@article{brooks_method_2013,
title = {A Method for Detecting Positive Growth Autocorrelation without Marking Individuals},
volume = {8},
url = {http://dx.doi.org/10.1371/journal.pone.0076389},
doi = {10.1371/journal.pone.0076389},
abstract = {In most ecological studies, within-group variation is a nuisance that obscures patterns of interest and reduces statistical power. However, patterns of within-group variability often contain information about ecological processes. In particular, such patterns can be used to detect positive growth autocorrelation (consistent variation in growth rates among individuals in a cohort across time), even in samples of unmarked individuals. Previous methods for detecting autocorrelated growth required data from marked individuals. We propose a method that requires only estimates of within-cohort variance through time, using maximum likelihood methods to obtain point estimates and confidence intervals of the correlation parameter. We test our method on simulated data sets and determine the loss in statistical power due to the inability to identify individuals. We show how to accommodate nonlinear growth trajectories and test the effects of size-dependent mortality on our method's accuracy. The method can detect significant growth autocorrelation at moderate levels of autocorrelation with moderate-sized cohorts (for example, statistical power of 80\% to detect growth autocorrelation ρ2 = 0.5 in a cohort of 100 individuals measured on 16 occasions). We present a case study of growth in the red-eyed tree frog. Better quantification of the processes driving size variation will help ecologists improve predictions of population dynamics. This work will help researchers to detect growth autocorrelation in cases where marking is logistically infeasible or causes unacceptable decreases in the fitness of marked individuals.},
number = {10},
urldate = {2013-10-29},
journal = {{PLoS} {ONE}},
author = {Brooks, Mollie E. and {McCoy}, Michael W. and Bolker, Benjamin M.},
month = oct,
year = {2013},
pages = {e76389},
pdf = {bbpapers/brooks_method_2013.pdf}
}
@article{pasch_interspecific_2013,
title = {Interspecific Dominance Via Vocal Interactions Mediates Altitudinal Zonation in Neotropical Singing Mice},
volume = {182},
copyright = {Copyright © 2013 The University of Chicago},
issn = {0003-0147},
url = {http://www.jstor.org/stable/10.1086/673263},
doi = {10.1086/673263},
abstract = {Abstract Interspecific aggression between ecologically similar species may influence geographic limits by mediating competitive exclusion at the range edge. Advertisement signals that mediate competitive interactions within species may also provide social information that contributes to behavioral dominance and spatial segregation among species. We studied the mechanisms underlying altitudinal range limits in Neotropical singing mice (Scotinomys), a genus of muroid rodent in which males vocalize to repel rivals and attract mates. We first delineated replacement zones and described temperature regimes on three mountains in Costa Rica and Panama where Chiriquí singing mice (S. xerampelinus) abruptly replace Alston’s singing mice (S. teguina). Next, we conducted interspecific behavioral trials and reciprocal removal experiments to examine if interspecific aggression mediated species replacement. Finally, we performed reciprocal playback experiments to investigate whether response to song matched competitive interactions. Behavioral trials and removal experiments suggest that S. xerampelinus is behaviorally dominant and excludes S. teguina from higher, cooler altitudes. Playback experiments indicate that subordinate S. teguina is silenced and repelled by heterospecific song, whereas S. xerampelinus responded to heterospecifics with approach and song rates comparable to responses to conspecifics. Thus, interspecific communication reflects underlying dominance and suggests that acoustic signaling contributes to altitudinal zonation of ecologically similar congeners. Our findings implicate the use of social information in structuring spatial distributions of animal communities across landscapes and provide insight into how large-scale patterns are generated by individual interactions.},
number = {5},
urldate = {2013-10-10},
journal = {The American Naturalist},
author = {Pasch, Bret and Bolker, Benjamin M. and Phelps, Steven M.},
month = nov,
year = {2013},
pages = {E161--E173},
pdf = {bbpapers/pasch_interspecific_2013.pdf}
}
@article{lebauer_translating_2013,
title = {Translating Probability Density Functions: From {R} to {BUGS} and Back Again},
volume = {5},
shorttitle = {Translating Probability Density Functions},
url = {http://people.bu.edu/dietze/manuscripts/lebauer-dietze-bolker.pdf},
number = {1},
urldate = {2013-08-20},
journal = {R Journal},
author = {{LeBauer}, David S. and Dietze, Michael C. and Bolker, Benjamin M.},
year = {2013},
pages = {207–209},
pdf = {bbpapers/lebauer_translating_2013.pdf}
}
@article{biesinger_gag_2013,
title = {Gag ({{\em Mycteroperca microlepis}}) space-use correlations with landscape structure and environmental conditions},
volume = {443},
issn = {00220981},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022098113000567},
doi = {10.1016/j.jembe.2013.02.004},
urldate = {2013-08-20},
journal = {Journal of Experimental Marine Biology and Ecology},
author = {Biesinger, Zy and Bolker, Benjamin M. and Marcinek, Douglas and Lindberg, William J.},
month = may,
year = {2013},
pages = {1--11},
pdf = {bbpapers/biesinger_gag_2013.pdf}
}
@article{biesinger_testing_2013,
title = {Testing an autonomous acoustic telemetry positioning system for fine-scale space use in marine animals},
volume = {448},
issn = {0022-0981},
url = {http://www.sciencedirect.com/science/article/pii/S0022098113002268},
doi = {10.1016/j.jembe.2013.06.007},
abstract = {Abstract
We tested the capabilities and limitations of a novel autonomous acoustic positioning telemetry system with data from fifteen field deployments off the Florida coast. Telemetry array coverage areas ranged between 100 and 300 m across. For fixed transmitters within the array, the fraction of transmissions leading to high-quality calculated position estimates averaged 44\%, with wide variation. Positional accuracy was about 2 m. The choice of filtering strictness represented a trade-off between the accuracy and frequency of positions. There was substantial temporal variation, but no clear pattern (e.g., daily or tidal correlations) in frequency of positions. There was no spatial bias within the array. Array performance for stationary transmitters was robust to user errors in sound speed and hydrophone position estimates. Performance was less robust for a transmitter attached to an autonomous underwater vehicle moving through the array, with 22\% of transmissions leading to position estimates. Overall the system produced reliable results, but as the use of acoustic telemetry in complex ecological studies increases it is important to recognize technological requirements and limitations.},
urldate = {2013-08-20},
journal = {Journal of Experimental Marine Biology and Ecology},
author = {Biesinger, Zy and Bolker, Benjamin M. and Marcinek, Douglas and Grothues, Thomas M. and Dobarro, Joseph A. and Lindberg, William J.},
month = oct,
year = {2013},
keywords = {Acoustic telemetry, Autonomous positioning, Autonomous underwater vehicle, Long-term tracking, Telemetry capabilities, Telemetry limitations},
pages = {46--56},
pdf = {bbpapers/biesinger_testing_2013.pdf}
}
@article{bolker_strategies_2013,
title = {Strategies for fitting nonlinear ecological models in {R}, {AD} {Model} {Builder}, and {BUGS}},
volume = {4},
issn = {{2041210X}},
url = {http://doi.wiley.com/10.1111/2041-210X.12044},
doi = {10.1111/2041-210X.12044},
number = {6},
urldate = {2013-06-11},
journal = {Methods in Ecology and Evolution},
author = {Bolker, Benjamin M. and Gardner, Beth and Maunder, Mark and Berg, Casper W. and Brooks, Mollie and Comita, Liza and Crone, Elizabeth and Cubaynes, Sarah and Davies, Trevor and de Valpine, Perry and Ford, Jessica and Gimenez, Olivier and Kéry, Marc and Kim, Eun Jung and Lennert-Cody, Cleridy and Magnusson, Arni and Martell, Steve and Nash, John and Nielsen, Anders and Regetz, Jim and Skaug, Hans and Zipkin, Elise},
editor = {Ramula, Satu},
month = jun,
year = {2013},
pages = {501--512},
pdf = {bbpapers/bolker_strategies_2013.pdf}
}
@article{brando_fire-induced_2012,
title = {Fire-induced tree mortality in a neotropical forest: the roles of bark traits, tree size, wood density and fire behavior},
author = {Brando, P.M. and Nepstad, D.C. and Balch, J.K. and Bolker, B. and Christman, M.C. and Coe, M. and Putz, F.E.},
journal = {Global Change Biology},
volume = {18},
number = {2},
pages = {630--641},
year = {2012},
pdf = {bbpapers/brando_fire-induced_2012.pdf},
doi = {10.1111/j.1365-2486.2011.02533.x}
}
@article{stier_predator_2013_oikos,
title = {Predator density and competition modify the benefits of group formation in a shoaling reef fish},
volume = {122},
issn = {1600-0706},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2012.20726.x/abstract},
pdf = {bbpapers/stier_predator_2013_oikos.pdf},
doi = {10.1111/j.1600-0706.2012.20726.x},
abstract = {{SynthesisPredation} risk experienced by individuals living in groups depends on the balance between predator dilution, competition for refuges, and predator interference or synergy. These interactions operate between prey species as well: the benefits of group living decline in the presence of an alternative prey species. We apply a novel model-fitting approach to data from field experiments to distinguish among competing hypotheses about shifts in predator foraging behavior across a range of predator and prey densities. Our study provides novel analytical tools for analyzing predator foraging behavior and offers insight into the processes driving the dynamics of coral reef {fish.Studies} of predator foraging behavior typically focus on single prey species and fixed predator densities, ignoring the potential importance of complexities such as predator dilution; predator-mediated effects of alternative prey; heterospecific competition; or predator–predator interactions. Neglecting the effects of prey density is particularly problematic for prey species that live in mixed species groups, where the beneficial effects of predator dilution may swamp the negative effects of heterospecific competition. Here we use field experiments to investigate how the mortality rates of a shoaling coral reef fish (a wrasse: Thalassoma amblycephalum), change as a result of variation in: 1) conspecific density, 2) density of a predator (a hawkfish: Paracirrhites arcatus), and 3) presence of an alternative prey species that competes for space (a damselfish: Pomacentrus pavo). We quantify changes in prey mortality rates from the predator's perspective, examining the effects of added predators or a second prey species on the predator's functional response. Our analysis highlights a model-fitting approach that discriminates amongst multiple hypotheses about predator foraging in a community context. Wrasse mortality decreased with increasing conspecific density (i.e. mortality was inversely density-dependent). The addition of a second predator doubled prey mortality rates, without significantly changing attack rate or handling time – i.e. there was no evidence for predator interference. The presence of a second prey species increased wrasse mortality by 95\%; we attribute this increase either to short-term apparent competition (predator aggregation) or to a decrease in handling time of the predator (e.g. through decreased wrasse vigilance). In this system, 1) prey benefit from intraspecific group living though a reduced predation risk, and 2) the benefit of group living is reduced in the presence of an alternative prey species.},
language = {en},
number = {2},
urldate = {2013-01-20},
journal = {Oikos},
author = {Stier, Adrian C. and Geange, Shane W. and Bolker, Benjamin M.},
year = {2013},
pages = {171–178}
}
@article{stier_predator_2013,
title = {Predator density and timing of arrival affect reef fish community assembly},
volume = {94},
issn = {0012-9658},
url = {http://www.esajournals.org.libaccess.lib.mcmaster.ca/doi/full/10.1890/11-1983.1},
pdf = {bbpapers/stier_predator_2013_ecology.pdf},
doi = {10.1890/11-1983.1},
abstract = {Most empirical studies of predation use simple experimental approaches to quantify the effects of predators on prey (e.g., using constant densities of predators, such as ambient vs. zero). However, predator densities vary in time, and these effects may not be well represented by studies that use constant predator densities. Although studies have independently examined the importance of predator density, temporal variability, and timing of arrival (i.e., early or late relative to prey), the relative contribution of these different predator regimes on prey abundance, diversity, and composition remains poorly understood. The hawkfish (Paracirrhites arcatus), a carnivorous coral reef fish, exhibits substantial variability in patch occupancy, density, and timing of arrival to natural reefs. Our field experiments demonstrated that effects of hawkfish on prey abundance depended on both hawkfish density and the timing of their arrival, but not on variability in hawkfish density. Relative to treatments without hawkfish, hawkfish presence reduced prey abundance by 50\%. This effect increased with a doubling of hawkfish density (an additional 33\% reduction), and when hawkfish arrived later during community development (a 34\% reduction). Hawkfish did not affect within-patch diversity (species richness), but they increased between-patch diversity (beta) based on species incidence (22\%), and caused shifts in species composition. Our results suggest that the timing of predator arrival can be as important as predator density in modifying prey abundance and community composition.},
number = {5},
urldate = {2013-09-09},
journal = {Ecology},
author = {Stier, Adrian C. and Geange, Shane W. and Hanson, Kate M. and Bolker, Benjamin M.},
month = nov,
year = {2012},
keywords = {coral reefs, diversity, Moorea, French Polynesia, Paracirrhites arcatus, Predation, priority effects, reef fish, variance},
pages = {1057--1068}
}
@article{belshe_tundra_2013,
title = {Tundra ecosystems observed to be {CO2} sources due to differential amplification of the carbon cycle},
copyright = {© 2013 John Wiley \& Sons {Ltd/CNRS}},
issn = {1461-0248},
url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12164/abstract},
doi = {10.1111/ele.12164},
abstract = {Are tundra ecosystems currently a carbon source or sink? What is the future trajectory of tundra carbon fluxes in response to climate change? These questions are of global importance because of the vast quantities of organic carbon stored in permafrost soils. In this meta-analysis, we compile 40 years of {CO2} flux observations from 54 studies spanning 32 sites across northern high latitudes. Using time-series analysis, we investigated if seasonal or annual {CO2} fluxes have changed over time, and whether spatial differences in mean annual temperature could help explain temporal changes in {CO2} flux. Growing season net {CO2} uptake has definitely increased since the 1990s; the data also suggest (albeit less definitively) an increase in winter {CO2} emissions, especially in the last decade. In spite of the uncertainty in the winter trend, we estimate that tundra sites were annual {CO2} sources from the mid-1980s until the 2000s, and data from the last 7 years show that tundra continue to emit {CO2} annually. {CO2} emissions exceed {CO2} uptake across the range of temperatures that occur in the tundra biome. Taken together, these data suggest that despite increases in growing season uptake, tundra ecosystems are currently {CO2} sources on an annual basis.},
language = {en},
urldate = {2013-09-10},
journal = {Ecology Letters},
author = {Belshe, E. F. and Schuur, E. A. G. and Bolker, B. M.},
year = {2013},
keywords = {Carbon flux, climate change, tundra},
pdf = {bbpapers/belshe_tundra_2013.pdf}
}
@article{belshe_incorporating_2012,
title = {Incorporating spatial heterogeneity created by permafrost thaw into a landscape carbon estimate},
volume = {117},
issn = {0148-0227},
url = {http://www.agu.org/pubs/crossref/2012/2011JG001836.shtml},
doi = {10.1029/2011JG001836},
abstract = {The future carbon balance of high-latitude ecosystems is dependent on the sensitivity of biological processes (photosynthesis and respiration) to the physical changes occurring with permafrost thaw. Predicting C exchange in these ecosystems is difficult because the thawing of permafrost is a heterogeneous process that creates a complex landscape. We measured net ecosystem exchange of C using eddy covariance {(EC)} in a tundra landscape visibly undergoing thaw during two 6 month campaigns in 2008 and 2009. We developed a spatially explicit quantitative metric of permafrost thaw based on variation in microtopography and incorporated it into an {EC} carbon flux estimate using a generalized additive model {(GAM).} This model allowed us to make predictions about C exchange for the landscape as a whole and for specific landscape patches throughout the continuum of permafrost thaw and ground subsidence. During June through November 2008, the {GAM} predicted that the landscape on average took up 337.1 g C m−2 via photosynthesis and released 289.5 g C m−2 via respiration, resulting in a net C gain of 47.5 g C m−2 by the tundra ecosystem. During April through October 2009, the landscape on average took up 498.7 g C m−2 and released 410.3 g C m−2, resulting in a net C gain of 87.8 g C m−2. On average, between the years, areas with the highest permafrost thaw and ground subsidence photosynthesized 17.7\% more and respired 3.3\% more C than the average landscape. Areas with the least thaw and subsidence photosynthesized 15\% less and respired 5.1\% less than the landscape on average. By incorporating spatial variation into the {EC} C estimate, we were able to estimate the C balance of a heterogeneous landscape and determine the collective effect of permafrost thaw on the plant and soil processes that drive ecosystem C flux. In these study years, permafrost thaw appeared to increase the amplitude of the C cycle by stimulating both C release and sequestration, while the ecosystem remained a C sink at the landscape scale.},
language = {English},
number = {G1},
urldate = {2012-12-02},
journal = {Journal of Geophysical Research},
author = {Belshe, E. F. and Schuur, E. A. G. and Bolker, B. M. and Bracho, R.},
month = mar,
year = {2012},
pages = {G01026}
}
@article{poulsen_experimental_2012,
title = {Experimental manipulation of seed shadows of an {Afrotropical} tree determines drivers of recruitment},
volume = {93},
issn = {0012-9658},
url = {http://www.esajournals.org.libaccess.lib.mcmaster.ca/doi/full/10.1890/10-2430.1},
doi = {10.1890/10-2430.1},
abstract = {The loss of animals in tropical forests may alter seed dispersal patterns and reduce seedling recruitment of tree species, but direct experimental evidence is scarce. We manipulated dispersal patterns of Manilkara mabokeensis, a monkey-dispersed tree, to assess the extent to which spatial distributions of seeds drive seedling recruitment. Based on the natural seed shadow, we created seed distributions with seeds deposited under the canopy (“no dispersal”), with declining density from the tree (“natural dispersal”), and at uniform densities (“good dispersal”). These distributions mimicked dispersal patterns that could occur with the extirpation of monkeys, low levels of hunting, and high rates of seed dispersal. We monitored seedling emergence and survival for 18 months and recorded the number of leaves and damage to leaves. {“Good} dispersal” increased seedling survival by 26\%, and “no dispersal” decreased survival by 78\%, relative to “natural dispersal.” Using a mixed-effects survival model, we decoupled the distance and density components of the seed shadow: seedling survival depended on the seed density, but not on the distance from the tree. Although community seedling diversity tended to decrease with longer dispersal distances, we found no conclusive evidence that patterns of seed dispersal influence the diversity of the seedling community. Local seed dispersal does affect seedling recruitment and survival, with better dispersal resulting in higher seedling recruitment; hence the loss of dispersal services that comes with the reduction or extirpation of seed dispersers will decrease regeneration of some tree species.},
number = {3},
urldate = {2012-12-02},
journal = {Ecology},
author = {Poulsen, John R. and Clark, Connie J. and Bolker, Benjamin M.},
month = mar,
year = {2012},
keywords = {Bayesian analysis, Congo, experiment, Janzen-Connell hypothesis, loss of seed dispersers, Manilkara mabokeensis, Seed dispersal, Seedling emergence, seedling survival, seed shadow, tropical trees},
pages = {500--510}
}
@article{debroy_bistability_2011,
title = {Bistability and Long-Term Cure in a Within-Host Model of Hepatitis {C}},
volume = {19},
issn = {0218-3390, 1793-6470},
url = {http://www.worldscientific.com/doi/abs/10.1142/S0218339011004135},
doi = {10.1142/S0218339011004135},
number = {04},
urldate = {2012-10-18},
journal = {Journal of Biological Systems},
author = {Debroy, Swati and Bolker, Benjamin M. and Martcheva, Maia},
month = dec,
year = {2011},
pages = {533--550}
}
@article{mckeon_multiple_2012,
title = {Multiple defender effects: synergistic coral defense by mutualist crustaceans},
volume = {169},
issn = {0029-8549},
shorttitle = {Multiple defender effects},
url = {http://www.springerlink.com/content/nm20758r6557v448/abstract/},
doi = {10.1007/s00442-012-2275-2},
abstract = {The majority of our understanding of mutualisms comes from studies of pairwise interactions. However, many hosts support mutualist guilds, and interactions among mutualists make the prediction of aggregate effects difficult. Here, we apply a factorial experiment to interactions of ‘guard’ crustaceans that defend their coral host from seastar predators. Predation was reduced by the presence of mutualists (15\% reduction in predation frequency and 45\% in volume of coral consumed). The frequency of attacks with both mutualists was lower than with a single species, but it did not differ significantly from the expected frequency of independent effects. In contrast, the combined defensive efficacy of both mutualist species reduced the volume of coral tissue lost by 73\%, significantly more than the 38\% reduction expected from independent defensive efforts, suggesting the existence of a cooperative synergy in defensive behaviors of ‘guard’ crustaceans. These emergent ‘multiple defender effects’ are statistically and ecologically analogous to the emergent concept of ‘multiple predator effects’ known from the predation literature.},
number = {4},
urldate = {2012-10-18},
journal = {Oecologia},
author = {McKeon, C. Seabird and Stier, Adrian and McIlroy, Shelby and Bolker, Benjamin},
year = {2012},
keywords = {Biomedical and Life Sciences},
pages = {1095--1103},
pdf = {bbpapers/mckeon_multiple_2012.pdf}
}
@article{hostetler+2012,
journal = {Oecologia},
volume = {168},
number = {1},
year = {2012},
pages = {289-300},
doi = {10.1007/s00442-011-2083-0},
title = {Does genetic introgression improve female reproductive
performance? {A} test on the endangered {Florida} panther},
author = {Jeffrey A. Hostetler and David P. Onorato and Benjamin M. Bolker
Warren E. Johnson and Stephen J. O'Brien and Deborah Jansen and
Madan K. Oli},
pdf = {bbpapers/hostetler_does_2011.pdf}
}
@article{padmanabha_food_2011,
title = {Food Availability Alters the Effects of Larval Temperature on {{\em Aedes aegypti}} Growth},
volume = {48},
issn = {0022-2585},
abstract = {Variation in temperature and food availability in larval habitats can influence the abundance, body size, and vector competence of the mosquito Aedes aegypti. Although increased temperature has energetic costs for growing larvae, how food resources influence the developmental response of this mosquito species to thermal conditions is unknown. We explored how rearing temperature and food affect allometric scaling between wing size and epidermal cell size in Ae. aegypti. Mosquitoes were reared at 22 and 28 degrees C across a gradient of field-collected detritus designed to simulate commonly observed natural larval food resources. Overall, reduced temperature and increased food level increased wing size, but only temperature affected cell size. Females fed the least food had the longest time to maturation, and their increases in wing size induced by cold temperature were associated with larger, rather than more, cells. By contrast, males fed the most food had the shortest time to maturation, and their increases in wing size induced by cold temperature were associated with more, rather than larger, cells. Therefore, food levels can alter the underlying physiological mechanisms generating temperature-size patterns in mosquitoes, suggesting that the control of development is sensitive to the combination of nutrient and thermal conditions, rather than each independently. Conditions prolonging development time may favor increased cell division over growth. We suggest that understanding the effects of climate change on Ae. aegypti vectorial capacity requires an improved knowledge of how water temperature interacts with limited food resources and competition in aquatic container habitats.},
number = {5},
journal = {Journal of Medical Entomology},
author = {Padmanabha, H. and Bolker, B. and Lord, C. C. and Rubio, C. and Lounibos, L. P.},
month = sep,
year = {2011},
url = {http://www.bioone.org/doi/abs/10.1603/ME11020},
doi = {10.1603/ME11020},
keywords = {Aedes aegypti, body-size, cell-size, climate change, competition, critical weight, culicidae, dengue, diptera, drosophila-melanogaster, life-history puzzle, nutritional reserves, reaction norms, resource limitation, Temperature},
pages = {974--984}
}
@article{Wayne+2011,
author = { Marta L. Wayne and Gabriela M. Blohm and Mollie E. Brooks and Kerry L. Regan and Brennin Y.
Brown and Michael Barfield and Robert D. Holt and Benjamin M. Bolker},
title = {The prevalence and persistence of sigma virus, a biparentally transmitted parasite
of {{\em Drosophila melanogaster}}},
journal = {Evolutionary Ecology Research},
year = {2011},
pages = {323-345},
volume = {13}
}
@article{poulsen_decoupling_2011,
title = {Decoupling the effects of logging and hunting on an {Afrotropical} animal community},
volume = {21},
issn = {1051-0761},
url = {http://www.esajournals.org/doi/full/10.1890/10-1083.1?prevSearch=%5BAllField%3A+decoupling%5D&searchHistoryKey=},
doi = {10.1890/10-1083.1},
journal = {Ecological Applications},
author = {Poulsen, J. R. and Clark, C. J. and Bolker, B. M.},
month = jul,
year = {2011},
pages = {1819--1836}
}
@article{biesinger_predicting_2011,
author = {Zy Biesinger and Benjamin M. Bolker and William J. Lindberg},
title = {Predicting local population distributions around a central shelter based on a predation risk-growth trade-off},
year = 2011,
journal = {Ecological Modelling},
volume = 222,
pages = {1448-1455},
doi = {10.1016/j.ecolmodel.2011.02.009}
}
@article{mccoy_predicting_2011,
author = {McCoy, M. W. and B. M. Bolker and K. Warkentin and J.R. Vonesh},
title = {Predicting predation through prey ontogeny using size-dependent functional response models},
journal = {American Naturalist},
year = 2011,
volume = 177,
number = 6,
pages = {752-766},
doi = {10.1086/659950}
}
@inproceedings{okuyama_tmiichap,
author = {Toshinori Okuyama and Benjamin M. Bolker},
title = {Model-based, response surface approaches to quantifying indirect interactions},
booktitle = {Ecology and Evolution of Trait-Mediated Indirect Interactions:
Linking Evolution, Community, and Ecosystem},
year = {2013},
editor = {Takayuki Ohgushi and Oswald Schmitz and Robert Holt},
publisher = {Cambridge University Press},
isbn = {1107001838},
pdf = {Okuyama_Bolker_corrected_proof.pdf}
}
@article{trager_benefits_2010,
author = {Trager, M.D. and S. Bhotika and J.A. Hostetler and G.V. Andrade and M.A. Rodriguez-Cabal and C.S. McKeon and C.W. Osenberg and B.M. Bolker},
title = {Benefits for plants in ant-plant protective mutualisms: A meta-analysis},
journal = {PLoS ONE},
volume = 5,
issue = 12,
year = 2010,
doi = {10.1371/journal.pone.0014308z},
pdf = {trager_benefits_2010.pdf}
}
@article{lomascolo_dispersers_2010,
title = {Dispersers shape fruit diversity in {{\em Ficus}} {(Moraceae)}},
volume = {107},
url = {http://www.pnas.org/content/107/33/14668.abstract},
doi = {10.1073/pnas.1008773107},
abstract = {Seed dispersal by vertebrates is one of the most common and important plant{\textendash}animal mutualisms, involving an enormous diversity of fruiting plants and frugivorous animals. Even though plant reproduction depends largely on seed dispersal, evolutionary ecologists have been unable to link co-occurring traits in fruits with differences in behavior, physiology, and morphology of fruit-eating vertebrates. Hence, the origin and maintenance of fruit diversity remains largely unexplained. Using a multivariate phylogenetic comparative test with unbiased estimates of odor and color in figs, we demonstrate that fruit traits evolve in concert and as predicted by differences in the behavior, physiology (perceptive ability) and morphology of their frugivorous seed dispersers. The correlated evolution of traits results in the convergence of general appearance of fruits in species that share disperser types. Observations at fruiting trees independently confirmed that differences in fig traits predict differences in dispersers. Taken together, these results demonstrate that differences among frugivores have shaped the evolution of fruit traits. More broadly, our results underscore the importance of mutualisms in both generating and maintaining biodiversity.},
number = {33},
journal = {Proceedings of the National Academy of Sciences},
author = {Silvia B. Lom\'{a}scolo and Douglas J. Levey and Rebecca T. Kimball and Benjamin M. Bolker and Hans T. Alborn},
year = {2010},
pages = {14668 --14672}
}
@article{vuilleumier+2010,
author = { Vuilleumier, S\'everine and Bolker, Benjamin M. and L\'ev\^eque, Olivier},
title = { Effects of colonization asymmetries on metapopulation persistence},
journal = {Theoretical Population Biology},
year = {2010},
volume = 78,
issue = 3,
pages = {225-238},
doi = {10.1016/j.tpb.2010.06.007}
}
@article{holdo_disease-mediated_2009,
title = {A Disease-Mediated Trophic Cascade in the {Serengeti} and its Implications for Ecosystem {C}},
volume = {7},
url = {http://dx.doi.org/10.1371/journal.pbio.1000210},
doi = {10.1371/journal.pbio.1000210},
abstract = {The removal of rinderpest had cascading effects on
herbivore populations, fire, tree density, and even
ecosystem carbon in the Serengeti ecosystem of East
Africa.},
number = {9},
journal = {{PLoS} Biol},
author = {Ricardo M. Holdo and Anthony R. E. Sinclair and
Andrew P. Dobson and Kristine L. Metzger and
Benjamin M. Bolker and Mark E. Ritchie and Robert
D. Holt},
year = {2009},
pages = {e1000210}
}
@article{Bolker+2009,
author = {Benjamin M. Bolker and Arjun Nanda and Dharmini Shah},
title = {Transient virulence of emerging pathogens},
journal = {J. Roy Soc. Interface},
year = 2010,
doi = {10.1098/rsif.2009.0384},
pages = { 811-822 },
volume = {7},
number = {46}
}
@article{deCastroBolker2005b,
author = {Francisco {de Castro} and Benjamin M. Bolker},
title = {Parasite establishment and host extinction in model communities},
journal = {Oikos},
year = {2005},
volume = {111},
pages = {501-513},
number = {3},
pdf = {bbpapers/DeCastroBolker2005b.pdf}
}
@article{Allen+2008,
author = {L. J. S. Allen and B. M. Bolker and Y. Lou and A. L. Nevai},
title = {Asymptotic Profiles of the Steady States for an {SIS} Epidemic Reaction-Diffusion
Model},
journal = {Discrete and Continuous Dynamical Systems},
year = {2008},
volume = {21},
pages = {145-164},
number = {1},
pdf = {bbpapers/Allen+2008.pdf}
}
@article{Allen+2007,
author = {L. J. S. Allen and B. M. Bolker and Y. Lou and A. L. Nevai},
title = {Asymptotic Profiles of the Steady States for an {SIS} Epidemic Patch
Model},
journal = {SIAM Journal on Applied Mathematics},
year = {2007},
volume = {67},
pages = {1283-1309},
number = {5},
doi = {10.1137/060672522},
keywords = {basic reproduction number,disease-free equilibrium,dispersal,endemic
equilibrium,habitat connectivity,spatial heterogeneity},
pdf = {bbpapers/Allen+2007.pdf},
url = {http://link.aip.org/link/?SMM/67/1283/1}
}
@article{Babbitt+2006,
author = {Babbitt, G. A. and Kiltie, R. and Bolker, B.},
title = {Are Fluctuating Asymmetry Studies Adequately Sampled? Implications
of a New Model for Size Distribution},
journal = {American Naturalist},
year = {2006},
volume = {167},
pages = {230-245},
number = {2},
doi = {10.1086/498621},
pdf = {bbpapers/Babbitt+2006.pdf}
}
@article{BjorBolk00,
author = {Bj{\o}rnstad, {Ottar N.} and Bolker, {Benjamin M.}},
title = {Canonical functions for dispersal-induced synchrony},
journal = {Proceedings of the Royal Society of London Series B: Biological Sciences},
year = {2000},
volume = {267},
pages = {1787-1794},
number = {1454},
doi = {10.1098/rspb.2000.1211},
pdf = {bbpapers/BjornstadBolker2000.pdf}
}
@incollection{bolk-mpchap-03,
author = {Benjamin Bolker},
title = {Continuous-space models for population dynamics},
booktitle = {Ecology, Genetics, and Evolution of Metapopulations},
publisher = {Elsevier Science},
year = {2004},
editor = {Ilkka Hanski and Oscar E. Gaggioti},
chapter = {3},
pages = { 45-69},
address = {San Diego, CA},
pdf = {bbpapers/Bolker-HGbook-2004.pdf}
}
@article{Bolker2005,
author = {Ben Bolker},
title = {Other People's Data},
journal = {BioScience},
year = {2005},
volume = {55},
pages = {550-551},
number = {7},
pdf = {bbpapers/Bolker2005.pdf}
}
@article{bolk04a,
author = {Benjamin Bolker},
title = {A smorgasbord of stochastic dynamics},
journal = {Trends in Ecology and Evolution},
year = {2004},
volume = {19},
pages = {11},
number = {1},
note = {(Book review of {{\em Stochastic Population Dynamics in Ecology and
Conservation}} by Russ Lande, Steinar Engen and Bernt-Erik S{\ae}ther,
OUP 2003)},
pdf = {bbpapers/Bolker-LES-2004.pdf}
}
@article{bolk93,
author = {B. Bolker},
title = {Chaos and complexity in measles models: a comparative numerical study},
journal = {IMA Journal of Mathematics Applied in Medicine and Biology},
year = {1993},
volume = {10},
pages = {83--95},
keyword = {chaos; complexity; measles; models; age structure; seasonality; simulation;},
pdf = {bbpapers/Bolker1993.pdf}
}
@article{jury,
author = {Benjamin Bolker and Ethan D. Bolker},
title = {Modeling juror decay in a high profile criminal trial},
journal = {Math Horizons},
year = {1997},
volume = {V},
pages = {12-16},
number = {Nov.},
note = {(Newsletter of the Mathematical Association of America)}
}
@article{bolk+03b,
author = {Benjamin Bolker and Marcel Holyoak and Vlastimil K{\v r}ivan and
Locke Rowe and Oswald Schmitz},
title = {Connecting theoretical and empirical studies of trait-mediated interactions},
journal = {Ecology},
year = {2003},
volume = {84},
pages = {1101-1114},
number = {5},
pdf = {bbpapers/Bolker+-2003-Ecol.pdf}
}
@article{bolk+03c,
author = {Benjamin Bolker and Toshinori Okuyama and Karen Bjorndal and Alan
Bolten},
title = {Stock estimation for sea turtle populations using genetic markers:
accounting for sampling error of rare genotypes},
journal = {Ecological Applications},
year = {2003},
volume = {13},
pages = {763-775},
number = {3},
pdf = {bbpapers/Bolker+-2003-EA.pdf}
}
@article{bolker03,
author = {Benjamin M. Bolker},
title = {Combining endogenous and exogenous spatial variability in analytical
population models},
journal = {Theoretical Population Biology},
year = {2003},
volume = {64},
pages = {255-270},
pdf = {bbpapers/Bolker2003.pdf}
}
@article{bol99,
author = {Benjamin M. Bolker},
title = {Analytic Models for the Patchy Spread of Plant Disease},
journal = {Bulletin of Mathematical Biology},
year = {1999},
volume = {61},
pages = {849-874},
abstract = {Basic application of spatial moment closure (power-1) to dynamics
of a simple epidemic. Considers the covariance dynamics in a Poisson-distributed
and aggregated host populations, and looks briefly at epidemics with
removal/recovery.},
pdf = {bbpapers/Bolker1999.pdf}
}
@phdthesis{bbthesis,
author = {Benjamin M. Bolker},
title = {Dynamics of measles epidemics in developed countries},
school = {Cambridge University},
year = {1993}
}
@article{Bolker+2008,
author = {Benjamin M. Bolker and Francisco {de Castro} and Andrew Storfer and
Stephen Mech and Erik Harvey and James P. Collins},
title = {Disease as a selective force precluding widespread cannibalism: A
case study of an iridovirus of tiger salamanders, {{\em Ambystoma
tigrinum}}},
journal = {Evolutionary Ecology Research},
year = {2008},
volume = {10},
pages = {105-128},
owner = {ben},
timestamp = {2007.07.02}
}
@incollection{spatwild,
author = {B. M. Bolker and M. Altmann and M. Aubert and F. Ball and N. D. Barlow
and R. G. Bowers and A. P. Dobson and J. S. Elkington and G. P. Garnett
and C. A. Gilligan and M. P. Hassell and V. Isham and J. A. Jacquez
and A. Kleczkowski and S. A. Levin and R. M. May and J. A.J. Metz
and D. Mollison and M. Morris and L. A. Real and L. Sattenspiel and
J.Swinton and P. White and B. G. Williams},
title = {Group report: Spatial Dynamics of Infectious Diseases in Natural
Populations},
booktitle = {Ecology of Infectious Diseases in Natural Populations},
publisher = {Cambridge University Press},
year = {1995},
editor = {B. T. Grenfell and A. P. Dobson},
address = {Cambridge, UK},
pdf = {bbpapers/Bolker+1995.pdf}
}
@article{bolk+97,
author = {B. M. Bolker and D. H. Deutschman and G. Hartvigsen and D. L. Smith},
title = {Individual-based modelling: What is the difference?},
journal = {Trends in Ecology and Evolution},
year = {1997},
volume = {12},
pages = {111},
number = {3},
pdf = {bbpapers/Bolker+1997.pdf}
}
@article{bolkgren96,
author = {B. M. Bolker and B. T. Grenfell},
title = {Impact of vaccination on the spatial correlation and persistence
of measles dynamics},
journal = {Proceedings of the National Academy of Sciences of the USA},
year = {1996},
volume = {93},
pages = {12648-12653},
number = {22},
pdf = {bbpapers/BolkerGrenfell1996.pdf}
}
@article{bolkgren95,
author = {Benjamin M. Bolker and Bryan T. Grenfell},
title = {Space, persistence and dynamics of measles epidemics},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
year = {1995},
volume = {348},
pages = {309--320},
pdf = {bbpapers/BolkerGrenfell1995.pdf}
}
@article{bolkgren93,
author = {B. M. Bolker and B. T. Grenfell},
title = {Chaos and biological complexity in measles dynamics},
journal = {Proceedings of the Royal Society of London Series B: Biological Sciences},
year = {1993},
volume = {251},
pages = {75--81},
keyword = {chaos; complexity; measles; dynamics;},
pdf = {bbpapers/BolkerGrenfell1993.pdf}
}
@article{bolkgren92,
author = {B. M. Bolker and B. T. Grenfell},
title = {Are measles epidemics chaotic?},
journal = {Biologist},
year = {1992},
volume = {39},
pages = {107-110},
note = {(Newsletter of the British Society for Biology)},
keyword = {measles; epidemics; chaotic;}
}
@article{Bolker+2007,
author = {Benjamin M. Bolker and Toshinori Okuyama and Karen A. Bjorndal and
Alan B. Bolten},
title = {Incorporating multiple mixed stocks in mixed stock analysis: 'many-to-many'
analyses},
journal = {Molecular Ecology},
year = {2007},
volume = {16},
pages = {685-695},
doi = {10.1111/j.1365-294X.2006.03161.x},
pdf = {bbpapers/Bolker+2007.pdf}
}
@article{bp98,
author = {B. M. Bolker and S. W. Pacala},
title = {Spatial moment equations for plant competition: understanding spatial
strategies and the advantages of short dispersal},
journal = {American Naturalist},
year = {1999},
volume = {153},
pages = {575-602},
abstract = {Analyzes the "spatial Lotka-Volterra model": two-species competition
in a point process model. Decomposes spatial covariances into a series
of terms that affect competitive invasion, attributing different
terms to competition-colonization tradeoffs, successional niches,
or phalanx growth. Uses power-1 closure and Bessel-function competition
and dispersal kernels to get analytically tractable invasion criteria.
(However, power-1 closure means that invasion criteria only act sensibly
when the invader would lose in the non-spatial case.)},
pdf = {bbpapers/BolkerPacala1999.pdf}
}
@article{bolkpaca97,
author = {B. M. Bolker and S. W. Pacala},
title = {Using moment equations to understand stochastically driven spatial
pattern formation in ecological systems},
journal = {Theoretical Population Biology},
year = {1997},
volume = {52},
pages = {179-197},
abstract = {Spatial moment equations (power-1 closure) for the spatial logistic
model, one-species competition. Analytical methods for solving for
equilibrium are presented (but these methods are somewhat clumsy,
and are superseded by those in Bolker and Pacala 1999). Predicts
when equilibrium population patterns will be even vs. aggregated.},
pdf = {bbpapers/BolkerPacala1997.pdf}
}
@article{bolk+95,
author = {B. M. Bolker and S. W. Pacala and F. A. Bazzaz and C. D. Canham and
S. A. Levin},
title = {Species diversity and ecosystem response to carbon dioxide fertilization:
conclusions from a temperate forest model},
journal = {Global Change Biology},
year = {1995},
volume = {1},
pages = {373-381},
pdf = {bbpapers/Bolker+1995-GCB.pdf}
}
@inproceedings{bpl97,
author = {Benjamin M. Bolker and Stephen W. Pacala and Simon A. Levin},
title = {Moment methods for stochastic processes in continuous space and time},
booktitle = {The Geometry of Ecological Interactions: Simplifying Spatial Complexity},
year = {2000},
editor = {U. Dieckmann and R. Law and J. A. J. Metz},
pages = {388-411},
address = {Cambridge, UK},
publisher = {Cambridge University Press},
pdf = {bbpapers/Bolker+2000-iiasa.pdf}
}
@article{bpn03,
author = {Benjamin M. Bolker and Stephen W. Pacala and Claudia Neuhauser},
title = {Spatial dynamics in model plant communities: what do we really know?},
journal = {American Naturalist},
year = {2003},
volume = {162},
pages = {135-148},
number = {2},
pdf = {bbpapers/Bolker+-AN-2003.pdf}
}
@article{bpp96,
author = {B. M. Bolker and S. W. Pacala and Parton, Jr., W. J.},
title = {Linear analysis of soil decomposition: insights from the {{\sc Century}}
model},
journal = {Ecological Applications},
year = {1998},
volume = {8},
pages = {425-439},
number = {2},
pdf = {bbpapers/Bolker+-1998-EA.pdf}
}
@article{bolk+02,
author = {Bolker, B. M. and C. M. {St. Mary} and C. W. Osenberg and R. J. Schmitt
and S. J. Holbrook},
title = {Management at a different scale: marine ornamentals and local processes},
journal = {Bulletin of Marine Science},
year = {2002},
volume = {70},
pages = {733-748},
number = {2}
}
@article{bowen+2004,
author = {B. W. Bowen and A. L. Bass and S.-M. Chow and M. Bostrom and K. A.
Bjorndal and A. B. Bolten and T. Okuyama and B. M. Bolker and S.
Epperly and E. LaCasella and D. Shaver and M. Dodd and S. R. Hopkins-Murphy
and J. A. Musick and M. Swingle and K. Rankin-Baransky and W. Teas
and W. N. Witzell and P. H. Dutton},
title = {Natal homing in juvenile loggerhead turtles ({{\em Caretta caretta}})},
journal = {Molecular Ecology},
year = {2004},
volume = {13},
pages = {3797-3808},
doi = {10.1111/j.1365-294X.2004.02356.x},
pdf = {bbpapers/Bowen+2004.pdf}
}
@article{brownbolker04,
author = {David H. Brown and Benjamin M. Bolker},
title = {The effects of disease dispersal and host clustering on the epidemic
threshold in plants},
journal = {Bulletin of Mathematical Biology},
year = {2004},
volume = {66},
pages = {341-371},
doi = {10.1016/j.bulm.2003.08.006},
pdf = {bbpapers/BrownBolker2004.pdf}
}
@article{Buckley+2007,
author = {Buckley, Yvonne M. and Bolker, Benjamin M. and Rees, Mark},
title = {Disturbance, invasion and re-invasion: managing the weed-shaped hole
in disturbed ecosystems},
journal = {Ecology Letters},
year = {2007},
volume = {10},
pages = {809--817},
number = {9},
month = {September},
citeulike-article-id = {1527173},
doi = {10.1111/j.1461-0248.2007.01067.x},
issn = {1461-023X},
keywords = {math},
publisher = {Blackwell Publishing}
}
@article{DeCastroBolker2005,
author = {de Castro, Francisco and Bolker, Benjamin},
title = {Mechanisms of disease-induced extinction},
journal = {Ecology Letters},
year = {2005},
volume = {8},
pages = {117-126},
doi = {10.1111/j.1461-0248.2004.00693.x},
pdf = {bbpapers/DeCastroBolker2005.pdf}
}
@article{Clark+2005,
author = {C. J. Clark and J. R. Poulsen and B. M. Bolker and E. F. Connor and
V. T. Parker},
title = {Comparative seed shadows of bird-, monkey-, and wind-dispersed trees},
journal = {Ecology},
year = {2005},
volume = {86},
pages = {2684-2694},
number = {10},
pdf = {bbpapers/Clark+2005.pdf}
}
@article{earn+00,
author = {David J. D. Earn and Pejman Rohani and Benjamin M. Bolker and Bryan
T. Grenfell},
title = {A simple model for complex dynamical transitions in epidemics},
journal = {Science},
year = {2000},
volume = {287},
pages = {667-670},
pdf = {bbpapers/Earn+2000.pdf}
}
@incollection{gbk93,
author = {Bryan Grenfell and Ben Bolker and Adam Kleczkowski},
title = {Seasonality, demography, and the dynamics of measles in developed
countries},
booktitle = {Epidemic Models: Their Structure and Relation to Data},
publisher = {Cambridge University Press},
year = {1993},
editor = {Denis Mollison},
pages = {248-268},
address = {Cambridge, UK},
keyword = {epidemic; epidemic models; models; seasonality; demography; dynamics;
measles; countries;}
}
@incollection{gren94,
author = {Bryan T. Grenfell and Benjamin M. Bolker},
title = {Population dynamics of measles},
booktitle = {Parasitic and Infectious Diseases: Epidemiology and Ecology},
publisher = {Academic Press},
year = {1994},
editor = {Marilyn E. Scott and Gary Smith},
address = {San Diego},
keyword = {parasite; epidemiology; measles;}
}
@article{GrenBolk98,
author = {B. T. Grenfell and B. M. Bolker},
title = {Cities and villages: infection hierarchies in a measles metapopulation},
journal = {Ecology Letters},
year = {1998},
volume = {1},
pages = {63-70},
number = {1},
month = jul,
abstract = {An important issue in the dynamics of directly transmitted microparasites
is the relationship between infection probability and host density.
We use models and extensive spatio-temporal data for the incidence
of measles to examine evidence for spatial heterogeneity in transmission
probability, in terms of urban-rural hierarchies in infection rate.
Pre-vaccination measles data for England and Wales show strong evidence
for urban-rural heterogeneities in infection rate -the proportion
of urban cases rises significantly before major epidemics. The model
shows that this effect is consistent with a higher infection rate
in large cities, though small towns have epidemic characteristics
intermediate between town and country. Surprisingly, urban and rural
areas of the same population size have a similar propensity for local
extinction of infection. A spatial map of urban-rural correlations
reveals complex regional patterns of synchronization of towns and
cities. The hierarchical heterogeneities in infection persist into
the vaccine era; their implications for disease persistence and control
are discussed},
pdf = {bbpapers/GrenfellBolker1998.pdf}
}
@article{gbk95,
author = {Grenfell, B. T. and Bolker, B. M. and Kleczkowski, A.},
title = {Seasonality and extinction in chaotic metapopulations},
journal = {Proceedings of the Royal Society of London Series B: Biological Sciences},
year = {1995},
volume = {259},
pages = {97-103},
number = {1354},
bids-rf = {0893_93 1 sexual mixing patterns; measles epidemics; hepatitis-b immunization;
spread of hiv; mass vaccination 2283_93 1 chaotic time- series; lyapunov
exponents; nonlinear dynamics; attractor dimension 6340_93 1 host
parasitoid system; prey density; water mite predation; distribution
of an armored scale insect; spatial heterogeneity; models for patchy
populations},
keywords = {measles dynamics, time-series, epidemics, oscillations, outbreaks,
models, noise},
pdf = {bbpapers/Grenfell+1995.pdf}
}
@article{gren+94,
author = {B. T. Grenfell and A. Kleczkowski and S. P. Ellner and B. M. Bolker},
title = {Measles as a case study in nonlinear forecasting and chaos},
journal = {Philosophical Transactions of the Royal Society A},
year = {1994},
volume = {348},
pages = {515-530},
note = {Also published in \emph{Chaos and Forecasting: Proceedings of the
Royal Society Discussion meeting} (1995), ed. H. Tong (World Scientific:
River Edge, NJ), pp. 321-345.},
pdf = {bbpapers/Grenfell+1994.pdf}
}
@article{gren+95b,
author = {B. T. Grenfell and A. Kleczkowski and C. A. Gilligan and B. M. Bolker},
title = {Spatial heterogeneity, nonlinear dynamics and chaos in infectious
diseases},
journal = {Statistical Methods in Medical Research},
year = {1995},
volume = {4},
pages = {160-183}
}
@article{grin+91,
author = {G. Grinstein and Yu He and C. Jayaprakash and B. Bolker},
title = {Collective behavior of a coupled-map system with a conserved quantity},
journal = {Physical Review A},
year = {1991},
volume = {44},
pages = {4923-4936}
}
@article{Gruner+2008,
author = {Gruner, D. S. and Smith, J. E. and Seabloom, E. W. and Sandin, S.
A. and Ngai, J. T. and Hillebrand, H. and Harpole, W. S. and Elser,
J. J. and Cleland, E. E. and Bracken, M. E. S. and Borer, E. T. and
Bolker, B. M.},
title = {A cross-system synthesis of consumer and nutrient resource control
on producer biomass},
journal = {Ecology Letters},
year = {2008},
volume = {11},
pages = {740--755},
number = {7},
sn = {1461-023X},
tc = {0},
ut = {MEDLINE:18445030},
owner = {ben},
timestamp = {2008.08.01}
}
@article{Hastings+2005,
author = {Alan Hastings and Peter Arzberger and Ben Bolker and Scott Collins
and Anthony R. Ives and Norman A. Johnson and Margaret A. Palmer},
title = {Quantitative Bioscience for the 21st Century},
journal = {BioScience},
year = {2005},
volume = {55},
pages = {511-517},
number = {6}
}
@inproceedings{hubb+88,
author = {L. M. Hubbard and B. Bolker and R. H. Socolow and D. Dickerhoff},
title = {Radon dynamics in a house heated alternately by forced air and by
electric resistance},
booktitle = {Proceedings of the 1988 EPA Symposium on Radon and Radon Reduction
Technology},
year = {1988},
address = {Denver, CO}
}
@article{kbb02,
author = {Klaus Keller and Benjamin Bolker and David Bradford},
title = {Uncertain climate thresholds and optimal economic growth},
journal = {Journal of Environmental Economics and Management},
year = {2004},
volume = {48},
pages = {723-741},
doi = {10.1016/j.jeem.2003.10.003},
pdf = {bbpapers/Keller+-2004.pdf}
}
@article{kb03,
author = {K. Kitajima and B. M. Bolker},
title = {Testing performance rank reversals among coexisting species: crossover
point irradiance analysis by {Sack} \& {Grubb} (2001) and alternatives},
journal = {Functional Ecology},
year = {2003},
volume = {17},
pages = {276-281},
pdf = {bbpapers/KitajimaBolker2003.pdf}
}
@article{khb92,
author = {E. O. Knutson and L. M. Hubbard and B. Bolker},
title = {Determination of the surface to volume ratio in homes: measurements
of radon and its progeny},
journal = {Radiation Protection Dosimetry},
year = {1992},
volume = {42},
pages = {121-126}
}
@article{Levey+2005,
author = {Douglas J. Levey and Benjamin M. Bolker and Joshua J. Tewksbury and
Sarah Sargent and Nick M. Haddad},
title = {Effects of landscape corridors on seed dispersal by birds},
journal = {Science},
year = {2005},
volume = {309},
pages = {146-148},
pdf = {bbpapers/Levey+2005.pdf}
}
@article{Levey+2008,
author = {Levey, D. J. and Tewksbury, J. J. and Bolker, B. M.},
title = {Modelling long-distance seed dispersal in heterogeneous landscapes},
journal = {Journal of Ecology},
year = {2008},
volume = {96},
pages = {599--608},
number = {4},
doi = {10.1111/j.1365-2745.2008.01401.x},
owner = {ben},
sn = {0022-0477},
tc = {4},
timestamp = {2008.08.01},
ut = {WOS:000256635800005}
}
@article{MartchevaBolker2007,
author = {Maia Martcheva and Benjamin M. Bolker},
title = {The Impact of the {Allee} Effect in Dispersal and Patch-Occupancy
Age on the Dynamics of Metapopulations},
journal = {Bulletin of Mathematical Biology},
year = {2007},
volume = {69},
pages = {135-156},
number = {1},
doi = {10.1007/s11538-006-9075-y},
pdf = {bbpapers/MartchevaBolker2007.pdf}
}
@article{Martcheva+2007,
author = {Maia Martcheva and Benjamin M. Bolker and Robert D. Holt},
title = {Vaccine-induced pathogen strain replacement: what are the mechanisms?},
journal = {J. Roy. Soc. Interface},
year = {2007},
doi = {10.1098/rsif.2007.0236},
owner = {ben},
timestamp = {2007.07.02}
}
@article{may+92,
author = {R. M. May and V. Isham and B. Bolker and E. Renshaw and A. J. Lawrance
and N. M. Spencer and L. A. Smith and A. J. Mayne and G. P. King
and V. Albrecht and K. S. Lim and I. Dvorak and J. Basterfield and
Salahuddin and D. Mollison and K. S. Chan and H. Tong and R. C.L.
Wolff and G. Lord and G. Nason and D. Tjostheim and M. Casdagli and
R. L. Smith and D. S. Broomhead and J. P. Huke and M. R. Muldoon
and D. Nychka and S. Ellner and A. R. Gallant and D. McCaffrey and
B. Cheng},
title = {{Royal Statistical Society} meeting on chaos: discussion},
journal = {Journal of the Royal Statistical Society B},
year = {1992},
volume = {54},
pages = {451-474}
}
@inproceedings{lin97,
author = {Ryan McAllister and Juan Lin and Benjamin Bolker and Stephen W. Pacala},
title = {Spatial correlations in population models with competition and dispersal},
booktitle = {Proceedings of the Symposium on Biological Complexity},
year = {1997},
address = {DIRAC Facultad de Ciencias, Montevideo, Uruguay}
}
@article{McCoyBolker2008,
author = {McCoy, M. W. and Bolker, B. M.},
title = {Trait-mediated interactions: influence of prey size, density and
experience},
journal = {Journal of Animal Ecology},
year = {2008},
volume = {77},
pages = {478--486},
number = {3},
doi = {10.1111/j.1365-2656.2008.01372.x},
owner = {ben},
sn = {0021-8790},
tc = {0},
timestamp = {2008.08.01},
ut = {WOS:000254990300007}
}
@article{McCoy+2006,
author = {Michael W. McCoy and Benjamin M. Bolker and Craig W. Osenberg and
Benjamin G. Miner and James R. Vonesh},
title = {Size correction: comparing morphological traits among populations
and environments},
journal = {Oecologia},
year = {2006},
volume = {148},
pages = {547-554},
doi = {10.1007/s00442-006-0403-6},
pdf = {bbpapers/McCoy+2006.pdf}
}
@article{OkuyamaBolker2007,
author = {Toshinori Okuyama and Benjamin M. Bolker},
title = {On quantitative measures of indirect effects},
journal = {Ecology Letters},
year = {2007},
volume = {10},
pages = {264-271},
number = {4},
abstract = {Indirect effects, whether density-mediated (DMII) or trait-mediated
(TMII), have been recognized as potentially important drivers of
community dynamics. However, empirical studies that have attempted
to detect TMII or to quantify the relative strength of DMII and TMII
in short-term studies have used a range of different metrics. We
review these studies and assess both the consistency of a variety
of different metrics and their robustness to (or ability to detect)
ecological phenomena such as the dependence of forager behaviour
on conspecific density. Quantifying indirect effects over longer
time scales when behaviour and population density vary is more challenging,
but also necessary if we really intend to incorporate indirect effects
into predictions of long-term community dynamics; we discuss some
problems associated with this effort and conclude with general recommendations
for quantifying indirect effects.}
}
@article{OkuyamaBolker2005,
author = {Okuyama, Toshinori and Bolker, Benjamin M.},
title = {Combining genetic and ecological data to estimate sea turtle origins},
journal = {Ecological Applications},
year = {2005},
volume = {15},
pages = {315-325},
number = {1},
pdf = {bbpapers/OkuyamaBolker2005.pdf}
}
@incollection{Osenberg+2006,
author = {C. W. Osenberg and B. M. Bolker and J. S. White and C. M. {St. Mary}
and J. Shima},
title = {Statistical Issues and Study Design in Ecological Restorations: Lessons
Learned from Marine Reserves},
booktitle = {Foundations of Restoration Ecology},
publisher = {Island Press},
year = {2006},
editor = {D. Falk and M. Palmer and J. Zedler},
chapter = {13},
address = {Washington, DC}
}
@article{Romero+2009,
year = {2009},
title = {Stem responses to damage: the evolutionary ecology of tree species in contrasting fire regimes},
author = {Romero, Claudia and Bolker, Benjamin M. and Edwards, Christine E.},
journal = {New Phytologist},
volume = {182},
pages = {261-271},
doi = {10.1111/j.1469-8137.2008.02733.x}
}
@article{Bolker2008b,
title = {Learning hierarchical models: advice for the rest of us
(Forum response)},
author = {Benjamin M. Bolker},
journal = {Ecological Applications},
volume = 19,
number = 3,
year = 2009,
pages = {588-592}
}
@article{Ozgul+2009,
author = {Arpat Ozgul and Madan Oli and Benjamin M. Bolker and Carolina Perez-Heydrich},
title = {Upper respiratory tract disease, force of infection, and multifactorial
effects on survival of gopher tortoises},
journal = {Ecological Applications},
volume = 19,
number = 3,
pages = {786-798},
year = 2009,
owner = {ben},
doi = {10.1890/08-0219.1},
timestamp = {2008.02.28}
}
@article{Bolker+2009b,
author = {Benjamin M. Bolker
and Mollie E. Brooks and Connie J. Clark
and Shane W. Geange and John R. Poulsen and M. Henry H. Stevens and
JadaSimone S. White},
title = {Generalized linear mixed models: a practical guide
for ecology and evolution},
doi = {10.1016/j.tree.2008.10.008},
year = {2009},
journal = {Trends in Ecology and Evolution},
volume = 24,
number = 3,
pages = {127-135},
pdf = {bbpapers/Bolker+2009-glmm.pdf}
}
@incollection{bolker2009,
author = {Benjamin M. Bolker},
title = {Evolution of dispersal scale and shape in heterogeneous
environments: a correlation equation approach},
editor = {Stephen Cantrell and Chris Cosner and Shigui Ruan},
booktitle = {Spatial Ecology},
chapter = 12,
isbn = {1420059858},
publisher = {Chapman \& {Hall}/{CRC}},
month = aug,
year = {2009}
}
@article{Poulsen+2007,
author = {Poulsen, J. R. and Osenberg, C. W. and Clark, C. J. and Levey, D.
J. and Bolker, B. M.},
title = {Plants as reef fish: fitting the functional form of seedling recruitment},
journal = {American Naturalist},
year = {2007},
volume = {170},
pages = {167-183},
number = {2}
}
@article{RomeroBolker2008,
author = {Romero, C. and Bolker, B. M.},
title = {Effects of stem anatomical and structural traits on responses to
stem damage: an experimental study in the {Bolivian} {Amazon}},
journal = {Canadian Journal of Forest Research},
year = {2008},
volume = {38},
pages = {611--618},
number = {3},
doi = {10.1139/X07-205},
owner = {ben},
sn = {0045-5067},
tc = {0},
timestamp = {2008.08.01},
ut = {WOS:000253774400019}
}
@article{seabloom+2005,
author = {Eric Seabloom and Ottar Bj{\o}rnstad and Benjamin Bolker and Omar
J. Reichman},
title = {The spatial signature of environmental heterogeneity, dispersal,
and competition in successional grasslands},
journal = {Ecological Monographs},
year = {2005},
volume = {75},
pages = {199-214},
number = {2},
pdf = {bbpapers/Seabloom+2005.pdf}
}
@article{Tiwari+2006,
author = {Tiwari, Manjula and Bjorndal, Karen A. and Bolten, Alan B. and Bolker,
Benjamin M.},
title = {Evaluation of density-dependent processes and green turtle {{\em
Chelonia mydas}} hatchling production at {Tortuguero}, {Costa Rica}},
journal = {Marine Ecology Progress Series},
year = {2006},
volume = {326},
pages = {283-293}
}
@article{Tiwari+2005,
author = {Manjula Tiwari and Karen A. Bjorndal and Alan B. Bolten and Benjamin
M. Bolker},
title = {Intraspecific application of the mid-domain effect model: spatial
and temporal nest distributions of green turtles, {{\em Chelonia
mydas}}, at {Tortuguero}, {Costa Rica}},
journal = {Ecology Letters},
year = {2005},
volume = {8},
pages = {918-924},
number = {9},
doi = {10.1111/j.1461-0248.2005.00793.x},
pdf = {bbpapers/Tiwari+2005.pdf}
}
@article{VoneshBolker2005,
author = {James R. Vonesh and Benjamin M. Bolker},
title = {Compensatory larval responses shift trade-offs associated with predator-induced
hatching plasticity},
journal = {Ecology},
year = {2005},
volume = {86},
pages = {1580-1591},
number = {6},
pdf = {bbpapers/VoneshBolker2005.pdf}
}
@article{Fiske+2008,
author = {Fiske, Ian J. and Bruna, Emilio M. and Bolker, Benjamin M.},
title = {Effects of Sample Size on Estimates of Population Growth Rates Calculated with Matrix Models},
journal = {PLoS ONE},
year = {2008},
volume = {3},
number = {8},
pages = {e3080},
doi = {10.1371/journal.pone.0003080}
}
@book{Bolker2008,
author = {Benjamin M. Bolker},
title = {Ecological Models and Data in R},
publisher = {Princeton University Press},
year = {2008},
address = {Princeton, NJ}
}
@article{ma_estimating_2014,
year = 2014,
note = {("OnLine first" version; no real date yet)},
title = {Estimating Initial Epidemic Growth Rates},
issn = {0092-8240, 1522-9602},
url = {http://link.springer.com/article/10.1007/s11538-013-9918-2},
doi = {10.1007/s11538-013-9918-2},
abstract = {The initial exponential growth rate of an epidemic is an important measure of disease spread, and is commonly used to infer the basic reproduction number {TeX{\textbackslash}mathcal\{R\}\_\{0\}} . While modern techniques (e.g., {MCMC} and particle filtering) for parameter estimation of mechanistic models have gained popularity, maximum likelihood fitting of phenomenological models remains important due to its simplicity, to the difficulty of using modern methods in the context of limited data, and to the fact that there is not always enough information available to choose an appropriate mechanistic model. However, it is often not clear which phenomenological model is appropriate for a given dataset. We compare the performance of four commonly used phenomenological models (exponential, Richards, logistic, and delayed logistic) in estimating initial epidemic growth rates by maximum likelihood, by fitting them to simulated epidemics with known parameters. For incidence data, both the logistic model and the Richards model yield accurate point estimates for fitting windows up to the epidemic peak. When observation errors are small, the Richards model yields confidence intervals with better coverage. For mortality data, the Richards model and the delayed logistic model yield the best growth rate estimates. We also investigate the width and coverage of the confidence intervals corresponding to these fits.},
language = {en},
urldate = {2013-11-27},
journal = {Bulletin of Mathematical Biology},
author = {Ma, Junling and Dushoff, Jonathan and Bolker, Benjamin M. and Earn, David J. D.},
keywords = {Cell Biology, Exponential growth rate, Life Sciences, general, Mathematical and Computational Biology, Phenomenological models},
pages = {1--16},
file = {Snapshot:/home/bolker/.mozilla/firefox/gf2kp1m5.default/zotero/storage/4XV9B8EU/10.html:text/html},
pdf = {bbpapers/Ma_estimating_2013.pdf}
}
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