, 219, 223, 229, 321
Alvarado-Serrano, Diego F., 45-65
Amazonian forest
avian diversification, 26
expansion and contraction, 26, 30
lizard response to climate change, 2, 45-64
Amblyrhynchus cristatus, 75
American lion (Panthera leo atrox), 267
Andes, 24, 30, 40, 52, 223, 304
Andrews, Kimberly R., 5-21
Andrews, Thomas D., 257-273
Anolis punctatus, 45, 47, 48, 49, 51-58, 60-64
Antarctic Circumpolar Current, 14
Antilopine wallaroo (Macropus antilopinus), 178
Approximate Bayesian computation (ABC), 48, 54, 57, 58, 60, 141, 166, 167, 168, 169, 322
hierarchical (hABC), 38, 40, 52, 58, 59-60, 157, 160, 162-163, 322
Archaea, 198, 199, 200, 201, 202, 203, 204, 206, 209, 211, 212
Assembling, Visualizing, and Analyzing the Tree of Life, 328
Atlantic Forest
lizard response to climate change, 45-64
Atlantic Ocean (see also North Atlantic)
antitropical taxa, 16
Indo-Pacific connections, 12, 18
Australia
biodiversity hotspots, 20
comparative phylogeography, 176-179, 180, 181, 183
continental dispersals, 20, 25, 26-27, 28, 30, 35, 37, 40, 89, 159, 315, 322
gene tree heterogeneity among diverging lineages, 175
human phylogeography, 295, 297, 298, 299, 308
Kimberley fauna, 175, 176, 177, 178, 179-180
Kimberley-Top End Barrier, 176, 177, 178, 179
monsoonal tropics, 176-179, 180
Pama–Nyungan language family, 199
Top End fauna, 175, 176, 177, 178, 179-180
wet tropics, 28, 30, 40, 181, 315
Australopithecus species, 296
B
Backmigration, 70, 73, 79, 80, 81-82, 85
Bacteria, 191, 195, 198, 199, 200, 201, 202, 203, 204, 206, 207, 209, 211, 212
Baja California Peninsula, 28, 42, 281, 287, 288
Baleen whales (Mysticetes), 16
Balsam fir, 286
Baltic Province, 13-14
Barriers to dispersal and diversity
behavioral and cultural, 19-20, 306
Carpentarian Barrier, 171, 176, 177, 179-180
climatic, 16, 41, 46, 167, 219-220, 292, 301
continental biotas, 24, 26, 40, 42
ecological, 40, 176, 268, 291-292, 325-326
gene tree heterogeneity across, 179-180
geographic, 24, 26, 40, 41, 46, 156, 157, 160, 161, 166, 167, 171, 179-180, 223, 227, 229, 236, 248-250, 272, 295, 301, 320-321, 324, 328-329
geological, 18, 40, 42, 171, 219-220, 259-260, 262, 266, 292
human migrations, 301, 302, 306
Kimberley-Top End Barrier, 176
ocean biotas, 1, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19-20
phenotypic, 219-220, 223, 227, 229
and plant species concordance, 292-293
Batrachochytrium dendrobatidis, 231
Bell, Rayna C., 215-233
Benguela Current, 12
Bering Sea, 13
Beringia, 31, 40, 192, 258, 259-260, 262, 267, 268, 269, 272, 304
Biodiversity
biogeochemistry and, 196
and biotic resistance, 79
hotspots, 1, 6, 7, 11, 12, 20, 21, 43, 236
topographic complexity and, 42
trait-based phylogeographic, 216, 217, 218, 228, 232-233
tropical, 140
Biogeochemical
Biogeography
adaptation perspective, 326
advances in understanding, 320-323
areas of inquiry, 328-329
concordance between phylogeography and, 5, 6
continental, 24-27
data acquisition, 327-328
and divergence, 324-326
ecological and evolutionary considerations, 323-326
equilibrium theory, 79-80
of microbial nitrogen cycling traits in soil, 195-213
population genetics and, 43
of speciation, 323-326
and species delimitation, 324-326
theory and analytic methods, 327
Biological carrying capacity, 53, 60, 61-63, 64, 167, 260, 263
Biotic turnover, 72, 79-80, 83-84, 85, 86, 218, 326
Bison phylogeography
and chronology of Ice-Free Corridor, 261-262
consensus sequence construction, 271-272
data availability, 273
DNA processing, 271-279
genealogy estimation, 262-268
phylogeographic analysis, 272-273
as proxy for human prehistory, 268-269
radiocarbon dating, 258, 259, 260, 261, 262, 263, 270, 272
Blanco, Marina B., 235-255
Blue marlin, 18
Blue tits, 223
Blue whales, 16
Bowen, Brian W., 5-21
Bragg, Jason G., 171-189
Brazil, Pleurodema (four-eyed frog) system case study, 142-151
Briggs, John C., 5-21
Bristlecone pine (Pinus longaeva), 281-282
Brown, Jason L., 45-65
Bryant, David, 113-135
Bulimulid land snails, 75
C
Pleurodema system, 142-147, 150-151
California Floristic Province, 282, 287
California plant phylogeography
environmental influence on gene flow and, 275, 280-281
leptokurtic pattern of gene flow and, 192, 275, 277, 278-279, 280, 287
longevity and, 192, 275, 277, 281-282, 287, 289-290
Quercus lobate (valley oak) case study, 192, 273, 282-287, 288
Ramalina menziesii (strap lichen) case study, 192, 276, 287-292
reproductive output and, 192, 275, 277, 279-280, 281, 287, 290, 291
sessility and, 192, 275, 277-278, 280, 287, 288, 291
Campbell, C. Ryan, 235-255
Canada, 159
Charlie Lake Cave site, 259, 262-263, 264-265, 266, 268, 269
Clover Bar site, 259, 262, 263
Ice-Free Corridor dispersals, 257-273
Carbon
and climate change, 46, 48-49, 55
in soil, 195, 202, 204, 209, 211-212
Caribbean Province, 6, 7, 303-304
Caribou (Rangifer tarandus), 267
Carlia skinks, 177, 178, 179, 180, 187
Carnaval, Ana C., 45-65
Carolina Province, 14
Carpentarian Barrier, 171, 176, 177, 178, 179-180, 183
Carstens, Bryan C., 137-154
Cellana limpets, 15
Cephalopholis argus, 11
Chaetodon auriga, 8-9
Chaetodon ornatissimus, 8-9
Chaetognaths, 19
Chen, Jin-Ming, 275-293
Cladogenesis, 67, 70, 72, 73, 76
Climacteris treecreepers, 177
Climate dynamics (see also Glacial–interglacial climate regimes)
arid conditions, 76, 176, 179, 219, 237
carbon emissions, 46, 48-49, 55
carrying capacity, 53, 60, 61-63, 64
demographic responses of Neotropical forest lizards, 45-64
dispersal barriers, 16, 41, 46
and distribution of taxa, 13
diversification evaluation with hABC, 162-163
future changes, 52-55, 60-61, 64
and genetic diversity, 46, 47, 49, 52-55, 56-57, 60-61, 63-64
Hadley Centre Climate model, 61
population size shifts, 48, 49, 51-52, 55, 57-60, 63, 64
precipitation fluctuations, 45, 47-48, 49, 52, 60, 142, 151, 202, 204, 211, 212, 218, 236, 282, 288
Representative Concentration Pathway model, 48-49, 61
sea level changes, 6, 10, 13, 14, 157, 162-163, 259, 298, 301, 302
sequencing protocols and phylogenetic analyses, 56
spatial genetic responses, 47, 63-64, 159
species differences in responses, 49-52
species distribution models, 53, 54, 60-62
Clupea herring, 13
Coalescence theory and models
backward-in-time simulations, 49, 114, 117
and climate dynamics from historical demography, 47, 48, 49, 51-52, 57, 58-59, 63
and gene/species tree analysis, 172, 173, 175, 176, 179, 180, 186, 187-188, 240, 241, 253-254, 292
glacial/ice sheet, 25, 26, 98, 258, 259-260, 261-262, 266, 268, 269, 272
and hybridization, 186
hypothesis testing and parameter estimation, 157, 160, 166, 168
lineage classes and, 116-117
marine lineages, 10
migration, 292
monophyly probability, 88, 113, 114, 116-127, 129, 131
multiple-merger events, 103
multispecies model, 114, 116, 186, 253-254
population pedigree and, 87, 93, 96-97, 98, 99, 100-103, 105, 106, 107, 108, 109-111
sequences of, 119, 120, 121, 122-123, 124
sequentially Markovian, 187-188
skygrid model, 272
species-merging event, 117
species-specific demographic models, 157, 160, 166, 167, 169
theory, 114, 138, 188, 204, 311, 327
tropical diversity, 47
within-deme events, 63
Codistributed species, 26, 27, 28 (see also Forest lizards)
case-history approach, 2
climate-driven diversification, 162, 167, 176
and community assembly, 68, 69, 77
congruence implications, 69, 157, 160
cryptic diversity, 29
discordant patterns, 88, 158, 159, 169, 217, 219-220
ecological relationships, 31, 38, 41
microcomplement fixation of serum albumin, 26-27
pseudocongruence, 40
species distribution modeling, 38
vertebrate focus of studies, 35-36
vicariance, 24
Common dolphinfish, 18
Common wallaroo (Macropus robustus), 178
Community assembly, 67, 68-69, 77-80, 83-84, 85-86, 322
Community lockup dynamics, 80, 81
Complementarity effect, 79
Concordance
abiotic versus biotic factors, 156, 158, 159, 161, 164, 169
differentiation with geographical isolation of populations, 75
historical emphasis on, 156-157
interpreting discordance, 158-159, 160-161
knowledge gaps, 160-161
limitations of criteria, 157-161
predictive power of generic expectations, 160, 162-163
Congruence (see also Pseudocongruence)
of demographic trends, 48, 276
genome, 29, 46, 47, 159, 241, 242, 291
quantification method, 157, 159, 160, 169
taxon, 29, 31, 33, 69, 157, 178
Conservation biology, 7, 15, 28, 31, 43, 48, 53, 55, 113, 114, 157, 311, 317, 327
Continental biogeography, 24-27
Continental comparative phylogeography
Australian dispersal patterns, 20, 25, 26-27, 28, 30, 35, 37, 40, 89, 159, 315, 322
biological relationships, 31, 33
climate and, 20, 24, 26, 33, 34, 35, 36-37, 41, 46, 47, 48, 176
context and content, 27-38
database, 27-28
ecological niche modeling, 38
ecological relationships, 31, 33, 40, 41-42, 46-47
evolutionary traits, 41-42
geological activity and, 2, 23, 24, 26, 31, 33, 35, 36-37, 40, 42
global representativeness of studies, 23, 28
idealized focal system, 29
and integrative evolutionary biogeography, 43-44
life history traits in, 42
marine phylogeography compared, 6, 20
multidisciplinary approach, 42
multilocus data from nuclear genome, 23, 29, 36, 37-38, 40, 75, 108, 171, 176-177, 178, 179, 186, 318, 319
Neogene period, 2, 23, 33-34, 35, 36-37, 42, 237
organelle (mtDNA) genomes, 23, 24, 29, 36, 37-38, 40, 41, 46
physiological traits in, 41-42
pseudocongruence, 23-24, 29, 40, 42, 43
Quaternary period, 2, 23, 33-34, 35, 36-37, 45, 48, 157, 180, 237, 240, 245, 269
range dynamics, 2, 23, 26, 32, 33, 35, 36, 41
refugia, 2, 23, 26, 35, 36, 37, 41, 157, 165, 176, 227, 276, 279, 292-293, 315, 322
species distribution modeling, 23, 38, 39-40, 41, 49, 53, 54, 60-62
study hotspots, 29-31
taxa focus of studies, 23, 35, 37
transition zones, 1, 24, 26, 30-31, 42
vicariance paradigms, 2, 23-24, 26, 35, 36, 37, 40-41, 42, 43-44, 179, 180
Corallochaetodon species, 8-9
Cordilleran Ice Sheet, 258, 259, 260
Crab spider (Misumenops rapaensis), 74
Cracticus butcherbirds, 176
Cryptic species/lineages, 19, 24, 39, 42, 81, 178, 181-182, 222, 227
Cultural diversity
barriers to dispersal, 19-20, 306
and environment, 300, 305-306, 308-310
inheritance of fertility, 105
D
Damselfish (Dascyllus aruanus), 10
Damselfly (Coenagrion scitulum),317-318
Darwin’s finches, 75
Deltaproteobacteria, 195, 203, 207
Demography
coalescent theory and models, 47, 48, 49, 51-52, 57, 58-59, 63, 157, 160, 166, 167, 169
historical, and climate dynamics, 47, 48, 49, 51-52, 57, 58-59, 63
large family and population pedigree, 88, 91, 94, 98, 99-104, 105, 109-110
Neotropical forest lizard response to climate change, 2, 45-64
spatial simulations, 47, 62-63
species-specific models, 157, 160, 166, 167, 169
Di Battista, Joseph D., 5-21
Dipodomys deserti, 41
Dipodomys merriami, 41
Discordance
interpreting, 158-159, 160-161
Dispersal
capabilities, 2, 9, 13, 15, 16, 69, 72
“sweepstakes,” 68
vectors, 78
Divergence
across Australian monsoonal tropics, 176-179
gene tree heterogeneity across Carpentarian Barrier, 179-180
molecular markers, 183-185
processes in nature, 176-183
reconstructing processes in next-generation era, 183-185
speciation genomics, 182-183
Dobzhansky, Theodosius, 313, 314, 315, 316, 327
Dobzhansky-Muller incompatibilities, 227
Dos Reis, Mario, 235-255
Driver, Jonathan C., 257-273
Drosophila melanogaster, 96
Drosophila pseudoobscura, 313, 315, 316
Dugongs, 10
Dysdera spiders, 76
E
East Pacific Ocean, 8, 11-12, 17
Easter Island, 10
Echinothrix diadema, 12
Ecological dynamics
barriers to dispersal and diversity, 40, 176, 268, 291-292, 325-326
biotic resistance, 77-79, 80, 83-84, 85
biotic turnover, 72, 79-80, 83-84, 85, 86
codistributed species, 31, 38, 41
community assembly, 67, 68-69, 77-80, 85-86, 322
concerted versus individualistic responses, 158
continental relationships, 31, 33, 40, 41-42, 46-47
on island archipelagos, 72, 77-80, 83-84, 85, 86
metapopulation, 79-80
niche modeling, 38, 142, 150, 151, 152
niche preemption, 79
and reticulation, 180-182
transition zones, 1-2
Ecotypes, 17
Edwardsiella, 203
Endemism
and continental comparative phylogeography, 31, 32, 43
hotspots, 7, 9, 10, 12, 21, 43
and ocean phylogeography, 5, 6-7, 8, 9, 10, 12, 14, 21
secondary replacement of original fauna, 76
Epsilonproteobacteria, 203
Ethiopia, 25, 31, 37, 296, 298
Euphausiids, 19
Euphorbia lomelii,281
Extinctions, 24, 74, 79-80, 84, 162, 163, 231, 261, 263, 281, 282-283, 321, 327
F
Faroe Islands, 13
Fixed hotspot hypothesis, 74
Flightless beetles, 220
Forest lizards
carrying capacity, 53, 60, 61-63, 64
demographic responses to climate change, 2, 45-64
genetic diversity, 46, 47, 49, 52-55, 56-57, 60-61, 63-64
population size shifts, 48, 49, 51-52, 55, 57-60, 63, 64
sequencing protocols and phylogenetic analyses, 56
spatial demographic simulations, 62-63
spatial genetic simulations, 63-64
species differences in responses, 49-52
species distribution models, 60-62
Forests (see also Amazonian forest)
cloud forests, 223
contractions and expansions, 26, 40, 49, 50, 52
deforestation, 76-77
provenance studies, 278
Seasonally Dry Tropical Forests, 142-143, 150
Froese, Duane, 257-273
Frogs
Australian, 26-27
Brazilian four-eyed, 88, 137, 142-154
lowland leopard, 231
pathogen immunity, 231
toadlet, 178
Fungi, 36-37, 159, 198, 199, 200, 211, 231, 277, 289, 290-291, 292
G
Gadus cod, 13
Gaither, Michelle R., 5-21
Galagete lepidopterans, 75
Galapaganus flightless weevils, 75
Galapagos Islands, 24, 71, 75, 83, 85
Ganzhorn, Jörg U., 235-255
Genealogy (see Population pedigree)
Genealogy of Life, 328
Genetic diversity (see also Concordance; Phylogenetics)
abiotic factors, 41
climate dynamics and, 46, 47, 49, 52-55, 56-57, 60-61, 63-64
forest lizards, 46, 47, 49, 52-55, 56-57, 60-61, 63-64
to phenotypes, 221-228
spatial simulations, 47, 63-64
Genetic drift, 96, 108, 138, 308, 327
Genghis Khan, 99-103, 105, 109-110
Geochelone nigra (Galapagos giant tortoise), 75
Gillespie, Rosemary G., 67-86
Glacial–interglacial climate regimes
and biological carrying capacity, 167, 260, 263
and bison dispersal and viability, 257-273
continental distributional shifts, 20, 24, 33, 34, 35, 36, 41, 46, 47, 48, 176
cryptic populations, 227
and human expansions, 258, 260, 268-269, 299-300
Ice-Free Corridor, 257-273
ice sheet coalescence, 25, 26, 98, 258, 259-260, 261-262, 266, 268, 269, 272
and island radiations, 245
Last Glacial Maximum, 13, 33, 35, 142, 150, 151, 152, 166, 167, 176, 258, 259, 260, 261-262, 263, 267, 269, 281-282, 283-284, 285
models of postglacial expansion and colonization, 139, 142, 148, 151
ocean phylogeography, 7, 10, 12, 13, 15, 20, 21
and range dynamics, 35, 41, 46, 151
refugia, 2, 23, 26, 35, 36, 37, 41, 157, 165, 176, 227, 228, 276, 279, 292-293, 315, 322
vegetation distribution and diversity, 142, 159, 276, 281-282, 283, 285, 287, 292-293, 297
Global Biodiversity Information Facility, 327
Global Map project, 327
Golden-crowned sifaka (Propithecus tattersalli), 251
Goodman, Steven M., 235-255
Grant, W. Stewart, 5-21
Gugger, Paul F., 275-293
H
Habitat (see also Microbial nitrogen-cycling traits in soil)
fragmentation and loss, 74, 76-77, 142, 162, 236, 245, 247, 250, 251
selection/preference, 19, 161, 162, 163, 209, 219, 220, 232, 281, 291
Hadza peoples, 301
Hall, Elizabeth, 257-273
Harcourt, Alexander H., 295-310
Hare, P. Gregory, 257-273
Havaika spiders, 78
Hawaiian Archipelago
endemism, 73
human migration, 305
ocean phylogeography, 6, 7, 8-9, 10, 14, 15, 20
progression rule, 70, 71, 73, 78, 81, 82, 83, 85
Hawaiian silverswords, 73
Hawksbill turtle, 18
Hector’s dolphins, 17
Heintzman, Peter D., 257-273
Helicobacter pylori, 307
Helmeted musk oxen (Bootherium bombifrons), 267
Hickerson, Michael J., 45-65
Holocene, 35, 150, 151, 152, 251, 258, 263, 267, 270
Hotspots
biodiversity, 1, 6, 7, 11, 12, 20, 21, 43, 236
continental progressions, 1-2, 20, 29-31, 49
ecological transition zones, 1-2
endemism, 7, 9, 10, 12, 21, 43
island archipelago progressions, 2, 67, 69, 71-78, 83, 84
marine progressions, 1, 6, 7, 9, 10, 11, 12, 20, 21
proliferation, 29-31
value of studies in, 41-42, 43, 217
Human phylogeography
Americas, 258-259, 260, 261-262, 268-269, 302-304
Anzick child burial, 269
climate and, 258, 260, 268-269, 297, 299-300
Clovis sites, 258-259, 260, 268-269, 302
commensal movements, 307-308
cultural diversity and environment, 300, 305-306, 308-310
cultural inheritance of fertility, 105
Ice-Free Corridor and, 258-259, 260, 261-262, 268-269
modern migrations and their barriers, 306
ocean archipelagos, 304-306
Old World outside Africa, 269, 295, 299-301
paleogenetic data, 261
parallel adaptations, 222, 226
pedigree effects of a large family, 88, 91, 94, 98, 99-104, 105, 109-110
sex-specific, 306-307
Siberia, 300-301, 302, 303, 304, 308
species’ global diaspora, 296-308
tropical diversity, 308-310
within and into Africa, 301-302
Humpback dolphins, 17
Humpback whales, 16
Hunnicutt, Kelsie E., 235-255
Hybridization (admixture), 26, 32, 80, 81, 83, 84-85, 94, 180, 182, 183-184, 186, 229, 315, 319
Hyposmocoma moths, 73
I
Iacchei, Matthew, 5-21
Ice-Free Corridor, 258, 261, 269
inferring chronology for opening, 262-268
North American human prehistory, 268-269
iDigBio, 327
Indian Ocean, 10
Indo-Malay Archipelago, 10, 11
Indonesia, 305-306
Indo-Pacific Barrier, 8, 9, 10, 11
Indo-Pacific Province, 7, 8, 9, 11-12, 17, 18, 20
Indo-Polynesian Province (IPP), 8, 9, 10
Introgression
of adaptive alleles, 182
broad-scale, 178-179
contrasting processes and views of, 181
cryptic lineages, 181-182
and gene tree heterogeneity, 175, 179
mtDNA analysis and, 319
and network models of diversification, 174
priority effects and, 80
and reticulation, 89, 171-172, 174, 176, 180-182, 186-187
secondary contact and, 180, 315
timing of events, 180
Islands and island archipelagos (see also specific islands)
backmigration, 70, 73, 79, 80, 81-82, 85
biotic resistance on evolutionary timescale, 77-79, 80, 83-84, 85
biotic turnover on ecological timescale, 72, 79-80, 83-84, 85, 86
community assembly, 67, 68-69, 77-80, 83-84, 85-86
equilibrium theory of biogeography, 79-80
geological origins, 69
insights into continental biotas, 25-26
persistence of progression pattern, 77-80
progression rule, 67, 71-77, 81-83
sea level changes and diversification, 162-163
within-island speciation, 73
Ituri pygmoid peoples, 301
Ives, John W., 257-273
J
Jass, Christopher N., 257-273
K
Kangaroo rat (Dipodomys), 41
Kappeler, Peter M., 235-255
Katydids (Banza), 73
Khoi peoples, 301
Khoisan/San peoples, 301
Killer whales, 17
King, Léandra, 91-111
King crab (Lithodes), 13
Knowles, L. Lacey, 155-170
L
Landscape genetics
differences from phylogeography, 159, 318-320
history of phylogeography and, 314-318
molecular markers and methodology, 319-320
spatial scale, 320
temporal scale, 319
Laparocerus weevils, 83
Larsen, Peter A., 235-255
Last Glacial Maximum (LGM), 13, 33, 35, 142, 150, 151, 152, 166, 167, 176, 258, 259, 260, 261-262, 263, 267, 269, 281-282, 283-284, 285
Laupala crickets, 73, 81, 82, 83, 85
Laurentide Ice Sheet, 258, 259, 260
Leatherback turtle, 18
Leptokurtic pattern of gene flow, 192, 275, 277, 278-279, 280, 287
Letts, Brandon, 257-273
Limpets (Cellana), 15
Linanthus parryae, 313, 314, 315
Lipinia noctua, 307
Lizards (see Forest lizards)
Loxosceles spiders, 76
Lutjanus fulvus, 8-9
Lutjanus kasmira, 8-9
M
MacKay, Glen, 257-273
Madagascar
Ambohitantely protected area, 245-246
Anjohibe Cave, 237
Ankafobe, 245-246
Central Highland conduit for dispersal, 192, 235-240, 241, 242, 244-247, 250, 251
climate and biome, 236-237, 238, 239
forest hypothesis, 237, 240, 251
geogenetic patterns in mouse lemurs, 192, 240-255
grassland hypothesis, 238-239, 240, 251
human origins and activity in, 236-237, 305, 323-324
Lake Tritrivakely, 239
mosaic hypothesis, 239, 240, 241, 246, 247, 251
species richness, 237-238
Madeira Islands, 83
Maize (Zea mays), 113, 116, 131-135
Marine biogeography (see also Ocean phylogeography)
provinces, 7-15
Marquesas Islands, 8-9, 10, 71, 75, 83
Martiny, Adam C., 195-213
Martiny, Jennifer B. H., 195-213
Mason, Nicholas A., 215-233
Mediterranean Province, 13-14, 30, 31, 224, 279, 282
Megalagrion damselflies, 73
Mehta, Rohan S., 113-135
Metapopulation ecology, 79-80
Mexico, Cuatro Ciénegas Valley, 225
Microbial nitrogen-cycling traits in soil
dataset and curation, 196-197, 207, 210-211
drivers of N pathway frequencies, 195, 202-203
drivers of taxonomic composition by N pathway, 195, 208
environmental metadata, 211-212
frequency of N pathways, 195, 197, 198, 199-201, 202-203, 204, 208, 209-210, 212
identification of N cycle pathways, 211
metagenomic data, 197-198, 208, 209, 210-211
phylogenetic visualization, 195, 213
standardization of data, 211
statistical analyses, 212-213
taxonomic and phylogenetic distribution of N pathways, 196, 197, 203-208
Microcebus (see Mouse lemurs)
Microcomplement fixation of serum albumin, 26-27
Microlophus lava lizards, 75
Mocking birds, 75
Model selection for phylogeography
Bayesian framework, 141-142, 150, 153, 157
coalescent theory, 138
and confirmation bias, 137, 139, 141, 154
divergence with gene flow model and, 153
inference process, 137-138, 139, 140, 141, 148, 150-153, 154
information theoretic frameworks, 88, 137, 141-142, 153
missing data, 146
nonmodel systems and, 140, 141, 151-153
parameter estimation, 137-138, 139, 140, 141, 143, 145, 146, 147-148, 149, 150, 151-153, 154
Pleurodema (four-eyed frog) system case study, 142-151
sampling and molecular protocols, 144-145
species delimitation tests, 153
statistical frameworks, 140-141, 154
uncertainty component, 138, 141
Models/modeling
climate effects, 48-49, 61, 150, 151
Clovis First archaeological, 258-259
ecological niche, 38, 142, 150, 151, 152
general linear models (GLMs), 168
human phylogeography, 140
integrating distributional, demographic, and coalescent modeling, 166-167, 168
isolation-by-distance, 93
missing data and, 56-57, 135, 146, 272
monophyly probabilities, 116-120
Pleistocene Aggregate Island Complex model of diversification, 162
population genetics, 88, 91, 92, 94-99, 108, 109-111
postglacial expansion and colonization, 139, 142, 148, 151
sequentially Markovian coalescent, 187
source-sink migration, 142
spatial demographic simulations, 47, 62-63
spatial genetic simulations, 47, 63-64
species distribution, 23, 38, 39-40, 41, 49, 53, 54, 60-62
Wright–Fisher model of random mating, 109
Modern Synthesis, 315, 317, 320
Monophyly probabilities on species tree
bounds of summation, 121
branch length and, 113, 116, 118, 126-128, 129
central recursion, 120-124, 125
coalescence sequences, 88, 113, 114, 116-127, 129, 131
combinatorial functions, 120, 121-122, 123
height of species tree and, 126-127, 129, 133
lineage classes, 116-117, 118, 121-122, 123, 124, 126, 127-128, 129, 130, 131, 132-133
maize and teosinte application, 113, 116, 131-135
model and notation, 116-120
monophyly events, 117, 118, 125
node output probability, 118, 120, 121-124, 133
pooling effect, 115, 129-131, 133
reciprocal monophyly, 114, 115, 118, 119, 123, 124-125, 129, 131
species-merging events, 117-119
Montastraea corals, 12
Moritz, Craig, 171-189
Morphobank, 327
Mosaic
environment, 223, 236, 247, 251
hypothesis, 239, 240, 241, 247, 251
Mountain pine beetle, 159
Mouse lemurs (Microcebus sp.)
characteristics, 240
generation times, 240, 244-245, 253, 254
genotyping, 252-253
geogenetic analysis, 235-250, 255
purpose of study, 240-241
sample collection, 251-252
species tree estimation and divergence times, 242-245, 250-251, 253-254
Mulloidichthys goatfishes,8-9, 10, 12
Myripristis berndti, 11
N
Native Americans, 302
Nearctic region, 24, 26, 30-31, 33, 35, 40
Nelson, Michaeline B., 195-213
Neogene period, 2, 23, 33-34, 35, 36-37, 42, 237
Neoniphon samara, 8-9
Neotropical, 20, 25, 26, 28, 30-31, 33, 35, 37, 40, 222
biogeographic transition zone, 24
forest lizards, 45-65
Nerita albicilla,11
New Guinea, 7, 176, 298, 299, 304
New Zealand, 14, 295, 305, 307-308
Nitrogen (see Microbial nitrogen-cycling traits in soil)
North America (see also Bison phylogeography)
biodiversity hotspots, 43
human phylogeography, 258-259, 260, 261-262, 268-269, 302-304
Ice-Free-corridor, 257-273
pseudocongruence, 41
topographic complexity and diversity, 42
North Atlantic, 13-14, 15, 16, 320
North Sea Province, 13-14
O
Oak gall wasps, 33
Ocean phylogeography
Atlantic and Indo-Pacific connections, 12, 18
barriers to dispersal, 1, 8, 9, 10, 11, 12, 13, 15, 17, 18, 19
biodiversity hotspots, 1, 6, 7, 11, 12, 20, 21
biogeochemical provinces, 18-19, 20
biogeographic provinces, 5, 7-15
Caribbean Province, 6
climate change and, 7, 10, 12, 13, 15, 20, 21
concordant discontinuities between Gulf of Mexico and Atlantic populations, 157
endemism and, 5, 6-7, 8, 9, 10, 12, 14, 21
North Atlantic, 13-14
North Pacific, 13
organelle (mtDNA), 10, 11, 12, 16, 17, 18, 37
Red Sea Province, 6-7, 8-9, 10, 11-12
sea level changes, 6, 10, 13, 14, 157, 162-163, 259, 298, 301, 302
species patterns within, 14-15
taxon-specific patterns, 5-6, 14-20
temperate and polar seas, 13-14
terrestrial versus marine, 6, 20
tropical oceans, 7-12
Odontocetes (toothed whales), 16-17
Orb web spider (Tangaroa tahitiensis), 74
Oriental region, 25, 28, 30, 31, 35
Oriental-Palearctic transition area, 33
Orsonwelles spiders, 73
Oscines, 222
P
Pacific Ocean (see also East Pacific Ocean; North Pacific)
antitropical taxa, 16
Pacific rat (Rattus exulans), 307
Panulirus penicillatus (pronghorn spiny lobster), 8-9, 11-12
Papadopoulou, Anna, 155-170
Paper mulberry (Broussonetia papyrifera), 307
Paralithodes king crab, 13
Parupeneus multifasciatus, 8-9
Phenoscape, 327
Phenotypes (see also Microbial nitrogen-cycling traits in soil; Trait-based comparative phylogeography)
adaptive, 85, 188, 217, 219, 222, 223-224, 225-226, 228, 229, 230, 231, 232-233
barriers to gene flow, 219-220, 223, 227, 229
cryptic lineages, 19, 24, 39, 42, 81, 178, 181-182, 222, 227
data from field studies and natural history collections, 216, 219, 232-233
Dobzhansky-Muller incompatibilities, 227
evolutionary mechanisms linking genetic diversification to, 191, 215, 216-217, 219, 221-228
genotype associations, 188, 228, 230, 231-232
geographically clustered, 191-192, 219, 220, 221, 222, 223-225, 226
geographically dispersed, 217-218, 219-220, 221, 222, 223, 225-227, 228
horizontal gene transfer, 174, 228
parallel evolution, 225-226, 229
phylogenetics and, 224, 226, 227, 231
with phylogeographic structure, 216, 219, 221, 222, 223-224, 225-226, 227
without phylogeographic structure, 221, 222, 224-225, 226-227, 228
plasticity, 85, 217, 222, 224-225, 226, 228, 329
species-specific traits and idiosyncratic patterns, 215, 217-220, 223
uniform, 227-228
Philippines, 7, 11, 162, 227, 297, 305
Pholcus spiders, 76
Phylogenetics, 39, 329 (see also Genetic diversity)
bison, 263
climate dynamics and, 49, 56, 178, 263, 321
coalescent models, 186
continuum, 89
and geogenetic patterns in mouse lemurs, 235, 237, 241, 242, 243, 247, 250-251
humans and commensals, 307, 308, 309
island progressions and speciation 72, 74, 75, 77, 85, 323-324
lace lichen, 291
microbial nitrogen-cycling traits in soil, 195, 213
molecular technologies and, 89, 173-174, 183, 184, 185, 187-188, 224, 311
monophyly probabilities, 114
and phenotypic variation, 224, 226, 227, 231
and phylogeography, 43-44, 172, 173, 174, 178, 179, 183, 185, 186-187, 188, 226, 231, 237, 263, 295
and population genetics, 138, 139, 173, 174, 183, 235
priority effects, 85
quantitative measures, 43
reticulation and, 186-187
statistical tests of trait-based hypotheses, 161
tropical species, 321-322
Picture-winged Drosophila, 73, 85
Plain-backed thrushes, 222
Plains bison (Bison bison bison), 261
Plant phylogeography (see California plant phylogeography; Vegetation distribution and diversity)
Plasmodium falciparum, 307
Pleistocene Aggregate Island Complex model, 162
Pleistocene dispersals
bison, 258, 261, 262, 263, 266-267, 269, 270
Carpentarian Barrier, 176
climate effects, 10, 13, 148, 159, 251, 259-260, 267, 276
Clovis First archaeological model, 258-259
extinction event, 261
Ice-Free Corridor, 258, 261, 262, 263, 266-267, 269
sea level changes, 13, 14, 157, 162
species-pump diversification hypothesis, 26, 162
trans-Andean divergence, 40
Pleurodema (four-eyed frog), 142-151
Poephila grassfinches, 177
Pogonomyrmex ant, 42
Polychrus marmoratus, 45, 47, 48, 49, 51, 52, 56, 57, 58
Pomarea flycatchers, 75
Pomatostomus babblers, 176
Population genetics
and biogeography, 43
concordance criterion and, 155
four-eyed frogs, 143
and landscape genetics, 44, 48, 311, 313, 314, 318, 319, 322
models, 88, 91, 92, 94-99, 108, 109-111, 176, 322
and phylogenetics, 49, 51, 138, 139, 173, 174, 183, 235, 311, 313, 317
phylogeography and, 172, 173, 188, 216
site fidelity and, 16
transition to speciation, 84
Population pedigree
coalescence probabilities and, 87, 93, 96-97, 98, 99, 100-103, 105, 106, 107, 108, 109-111
Genghis Khan, 99-103, 105, 109-110
large family and, 88, 91, 94, 98, 99-104, 105, 109-110
population genetics models, 88, 91, 92, 94-99, 108, 109-111
selective sweep and, 88, 91, 94, 103-108, 110-111
Spanish Hapsburg royal family, 98
Wright–Fisher model of random mating, 95, 98, 109
Porites lobate, 12
Prates, Ivan, 45-65
Priority effects, 78, 79, 80, 84, 85
Pristipomoides filamentosus, 8-9
Progression rule
biotic resistance on evolutionary timescale, 77-79, 80
biotic turnover on ecological timescale, 72, 79-80, 83-84, 85, 86
and community assembly, 67, 77-80
Galapagos Islands, 71, 75, 83, 85
Hawaiian Islands, 70, 71, 78, 81, 82, 83
high-density blocking, 80
island context, 71-77
reconciliation of biotic turnover with biotic resistance, 80
Pseudocongruence, 23-24, 29, 40, 42, 43
Psychotria, 73
Pygoplites diacanthus, 8-9
Q
Qinghai-Tibetan Plateau, 31
Quaternary dispersals (see also Pleistocene dispersals)
climate drivers, 33, 35, 36-37, 41, 45, 48, 180, 237, 240, 245
continental, 2, 23, 33-34, 35, 36-37, 45, 48, 157, 180, 237, 240, 245, 269
inferring refugia, 157
Last Glacial Maximum, 13, 33, 142, 176, 258, 269, 281-282, 283-284, 285
lemur diversity and speciation, 237, 239, 240, 245
Oriental-Palearctic transition, 33
reticulation, 180
vegetation distribution, 45, 48, 49, 237, 239, 240, 245
R
Rainforest skinks, 222
Ralison, José M., 235-255
Range dynamics
Rasoloarison, Rodin M., 235-255
Reciprocal monophyly, 7, 10, 12, 114, 115, 118, 119, 123, 124-125, 129, 131
Red Sea, 6-7, 8-9, 10, 11-12, 297-298
Red-backed fairywren (Malurus melanocephalus), 177, 178
Reed-warblers (Acrocephalus sp.), 74
Refugia, 2, 23, 26, 35, 36, 37, 41, 157, 165, 176, 227, 276, 279, 292-293, 315, 322
Reproductive isolation, 151, 181-182, 227, 315, 324
Resistance
adaptive phenotypes, 230
biotic, on island archipelagos, 77-79, 80, 83-84, 85
Resource specialization, 16
Reticulation
ecology- and introgression-driven, 180-182
gene tree outliers and, 185
introgression methods, 186-187
methods for detecting, 186-188
molecular markers, 183-185
and phylogenetic networks, 186-187
processes in nature, 176-183
recombination methods, 187-188
reconstructing processes in next-generation era, 183-185
sequentially Markovian coalescent models, 187-188
Rhagoletis (Crater Lake cichlids),324
Riddle, Brett R., 23-44
Right whales, 16
Rissler, Leslie J., 313-339
River barriers to dispersal, 46
Rock pocket mouse, 230-231
Rock-wallabies (Petrogale), 177, 178
Rocky Mountains, 24, 30, 159, 167, 258, 259, 281, 315
Rodrigues, Miguel T., 45-65
Rosenberg, Noah A., 113-135
S
Sackler, Arthur M., vii-viii
Samoana land snails, 75
Sardinops sardines, 13, 16, 17
Scalloped hammerhead shark, 18
Schiedea, 73
Sea level changes, 6, 10, 13, 14, 157, 162-163, 259, 298, 301, 302
Selective sweeps, 88, 91, 94, 103-108, 110-111, 184
Shaded-litter rainbow skink (Carlia munda), 177, 179, 180
Shapiro, Beth, 257-273
Shaw, Kerry L., 67-86
Side-blotched lizards, 222, 225
Simulium blackflies, 74
Sister species, 5, 7, 10, 11, 14, 15-16, 19, 84, 137, 142, 143, 223, 242, 321, 325
Site fidelity, 16-17, 18, 19, 219
Soares, André E. R., 257-273
Soil (see Microbial nitrogen-cycling traits in soil)
Sork, Victoria L., 275-293
Southern Africa dispersals
Southon, John R., 257-273
Spadefoot toads, 222
Speciation
allopatric, 1, 15, 18, 19, 20-21, 32, 180, 216, 219, 223, 229, 321
ecological dynamics, 1, 6, 15, 340
genomics, 182-183
island progressions and, 72, 74, 75, 77, 85, 323-324
population genetics transition to, 84
sympatric, 1, 17, 19, 21, 143, 324
within-island, 73
Species tree (see Monophyly probabilities on species tree)
Species-pump diversification hypothesis, 26, 41, 162
Spermophorides spiders, 76
Sphyrna lewini,11
Spinner dolphins, 17
Steppe bison (Bison priscus), 261, 271-272
Stiller, Mathias, 257-273
Strap lichen (Ramalina menziesii), 192, 276, 287-292
Straw-colored fruit bats, 222, 228
Succineid land snails, 73
Suchard, Marc A., 257-273
Surgeonfishes (Acanthurus), 8-9, 12
Suture zones, 26, 32, 42, 181, 315, 316
Swofford, David L., 235-255
Sympatric speciation, 1, 17, 19, 21, 143, 324
T
Taiwan, 305
Tasmania, 299
Temperature adaptations/tolerances, 13, 15, 16, 18, 46, 197, 218, 281, 282-283, 286, 321
Tethys Sea, 12
Tetragnatha spiders, 69
Tetramolopium plants, 78
Thomé, Maria Tereza C., 137-154
Threespine sticklebacks, 222, 226, 230, 231
Toonen, Robert J., 5-21
Trait-based comparative phylogeography
iDDC modeling approach, 166-167, 168
methodological challenges, 168-169
model-based framework, 165-168
study design, 165
Transequatorial dispersal, 16, 17
Trebouxia decolorans, 288, 290, 292
Tropical diversity, 140
Tundra muskoxen (Ovibos moschatus), 267
V
Valley oak (Quercus lobate), 192, 273, 282-287, 288
Vegetation distribution and diversity
climate change and, 142, 159, 276, 281-282, 283, 285, 287, 292-293, 297
montane plant taxa, 159
Verrucomicrobia, 206
W
Wakeley, John, 91-111
Wallace, Alfred Russel, 24, 25-26, 39, 40, 44, 191
Wari people, 304
Weisrock, Davis W., 235-255
Werth, Silke, 275-293
Western camel (Camelops hesternus), 267
Whale shark, 18
Wilton, Peter R., 91-111
Wolinella, 203
Wolves (Canis lupus), 267
Wood bison (Bison bison athabascae), 261
Woywitka, Robin, 257-273
Wrasses
Anampses, 12
Thalassoma, 12
Wright, Sewall, 314
Wright’s shifting balance theory, 314
Wright–Fisher model of random mating, 95, 98, 109
X
Xue, Alexander T., 45-65
Y
Yellowstripe goatfish (Mulloidichthys flavolineatus),8-9, 10
Yoder, Anne D., 235-255
Yukon Territory, 258, 260, 263, 265, 267
Z
Zamudio, Kelly R., 215-233
Zazula, Grant D., 257-273
