In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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From page 401... ...
avian diversification, 26 antitropical taxa, 16 expansion and contraction, 26, 30 Indo-Pacific connections, 12, 18 lizard response to climate change, 2, Austral Islands, 71, 74, 83 45-64 Australia Amblyrhynchus cristatus, 75 biodiversity hotspots, 20 American lion (Panthera leo atrox) , 267 Cape York fauna, 175, 176, 177, 178, Anaeromyxobacter, 203, 207 179-180 Andes, 24, 30, 40, 52, 223, 304 Carpentarian Barrier, 171, 176, 177, 178, Andrews, Kimberly R., 5-21 179-180, 183 Andrews, Thomas D., 257-273 401
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From page 402... ...
402 / Index comparative phylogeography, 176-179, phenotypic, 219-220, 223, 227, 229 180, 181, 183 and plant species concordance, 292-293 continental dispersals, 20, 25, 26-27, 28, Batrachochytrium dendrobatidis, 231 30, 35, 37, 40, 89, 159, 315, 322 Bell, Rayna C., 215-233 gene tree heterogeneity among Benguela Current, 12 diverging lineages, 175 Bering Sea, 13 human phylogeography, 295, 297, 298, Bering Strait, 14, 302 299, 308 Beringia, 31, 40, 192, 258, 259-260, 262, 267, Kimberley fauna, 175, 176, 177, 178, 268, 269, 272, 304 179-180 Biodiversity Kimberley-Top End Barrier, 176, 177, biogeochemistry and, 196 178, 179 and biotic resistance, 79 marine dispersals, 9, 10, 16 hotspots, 1, 6, 7, 11, 12, 20, 21, 43, 236 monsoonal tropics, 176-179, 180 lemur, 237, 239, 240, 245 Pama–Nyungan language family, 199 topographic complexity and, 42 Top End fauna, 175, 176, 177, 178, trait-based phylogeographic, 216, 217, 179-180 218, 228, 232-233 wet tropics, 28, 30, 40, 181, 315 tropical, 140 Australopithecus species, 296 Biogeochemical Azoarcus, 203, 207 cycles, 191, 196, 210 Azores, 71, 76-77, 83 marine provinces, 18, 20 Biogeography adaptation perspective, 326 B advances in understanding, 320-323 areas of inquiry, 328-329 Backmigration, 70, 73, 79, 80, 81-82, 85 concordance between phylogeography Bacteria, 191, 195, 198, 199, 200, 201, 202, and, 5, 6 203, 204, 206, 207, 209, 211, 212 continental, 24-27 Baja California Peninsula, 28, 42, 281, 287, data acquisition, 327-328 288 and divergence, 324-326 Baleen whales (Mysticetes) , 16 ecological and evolutionary Balsam fir, 286 considerations, 323-326 Baltic Province, 13-14 equilibrium theory, 79-80 Bantu peoples, 301, 307 of microbial nitrogen cycling traits in Barriers to dispersal and diversity soil, 195-213 behavioral and cultural, 19-20, 306 ocean provinces, 5, 7-15 Carpentarian Barrier, 171, 176, 177, population genetics and, 43 179-180 of speciation, 323-326 climatic, 16, 41, 46, 167, 219-220, 292, and species delimitation, 324-326 301 theory and analytic methods, 327 continental biotas, 24, 26, 40, 42 Biological carrying capacity, 53, 60, 61-63, ecological, 40, 176, 268, 291-292, 325-326 64, 167, 260, 263 gene tree heterogeneity across, 179-180 Biotic turnover, 72, 79-80, 83-84, 85, 86, 218, geographic, 24, 26, 40, 41, 46, 156, 157, 326 160, 161, 166, 167, 171, 179-180, 223, Bison phylogeography 227, 229, 236, 248-250, 272, 295, 301, and chronology of Ice-Free Corridor, 320-321, 324, 328-329 261-262 geological, 18, 40, 42, 171, 219-220, 259- consensus sequence construction, 260, 262, 266, 292 271-272 human migrations, 301, 302, 306 data availability, 273 Kimberley-Top End Barrier, 176 DNA processing, 271-279 ocean biotas, 1, 8, 9, 10, 11, 12, 13, 15, 17, genealogy estimation, 262-268 18, 19-20
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From page 403... ...
arid conditions, 76, 176, 179, 219, 237 Caatinga, 30, 47 carbon emissions, 46, 48-49, 55 Pleurodema system, 142-147, 150-151 carrying capacity, 53, 60, 61-63, 64 California Floristic Province, 282, 287 demographic responses of Neotropical California plant phylogeography forest lizards, 45-64 environmental influence on gene flow dispersal barriers, 16, 41, 46 and, 275, 280-281 and distribution of taxa, 13 leptokurtic pattern of gene flow and, diversification evaluation with hABC, 192, 275, 277, 278-279, 280, 287 162-163 longevity and, 192, 275, 277, 281-282, future changes, 52-55, 60-61, 64 287, 289-290 and genetic diversity, 46, 47, 49, 52-55, Quercus lobate (valley oak) case study, 56-57, 60-61, 63-64 192, 273, 282-287, 288 Hadley Centre Climate model, 61 Ramalina menziesii (strap lichen)
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From page 404... ...
253-254 of demographic trends, 48, 276 neutral, 88, 113 genome, 29, 46, 47, 159, 241, 242, 291 population pedigree and, 87, 93, 96-97, quantification method, 157, 159, 160, 98, 99, 100-103, 105, 106, 107, 108, 169 109-111 taxon, 29, 31, 33, 69, 157, 178 sequences of, 119, 120, 121, 122-123, 124 Conservation biology, 7, 15, 28, 31, 43, 48, sequentially Markovian, 187-188 53, 55, 113, 114, 157, 311, 317, 327 skygrid model, 272 Continental biogeography, 24-27 species-merging event, 117 Continental comparative phylogeography species-specific demographic models, Australian dispersal patterns, 20, 25, 157, 160, 166, 167, 169 26-27, 28, 30, 35, 37, 40, 89, 159, 315, theory, 114, 138, 188, 204, 311, 327 322 tropical diversity, 47 biological relationships, 31, 33 within-deme events, 63 climate and, 20, 24, 26, 33, 34, 35, 36-37, Codistributed species, 26, 27, 28 (see also 41, 46, 47, 48, 176 Forest lizards) conservation role, 28, 31, 43 case-history approach, 2 context and content, 27-38 climate-driven diversification, 162, 167, database, 27-28 176 dispersal paradigms, 2, 23 and community assembly, 68, 69, 77 ecological niche modeling, 38 congruence implications, 69, 157, 160 ecological relationships, 31, 33, 40, cryptic diversity, 29 41-42, 46-47 discordant patterns, 88, 158, 159, 169, endemism and, 31, 32, 43 217, 219-220 evolutionary traits, 41-42 ecological relationships, 31, 38, 41 future research approaches, 23-24, 39-44
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From page 405... ...
, 317-318 idealized focal system, 29 Dark-eyed juncos, 222, 224 and integrative evolutionary Darwin's finches, 75 biogeography, 43-44 Deltaproteobacteria, 195, 203, 207 life history traits in, 42 Demography marine phylogeography compared, 6, coalescent theory and models, 47, 48, 20 49, 51-52, 57, 58-59, 63, 157, 160, 166, multidisciplinary approach, 42 167, 169 multilocus data from nuclear genome, congruence of trends, 48, 276 23, 29, 36, 37-38, 40, 75, 108, 171, 176- historical, and climate dynamics, 47, 48, 177, 178, 179, 186, 318, 319 49, 51-52, 57, 58-59, 63 Neogene period, 2, 23, 33-34, 35, 36-37, large family and population pedigree, 42, 237 88, 91, 94, 98, 99-104, 105, 109-110 organelle (mtDNA) genomes, 23, 24, 29, Neotropical forest lizard response to 36, 37-38, 40, 41, 46 climate change, 2, 45-64 physiological traits in, 41-42 spatial simulations, 47, 62-63 pseudocongruence, 23-24, 29, 40, 42, 43 species-specific models, 157, 160, 166, Quaternary period, 2, 23, 33-34, 35, 167, 169 36-37, 45, 48, 157, 180, 237, 240, 245, Desert cichlids, 222, 225 269 Di Battista, Joseph D., 5-21 range dynamics, 2, 23, 26, 32, 33, 35, 36, Dipodomys deserti, 41 41 Dipodomys merriami, 41 refugia, 2, 23, 26, 35, 36, 37, 41, 157, Discordance 165, 176, 227, 276, 279, 292-293, 315, insights from, 161, 184 322 interpreting, 158-159, 160-161 species distribution modeling, 23, 38, Dispersal 39-40, 41, 49, 53, 54, 60-62 capabilities, 2, 9, 13, 15, 16, 69, 72 study hotspots, 29-31 "sweepstakes," 68 taxa focus of studies, 23, 35, 37 vectors, 78 topic diversity, 31, 32 Divergence transition zones, 1, 24, 26, 30-31, 42 across Australian monsoonal tropics, vicariance paradigms, 2, 23-24, 26, 35, 176-179 36, 37, 40-41, 42, 43-44, 179, 180 gene tree heterogeneity across Cook Islands, 74, 305 Carpentarian Barrier, 179-180 Coral Triangle, 7-9, 11, 14 molecular markers, 183-185 Corallochaetodon species, 8-9 processes in nature, 176-183 Cordilleran Ice Sheet, 258, 259, 260 reconstructing processes in nextCrab spider (Misumenops rapaensis)
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From page 406... ...
F Genealogy of Life, 328 Genetic diversity (see also Concordance; Faroe Islands, 13 Phylogenetics) Field voles, 222, 227 abiotic factors, 41 Firmicutes, 203, 207 climate dynamics and, 46, 47, 49, 52-55, Fixed hotspot hypothesis, 74 56-57, 60-61, 63-64
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From page 407... ...
, 267 models of postglacial expansion and Hickerson, Michael J., 45-65 colonization, 139, 142, 148, 151 Holocene, 35, 150, 151, 152, 251, 258, 263, ocean phylogeography, 7, 10, 12, 13, 15, 267, 270 20, 21 Hotspots and range dynamics, 35, 41, 46, 151 biodiversity, 1, 6, 7, 11, 12, 20, 21, 43, refugia, 2, 23, 26, 35, 36, 37, 41, 157, 165, 236 176, 227, 228, 276, 279, 292-293, 315, continental progressions, 1-2, 20, 29-31, 322 49 and sea levels, 6, 10 ecological transition zones, 1-2 vegetation distribution and diversity, endemism, 7, 9, 10, 12, 21, 43 142, 159, 276, 281-282, 283, 285, 287, island archipelago progressions, 2, 67, 292-293, 297 69, 71-78, 83, 84 Global Biodiversity Information Facility, marine progressions, 1, 6, 7, 9, 10, 11, 12, 327 20, 21 Global Map project, 327 proliferation, 29-31 Golden-crowned sifaka (Propithecus value of studies in, 41-42, 43, 217 tattersalli) , 251 volcanism, 2, 67, 69 Goodman, Steven M., 235-255 Human phylogeography Grant, W
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From page 408... ...
, 26, 32, 80, 81, progression rule, 67, 71-77, 81-83 83, 84-85, 94, 180, 182, 183-184, 186, sea level changes and diversification, 229, 315, 319 162-163 Hyposmocoma moths, 73 within-island speciation, 73 Isthmus of Panama, 12, 40 Ituri pygmoid peoples, 301 I Ives, John W., 257-273 Iacchei, Matthew, 5-21 Ice-Free Corridor, 258, 261, 269 J inferring chronology for opening, 262-268 Japan, 8, 16, 301 North American human prehistory, Jass, Christopher N., 257-273 268-269 Iceland, 13, 307 iDigBio, 327 K Indian Ocean, 10 Kangaroo rat (Dipodomys) , 41 Indo-Malay Archipelago, 10, 11 Kappeler, Peter M., 235-255 Indonesia, 305-306 Katydids (Banza)
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From page 409... ...
, 13, 33, 35, Mehta, Rohan S., 113-135 142, 150, 151, 152, 166, 167, 176, 258, Metapopulation ecology, 79-80 259, 260, 261-262, 263, 267, 269, 281- Mexico, Cuatro Ciénegas Valley, 225 282, 283-284, 285 Microbial nitrogen-cycling traits in soil Laupala crickets, 73, 81, 82, 83, 85 dataset and curation, 196-197, 207, Laurentide Ice Sheet, 258, 259, 260 210-211 Leatherback turtle, 18 drivers of N pathway frequencies, 195, Leptokurtic pattern of gene flow, 192, 275, 202-203 277, 278-279, 280, 287 drivers of taxonomic composition by N Letts, Brandon, 257-273 pathway, 195, 208 Limpets (Cellana) , 15 environmental metadata, 211-212 Linanthus parryae, 313, 314, 315 frequency of N pathways, 195, 197, 198, Lipinia noctua, 307 199-201, 202-203, 204, 208, 209-210, Lizards (see Forest lizards)
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From page 410... ...
, 168 Morphobank, 327 human phylogeography, 140 Mosaic integrating distributional, demographic, environment, 223, 236, 247, 251 and coalescent modeling, 166-167, genome, 67, 81-83, 85 168 hypothesis, 239, 240, 241, 247, 251 isolation-by-distance, 93 Mountain pine beetle, 159 missing data and, 56-57, 135, 146, 272 Mouse lemurs (Microcebus sp.) monophyly probabilities, 116-120 characteristics, 240 Pleistocene Aggregate Island Complex generation times, 240, 244-245, 253, 254 model of diversification, 162 genotyping, 252-253 population genetics, 88, 91, 92, 94-99, geogenetic analysis, 235-250, 255 108, 109-111 mtDNA tree, 241, 242, 252 postglacial expansion and colonization, purpose of study, 240-241 139, 142, 148, 151 sample collection, 251-252 sequentially Markovian coalescent, 187 species tree estimation and divergence source-sink migration, 142 times, 242-245, 250-251, 253-254 spatial demographic simulations, 47, Mulloidichthys goatfishes, 8-9, 10, 12 62-63 Myripristis berndti, 11 spatial genetic simulations, 47, 63-64 species distribution, 23, 38, 39-40, 41, 49, 53, 54, 60-62 N Wright–Fisher model of random Native Americans, 302 mating, 109 Neanderthal, 297, 298 Modern Synthesis, 315, 317, 320 Nearctic region, 24, 26, 30-31, 33, 35, 40 Mojave Desert, 43, 313, 314 Nelson, Michaeline B., 195-213 Mollies, 222, 226 Neogene period, 2, 23, 33-34, 35, 36-37, 42, Monophyly probabilities on species tree 237 bounds of summation, 121 Neoniphon samara, 8-9 branch length and, 113, 116, 118, 126 Neotropical, 20, 25, 26, 28, 30-31, 33, 35, 37, 128, 129 40, 222 central recursion, 120-124, 125 biogeographic transition zone, 24 coalescence sequences, 88, 113, 114, 116 forest lizards, 45-65 127, 129, 131
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From page 411... ...
, Arctic province, 14, 16, 209 307 Atlantic and Indo-Pacific connections, Paralithodes king crab, 13 12, 18 Paraphyly, 73, 118 barriers to dispersal, 1, 8, 9, 10, 11, 12, Parupeneus multifasciatus, 8-9 13, 15, 17, 18, 19 Pectobacterium, 203, 207 benthic fauna, 14, 225 Perch, 222, 225 biodiversity hotspots, 1, 6, 7, 11, 12, 20, Peru, 49, 223, 304 21 Phenoscape, 327 biogeochemical provinces, 18-19, 20 Phenotypes (see also Microbial nitrogen biogeographic provinces, 5, 7-15 cycling traits in soil; Trait-based Caribbean Province, 6 comparative phylogeography) cetaceans, 1, 16-17, 19-20 adaptive, 85, 188, 217, 219, 222, 223-224, climate change and, 7, 10, 12, 13, 15, 20, 225-226, 228, 229, 230, 231, 232-233 21 barriers to gene flow, 219-220, 223, 227, concordant discontinuities between 229 Gulf of Mexico and Atlantic cryptic lineages, 19, 24, 39, 42, 81, 178, populations, 157 181-182, 222, 227 endemism and, 5, 6-7, 8, 9, 10, 12, 14, 21 data from field studies and natural North Atlantic, 13-14 history collections, 216, 219, 232-233 North Pacific, 13 Dobzhansky-Muller incompatibilities, organelle (mtDNA)
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From page 412... ...
, 142-151 and geogenetic patterns in mouse Poephila grassfinches, 177 lemurs, 235, 237, 241, 242, 243, 247, Pogonomyrmex ant, 42 250-251 Polychrus marmoratus, 45, 47, 48, 49, 51, 52, humans and commensals, 307, 308, 309 56, 57, 58 island progressions and speciation 72, Polynesia, 8, 9, 69, 74, 308 74, 75, 77, 85, 323-324 Pomarea flycatchers, 75 lace lichen, 291 Pomatostomus babblers, 176 microbial nitrogen-cycling traits in soil, Population genetics 195, 213 and biogeography, 43 molecular technologies and, 89, 173-174, climate dynamics and, 49, 51 183, 184, 185, 187-188, 224, 311 concordance criterion and, 155 monophyly probabilities, 114 four-eyed frogs, 143 and phenotypic variation, 224, 226, 227, and landscape genetics, 44, 48, 311, 313, 231 314, 318, 319, 322 and phylogeography, 43-44, 172, 173, marine, 16, 20 174, 178, 179, 183, 185, 186-187, 188, models, 88, 91, 92, 94-99, 108, 109-111, 226, 231, 237, 263, 295 176, 322 and population genetics, 138, 139, 173, mouse lemurs, 235, 236 174, 183, 235 and phylogenetics, 49, 51, 138, 139, 173, priority effects, 85 174, 183, 235, 311, 313, 317 quantitative measures, 43 phylogeography and, 172, 173, 188, reticulation and, 186-187 216 statistical tests of trait-based site fidelity and, 16 hypotheses, 161 transition to speciation, 84 tropical species, 321-322
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From page 413... ...
, 74 72, 79-80, 83-84, 85, 86 Reef habitat, 7-8, 9 Canary Islands, 71, 76, 83 Refugia, 2, 23, 26, 35, 36, 37, 41, 157, 165, and community assembly, 67, 77-80 176, 227, 276, 279, 292-293, 315, 322 Galapagos Islands, 71, 75, 83, 85 Reproductive isolation, 151, 181-182, 227, Hawaiian Islands, 70, 71, 78, 81, 82, 315, 324 83 Resistance high-density blocking, 80 adaptive phenotypes, 230 island context, 71-77 biotic, on island archipelagos, 77-79, 80, Marquesas, 71, 75 83-84, 85 and mosaic genome, 67, 81-83 landscape, 280, 324 reconciliation of biotic turnover with Resource specialization, 16 biotic resistance, 80 Reticulation Society Islands, 71, 74, 83 ecology- and introgression-driven, Pseudocongruence, 23-24, 29, 40, 42, 43 180-182 Psychotria, 73 gene tree outliers and, 185 Pygoplites diacanthus, 8-9 introgression methods, 186-187 methods for detecting, 186-188 Q molecular markers, 183-185 and phylogenetic networks, 186-187 Qinghai-Tibetan Plateau, 31 processes in nature, 176-183 Quaternary dispersals (see also Pleistocene recombination methods, 187-188 dispersals) reconstructing processes in next climate drivers, 33, 35, 36-37, 41, 45, 48, generation era, 183-185 180, 237, 240, 245 sequentially Markovian coalescent continental, 2, 23, 33-34, 35, 36-37, 45, models, 187-188 48, 157, 180, 237, 240, 245, 269 Rhagoletis (Crater Lake cichlids)
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From page 414... ...
R., 257-273 Teosinte, 113, 116, 131-135 Social structure, 16, 17 Tethys Sea, 12 Society Islands, 71, 74, 83 Tetragnatha spiders, 69 Soil (see Microbial nitrogen-cycling traits Tetramolopium plants, 78 in soil) Thomé, Maria Tereza C., 137-154 Sonoran desert, 43, 281 Threespine sticklebacks, 222, 226, 230, 231 Sork, Victoria L., 275-293 Toonen, Robert J., 5-21 Southern Africa dispersals Trait-based comparative phylogeography marine, 12, 14, 16, 18 iDDC modeling approach, 166-167, 168 terrestrial, 237, 301 methodological challenges, 168-169 Southon, John R., 257-273 model-based framework, 165-168 Spadefoot toads, 222 study design, 165 Speciation Transequatorial dispersal, 16, 17 allopatric, 1, 15, 18, 19, 20-21, 32, 180, Trebouxia decolorans, 288, 290, 292 216, 219, 223, 229, 321 Tropical diversity, 140 ecological dynamics, 1, 6, 15, 340 Trout, 222, 226 genomics, 182-183 Tundra muskoxen (Ovibos moschatus)
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From page 415... ...
, 8-9, 10 Werth, Silke, 275-293 Yoder, Anne D., 235-255 Western camel (Camelops hesternus) , 267 Yukon Territory, 258, 260, 263, 265, 267 Whale shark, 18 Wilton, Peter R., 91-111 Wolinella, 203 Z Wolves (Canis lupus)
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