Cambridge University Press 978-0-521-88318-4 - Speciation and Patterns of Diversity Edited by Roger K. Butlin, Jon R. Bridle and Dolph Schluter Index More information Index Abiotic conditions, 278 successive substitution of beneficial mutations, 46 Adaptation to ecological niches Adaptive speciation, 165 Anolis radiation on Caribbean islands driven by, dietary, phenotypic and neutral genetic 102, 103, 109 differentiation, 166 Adaptive radiation, 102, 244 male colour phenotypes, variation in, 166 examples, 102 mating preferences by assortative mating, as extension of process of speciation, 102–103 variation in, 165 individual-based model of, 103 African cichlid fish radiations, 155 Adaptive radiation, classical, 46 Age-dependent probability, node as speciation Adaptive radiation, dynamic patterns of event, 287 discussion, 120–121 Arbitrary identification of real species, 15 diversification under random mating bias in reverse direction methods, 18–19 area effect, 109 challenges of using hypothesis tests for species hybridization and neutral gene flow, 110 diagnosis, 17–18 least action effect, 110 considering model-based approaches, 22–23 number of loci, effect of, 109 estimator bias and consistency, 19–20 over-shooting effect, 110 example using specific migration and splitting timing of speciation, 109 time cut-offs, 24–25 mathematical model insufficiency of overall summaries of habitat preference and dispersal, 106 differentiation, 21–22 individuals, 105 introduction to, 15–16 initial conditions, 108 nature of natural populations, 16–17 introduction to, 102 overcoming sample size effects using cut-off life-cycle, 105 criteria, 20–21 local extinction, 107 suggestions for criteria for species diagnosis, 23–24 mating preference, 107 offspring production, 107 Bacterial adaptation to complex environments, 47 parameter values, 108 genetic variance of fitness, estimating, 47 population genetic structure at imperfect generalists, 47 neutral loci, 108 Bacterial diversity in nature, 48–50 reproductive isolation and species, 108 DNA of soil bacteria, 49 space and environment, 104 Dykhuizen’s analysis, 50 viability selection, 105 mean abundance, 49 nonrandom mating evolution phylotypes, estimates of, 48 divergence in mating characters, 114 probability density distribution, 49 diversification stages, 120 Sheldon size spectrum, analysis of, 49 drift vs. selection (against hybridization), 112 soil bacteria, estimating, 50 hybridization, role of, 119 species richness, differences in, 50 local adaptation and speciation, 120 Batesian mimicry, 178 reinforcement, role of, 118 Bayesian and likelihood methods, 15 species diversity promoting speciation, 117 Bdelloids, 32 strength of nonrandom mating, 112 benefits of sex, 32 Adaptive radiation in bacteria, experimental, 46–47 range of species, 32 culture of bacteria, laboratory studies of, 46 rare recombination, 32 fitness rate, 46 reality of in Pseudomonas fluorescens, 46 testing morphological distinctiveness of, 33 © Cambridge University Press www.cambridge.org Cambridge University Press 978-0-521-88318-4 - Speciation and Patterns of Diversity Edited by Roger K. Butlin, Jon R. Bridle and Dolph Schluter Index More information INDEX 325 recognizability and structural analysis of, 32 species interactions contributing to community reproducing via parthenogenetic eggs, 32 diversity, 232 vs. monogonont rotifers, 32 biotic interactions stronger in tropics, 224–226 Bias in reverse direction methods, 18–19 latitudinal patterns in frequency of different, fixed difference between populations, 19 224–225 gene tree estimates approach, 19 latitudinal patterns in strength of, 225–226 sample size effect, 19 latitudinal patterns in traits involved in, 225 Population Aggregation Analysis (PAA) method, 19 climate, history and topography, 221–222 Binomial general linear model (logistic climatic factors associated with species regression), 284 richness and latitude, 221 Biodiversity and limits to adaptation in time and history and topography associated with species space, patterns of richness, importance of, 221–222 finite ranges in, 77–78 evolution and latitudinal gradient, 222–224 distributional limits, 77 biotic interactions hypothesis, 222–223 temporal or spatial persistence of species, evolutionary speed hypothesis, 222 factors limiting, 77 evolution of organisms, significant factors future prospects, 95 in, 223 integrating, 85–87 evolutionary implications of strong biotic population growth rate, calculating, 85 interactions, 226–228 species adapting to environmental change, 86 abiotic and biotic interactions, importance limits to adaptation determines species’ of, 226 distributions, 92–94 allocating resources for different adaptive habitat destruction and climate change, 93 challenges, 226 invasive species, studies of, 94 biotic drift, 228 range expansions of organisms, 92 coevolution, 227–228 limits to adaptation in space, 81–85 speciation rates higher in tropics, 232–233 demographic and genetic stochasticity on biotic interactions in maintenance of high adaptation, 84 tropical diversity, role of, 233 gene flow, effects of, 81, 82 tropical diversification and speciation rates, gene flow at range margins, 85 estimating higher, 233 genetic variance, evolution of, 84 strong biotic interactions lead to greater species geographical pattens of adaptation in species richness, 231–232 range, 81 Janzen-Connell effect, 232 models of evolution at range margins, 82 synopsis and future directions, 233–234 limits to adaptation in time, 78–81 biotic interactions in tropical regions, adaptation in response to environmental importance of, 233 change, 81 Red Queen hypothesis, 233 adaptation rate, determining, 78–79 Biotic interactions hypothesis, 222 genetic and demographic stochasticity by random sampling, 80–81 Catch-22, failure to recover correlations, 318 genetic variation in adaptation, role of, 78–80 Cenozoic individual-based simulation models, 81 climate changes effects, 310 rate of environmental change in time and diversity, trend, 312 extinction, relationship between, 78–79 Changing fitness landscapes, 140 predicting maximum rates of adaptation in Clade age natural populations analysis of, 249–249 condition-dependent sexual selection, 92 Clades, 41 genetic variation in fitness, amount of, 89–92 Cladogenesis, 282 phenotypic plasticity on rates of adaptation, effective rate, 282 effects of, 92 Climate changes, 317 rate and magnitude of change in optimum in Coalescent model, 36 space and time, 88–89 Coevolution, 227–228 strength of selection, 87–88 diversification of tropics, 227 Biotic drift, 228 tropical speciation, role in, 228 effects of, 228 Colour-based hybrid index, 157 Biotic interactions and speciation in tropics Complex temporal patterns, tests for, 288–292 biotic interactions facilitates speciation, 228–231 clade’s history, 279, 288 adaptive divergence of traits, 229 generalized additive models, 288 biotic factors to speciation in tropics, examples advantage, 289–290 of, 231 fitted rates and confidence intervals plotted reproductive isolation and geographic against time, 290 isolation, evolution of, 231 phylogeny underpinning, 290 © Cambridge University Press www.cambridge.org Cambridge University Press 978-0-521-88318-4 - Speciation and Patterns of Diversity Edited by Roger K. Butlin, Jon R. Bridle and Dolph Schluter Index More information 326 INDEX Complex temporal patterns, tests for (cont.) Diversification restriction, 289 in tropical regions results, 290 autocatalytic process, 219 limitations, 291–292 Diversification rates, 278 Constant diversification model, 262 American bird genera, 283– Constant rate models, 251 decrease in, 283 Continuous-time Markov model, 282 temporal patterns in, 278–279 “Coordinated stasis” hypothesis, 316 macroevolution, two approaches to, 279–282 Cretaceous-Tertiary boundary, 301 model system approach for macroevolution, limit to diversity, 301 292–296 mass extinction, 318 phylogenetic approach, problems with, 292 Cross-correlations tests for, 282–292, as effect of equilibrium, 318 Diversification under random mating between origination and extinction rates, 317 area effect, 109 Cut-off criteria, overcoming sample size effects intensive diversification, larger areas for, 109 using, 20–21 effect of number of loci, 109 cut-off values, 20 hybridization and neutral gene flow, 110 partly arbitrary, recommended, 21 blue butterfly species utilizing different hosts general hypotheses, 20 and diverged in morphology, 110 Cut-off values, 15, 20 least action effect, 110 over-shooting effect, 110 Demographic exchangeability, 39 timing of speciation, 109 Density-dependence/diversity-dependence, 278 Diversity, 301 Density-dependent diversification, 283 analysis, data, 309 Density dependent speciation, 252 geographic spread of sampling, 309 Diagnosis process, 15 Oligocene exclusion, 310 Dichotomous approach, 199 sample species, 310 Direct female mate choice of bacteria, estimating, 46 behavioural preferences for conspecific Cenozoic, trend in, 312 males, 160 community scale, 301 divergent female mating preferences restrict gene curves, 301 flow, 161 origination and extinction rates, relationship, 301 unimodal in male phenotype frequency and rank-order correlation, 310 distribution, 161 Sepkoski’s compendia, 306 Distinct population segment (DPS), 15 equilibrium, 317–319 Divergence measures, 26 population-level mechanism, locate, 319 Divergence population genetics of estimation, 305 chimpanzees, 24 SIB diversity, 307 cut-off values, 15 specimens, counting, 306, Pan troglodytes troglodytes versus