dmdScheme_papers.bib

@article{altermatt_big_2015,
	title = {Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution},
	volume = {6},
	copyright = {All rights reserved},
	url = {http://doi.wiley.com/10.1111/2041-210X.12312},
	doi = {10.1111/2041-210X.12312},
	number = {2},
	journal = {Methods in Ecology and Evolution},
	author = {Altermatt, Florian and Fronhofer, Emanuel and Garnier, Aurélie and Giometto, Andrea and Hammes, Frederik and Klecka, Jan and Legrand, Delphine and Mächler, Elvira and Massie, Thomas M. and Pennekamp, Frank and Plebani, Marco and Pontarp, Mikael and Schtickzelle, Nicolas and Thuillier, Virginie and Petchey, Owen L},
	month = nov,
	year = {2015},
	pages = {218--231},
	file = {Full Text:files/389/Altermatt et al. - 2015 - Big answers from small worlds a user's guide for .pdf:application/pdf}
}

@article{pennekamp_biodiversity_2018,
	title = {Biodiversity increases and decreases ecosystem stability},
	copyright = {All rights reserved},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/s41586-018-0627-8},
	doi = {10.1038/s41586-018-0627-8},
	language = {en},
	urldate = {2018-10-29},
	journal = {Nature},
	author = {Pennekamp, Frank and Pontarp, Mikael and Tabi, Andrea and Altermatt, Florian and Alther, Roman and Choffat, Yves and Fronhofer, Emanuel A. and Ganesanandamoorthy, Pravin and Garnier, Aurélie and Griffiths, Jason I. and Greene, Suzanne and Horgan, Katherine and Massie, Thomas M. and Mächler, Elvira and Palamara, Gian Marco and Seymour, Mathew and Petchey, Owen L.},
	month = oct,
	year = {2018},
	keywords = {Checked for experimental metadata},
	file = {Full Text:files/390/Pennekamp et al. - 2018 - Biodiversity increases and decreases ecosystem sta.pdf:application/pdf}
}

@article{mcgrady-steed_biodiversity_1997,
	title = {Biodiversity regulates ecosystem predictability},
	volume = {390},
	url = {http://www.nature.com/nature/journal/v390/n6656/abs/390162a0.html},
	journal = {Nature},
	author = {McGrady-Steed, J and Harris, PM},
	year = {1997},
	pages = {162--165},
	file = {Full Text:files/394/McGrady-Steed and Harris - 1997 - Biodiversity regulates ecosystem predictability.pdf:application/pdf}
}

@article{carrara_experimental_2015,
	title = {Experimental evidence for strong stabilizing forces at high functional diversity of microbial communities},
	volume = {in press},
	doi = {10.1890/14-1324.1},
	journal = {Ecology},
	author = {Carrara, Francesco and Giometto, Andrea and Seymour, Mathew and Rinaldo, Andrea and Altermatt, Florian},
	year = {2015},
	keywords = {Checked for experimental metadata},
	file = {Full Text:files/391/Carrara et al. - 2015 - Experimental evidence for strong stabilizing force.pdf:application/pdf}
}

@article{vasseur_phase-locking_2009,
	title = {Phase-locking and environmental fluctuations generate synchrony in a predator–prey community},
	volume = {460},
	copyright = {2009 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature08208},
	doi = {10.1038/nature08208},
	abstract = {Spatially synchronized fluctuations in system state are common in physical and biological systems ranging from individual atoms1 to species as diverse as viruses, insects and mammals2,3,4,5,6,7,8,9,10. Although the causal factors are well known for many synchronized phenomena, several processes concurrently have an impact on spatial synchrony of species, making their separate effects and interactions difficult to quantify. Here we develop a general stochastic model of predator–prey spatial dynamics to predict the outcome of a laboratory microcosm experiment testing for interactions among all known synchronizing factors: (1) dispersal of individuals between populations; (2) spatially synchronous fluctuations in exogenous environmental factors (the Moran effect); and (3) interactions with other species (for example, predators) that are themselves spatially synchronized. The Moran effect synchronized populations of the ciliate protist Tetrahymena pyriformis; however, dispersal only synchronized prey populations in the presence of the predator Euplotes patella. Both model and data indicate that synchrony depends on cyclic dynamics generated by the predator. Dispersal, but not the Moran effect, ‘phase-locks’ cycles, which otherwise become ‘decoherent’ and drift out of phase. In the absence of cycles, phase-locking is not possible and the synchronizing effect of dispersal is negligible. Interspecific interactions determine population synchrony, not by providing an additional source of synchronized fluctuations, but by altering population dynamics and thereby enhancing the action of dispersal. Our results are robust to wide variation in model parameters representative of many natural predator–prey or host–pathogen systems. This explains why cyclic systems provide many of the most dramatic examples of spatial synchrony in nature.},
	language = {en},
	number = {7258},
	urldate = {2018-02-08},
	journal = {Nature},
	author = {Vasseur, David A. and Fox, Jeremy W.},
	month = aug,
	year = {2009},
	keywords = {Checked for experimental metadata},
	pages = {1007--1010},
	file = {Full Text:files/392/Vasseur and Fox - 2009 - Phase-locking and environmental fluctuations gener.pdf:application/pdf}
}

@article{petchey_prey_2000,
	title = {Prey diversity, prey composition, and predator population dynamics in experimental microcosms},
	volume = {69},
	copyright = {All rights reserved},
	url = {http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2656.2000.00446.x},
	doi = {10.1046/j.1365-2656.2000.00446.x},
	number = {5},
	journal = {Journal of Animal Ecology},
	author = {Petchey, Owen L.},
	month = sep,
	year = {2000},
	pages = {874--882},
	file = {Full Text:files/393/Petchey - 2000 - Prey diversity, prey composition, and predator pop.pdf:application/pdf}
}

@article{leary_impact_2012,
	title = {The impact of environmental variability and species composition on the stability of experimental microbial populations and communities},
	volume = {121},
	copyright = {All rights reserved},
	url = {http://doi.wiley.com/10.1111/j.1600-0706.2011.19523.x},
	doi = {10.1111/j.1600-0706.2011.19523.x},
	number = {3},
	journal = {Oikos},
	author = {Leary, Daniel J. and Rip, Jason M. K. and Petchey, Owen L.},
	month = mar,
	year = {2012},
	keywords = {Checked for experimental metadata},
	pages = {327--336},
	file = {Full Text:files/388/Leary et al. - 2012 - The impact of environmental variability and specie.pdf:application/pdf}
}

@article{jiang_community_2008,
	title = {Community {Assembly} in the {Presence} of {Disturbance}: {A} {Microcosm} {Experiment}},
	volume = {89},
	copyright = {© 2008 by the Ecological Society of America},
	issn = {1939-9170},
	shorttitle = {Community {Assembly} in the {Presence} of {Disturbance}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/07-1263.1},
	doi = {10.1890/07-1263.1},
	abstract = {Ecologists know relatively little about the manner in which disturbance affects the likelihood of alternative community stable states and how the history of community assembly affects the relationship between disturbance and species diversity. Using microbial communities comprising bacterivorous ciliated protists assembled in laboratory microcosms, we experimentally investigated these questions by independently manipulating the intensity of disturbance (in the form of density-independent mortality) and community assembly history (including a control treatment with simultaneous species introduction and five sequential assembly treatments). Species diversity patterns consistent with the intermediate disturbance hypothesis emerged in the controls, as several species showed responses indicative of a trade-off between competitive ability and ability to recover from disturbance. Species diversity in communities with sequential assembly, however, generally declined with disturbance, owing to the increased extinction risk of later colonizers at the intermediate level of disturbance. Similarities among communities subjected to different assembly histories increased with disturbance, a result due possibly to increasing disturbance reducing the importance of competition and hence priority effects. This finding is most consistent with the idea that increasing disturbance tends to reduce the likelihood of alternative stable states. Collectively, these results indicate the strong interactive effects of disturbance and assembly history on the structure of ecological communities.},
	language = {en},
	number = {7},
	urldate = {2018-11-07},
	journal = {Ecology},
	author = {Jiang, Lin and Patel, Shivani N.},
	month = jul,
	year = {2008},
	pages = {1931--1940},
	file = {Full Text PDF:files/398/Jiang and Patel - 2008 - Community Assembly in the Presence of Disturbance.pdf:application/pdf;Snapshot:files/397/07-1263.html:text/html}
}

@article{delong_experimental_2012,
	title = {Experimental demonstration of a ‘rate–size’ trade-off governing body size optimization},
	volume = {14},
	issn = {1522-0613},
	url = {http://www.evolutionary-ecology.com/abstracts/v14/2742.html},
	language = {English},
	number = {3},
	urldate = {2018-11-08},
	journal = {Evolutionary Ecology Research},
	author = {DeLong, John P.},
	year = {2012},
	keywords = {Checked for experimental metadata},
	pages = {343--352},
	file = {Full Text PDF:files/401/DeLong - 2012 - Experimental demonstration of a ‘rate–size’ trade-.pdf:application/pdf;Snapshot:files/402/2742.html:text/html}
}

@article{fox_testing_2002,
	title = {Testing a {Simple} {Rule} for {Dominance} in {Resource} {Competition}.},
	volume = {159},
	issn = {0003-0147},
	url = {https://www.journals.uchicago.edu/doi/10.1086/338543},
	doi = {10.1086/338543},
	abstract = {Competition for limiting resources long has been considered an important factor generating community structure. A minimal model of resource competition predicts that the species that reduces the limiting resource R to the lowest level (R∗R{\textasciicircum}\{*\}) will exclude its competitors. Whether this “R∗R{\textasciicircum}\{*\} rule” is robust to violations of model assumptions remains largely unknown. I conducted a competition experiment with four species of bacterivorous protists in laboratory microcosms and predicted the outcome from each species’ R∗R{\textasciicircum}\{*\} value. I also examined how the outcome of competition, species abundances, and the effect of protists on bacterial density varied with productivity. Microcosms were unstirred batch cultures containing a variety of bacteria, challenging the robustness of the simplest competition models. Protists with low R∗R{\textasciicircum}\{*\} values were less affected by competition, although competing protists often coexisted. The values of R∗R{\textasciicircum}\{*\} can predict competitive dominance, even in the absence of competitive exclusion. Other model predictions were less robust. Contrary to expectation, densities of grazed bacteria increased with productivity, and the effect of some protists on bacterial density did not vary with productivity. Bacterial heterogeneity may account for deviations from model predictions. Further experiments should examine the conditions under which simple rules can be expected to identify dominant species.},
	number = {3},
	urldate = {2018-11-08},
	journal = {The American Naturalist},
	author = {Fox, Jeremy W.},
	month = mar,
	year = {2002},
	keywords = {Checked for experimental metadata},
	pages = {305--319},
	file = {Full Text PDF:files/404/Fox - 2002 - Testing a Simple Rule for Dominance in Resource Co.pdf:application/pdf;Snapshot:files/405/338543.html:text/html}
}

@article{griffiths_linking_2018,
	title = {Linking intraspecific trait variation to community abundance dynamics improves ecological predictability by revealing a growth–defence trade-off},
	volume = {32},
	copyright = {© 2017 The Authors.           Functional Ecology published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {1365-2435},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.12997},
	doi = {10.1111/1365-2435.12997},
	abstract = {Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in interspecific interactions and population dynamics. In turn, variation in species’ interactions and densities can alter the strength and direction of trait change. The resulting feedback between species’ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator–prey–resource system. Using this data, we parameterised a trait-dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait–abundance feedbacks into our population model improved the predictability of ecological dynamics from r2 of 34\% to 57\% and confirmed theoretical expectations of density-dependent population growth and species interactions in the system. Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. Modelling trait–abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait–abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics. A plain language summary is available for this article.},
	language = {en},
	number = {2},
	urldate = {2018-11-09},
	journal = {Functional Ecology},
	author = {Griffiths, Jason I. and Petchey, Owen L. and Pennekamp, Frank and Childs, Dylan Z.},
	month = feb,
	year = {2018},
	keywords = {community dynamics, density-dependent trait change, generalised additive models, growth–defence trade-offs, predator–prey experiment, trait-dependent interaction, trait–abundance feedbacks},
	pages = {496--508},
	file = {Full Text:files/411/Griffiths et al. - 2018 - Linking intraspecific trait variation to community.pdf:application/pdf;Snapshot:files/409/1365-2435.html:text/html}
}