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research_proposal.bib
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@article{stouffer2007evidence,
title={Evidence for the existence of a robust pattern of prey selection in food webs},
author={Stouffer, Daniel B and Camacho, Juan and Jiang, Wenxin and Amaral, Lu{\'\i}s A Nunes},
journal={Proceedings of the Royal Society B: Biological Sciences},
volume={274},
number={1621},
pages={1931--1940},
year={2007},
publisher={The Royal Society}
}
@article{Billionnet01012013,
author = {Billionnet, Alain},
title = {Solution of the Generalized Noah's Ark Problem},
volume = {62},
number = {1},
pages = {147-156},
year = {2013},
doi = {10.1093/sysbio/sys081},
abstract ={The phylogenetic diversity (PD) of a set of species is a measure of the evolutionary distance among the species in the collection, based on a phylogenetic tree. Such a tree is composed of a root, internal nodes, and leaves that correspond to the set of taxa under study. With each edge of the tree is associated a non-negative branch length (evolutionary distance). If a particular survival probability is associated with each taxon, the PD measure becomes the expected PD measure. In the Noah's Ark Problem (NAP) introduced by Weitzman (1998), these survival probabilities can be increased at some cost. The problem is to determine how best to allocate a limited amount of resources to maximize the expected PD of the considered species. It is easy to formulate the NAP as a (difficult) nonlinear 0–1 programming problem. The aim of this article is to show that a general version of the NAP (GNAP) can be solved simply and efficiently with any set of edge weights and any set of survival probabilities by using standard mixed-integer linear programming software. The crucial point to move from a nonlinear program in binary variables to a mixed-integer linear program, is to approximate the logarithmic function by the lower envelope of a set of tangents to the curve. Solving the obtained mixed-integer linear program provides not only a near-optimal solution but also an upper bound on the value of the optimal solution. We also applied this approach to a generalization of the nature reserve problem (GNRP) that consists of selecting a set of regions to be conserved so that the expected PD of the set of species present in these regions is maximized. In this case, the survival probabilities of different taxa are not independent of each other. Computational results are presented to illustrate potentialities of the approach. Near-optimal solutions with hypothetical phylogenetic trees comprising about 4000 taxa are obtained in a few seconds or minutes of computing time for the GNAP, and in about 30 min for the GNRP. In all the cases the average guarantee varies from 0% to 1.20%.},
URL = {http://sysbio.oxfordjournals.org/content/62/1/147.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/62/1/147.full.pdf+html},
journal = {Systematic Biology}
}
@article{witting1995optimization,
title={The optimization of biodiversity conservation},
author={Witting, Lars and Loeschcke, Volker},
journal={Biological Conservation},
volume={71},
number={2},
pages={205--207},
year={1995},
publisher={Elsevier}
}
@article{faller2012trait,
title={Trait-dependent extinction leads to greater expected biodiversity loss},
author={Faller, Be{\'a}ta and Steel, Mike},
journal={SIAM Journal on Discrete Mathematics},
volume={26},
number={2},
pages={472--481},
year={2012},
publisher={SIAM}
}
@article{steel2009markovian,
title={Markovian log-supermodularity, and its applications in phylogenetics},
author={Steel, Mike and Faller, Be{\'a}ta},
journal={Applied Mathematics Letters},
volume={22},
number={7},
pages={1141--1144},
year={2009},
publisher={Elsevier}
}
@article{bordewich2008nature,
title={Nature reserve selection problem: a tight approximation algorithm},
author={Bordewich, Magnus and Semple, Charles},
journal={Computational Biology and Bioinformatics, IEEE/ACM Transactions on},
volume={5},
number={2},
pages={275--280},
year={2008},
publisher={IEEE}
}
@article{faller2011optimizing,
title={Optimizing phylogenetic diversity with ecological constraints},
author={Faller, Be{\'a}ta and Semple, Charles and Welsh, Dominic},
journal={Annals of Combinatorics},
volume={15},
number={2},
pages={255--266},
year={2011},
publisher={Springer}
}
@article{moulton2007optimizing,
title={Optimizing phylogenetic diversity under constraints},
author={Moulton, Vincent and Semple, Charles and Steel, Mike},
journal={Journal of theoretical biology},
volume={246},
number={1},
pages={186--194},
year={2007},
publisher={Elsevier}
}
@article{hartmann2006maximizing,
title={Maximizing phylogenetic diversity in biodiversity conservation: greedy solutions to the Noah's Ark problem},
author={Hartmann, Klaas and Steel, Mike},
journal={Systematic Biology},
volume={55},
number={4},
pages={644--651},
year={2006},
publisher={Oxford University Press}
}
@article{weitzman1998noah,
title={The Noah's ark problem},
author={Weitzman, Martin L},
journal={Econometrica},
pages={1279--1298},
year={1998},
publisher={JSTOR}
}
@article{faith1992conservation,
title={Conservation evaluation and phylogenetic diversity},
author={Faith, Daniel P},
journal={Biological Conservation},
volume={61},
number={1},
pages={1--10},
year={1992},
publisher={Elsevier}
}
@article{prill2005dynamic,
title={Dynamic properties of network motifs contribute to biological network organization},
author={Prill, Robert J and Iglesias, Pablo A and Levchenko, Andre},
journal={PLoS biology},
volume={3},
number={11},
pages={e343},
year={2005},
publisher={Public Library of Science}
}
@incollection{raup1984evolutionary,
title={Evolutionary radiations and extinctions},
author={Raup, DM},
booktitle={Patterns of Change in Earth Evolution},
pages={5--14},
year={1984},
publisher={Springer}
}
@article{berg2011using,
title={Using sensitivity analysis to identify keystone species and keystone links in size-based food webs},
author={Berg, Sofia and Christianou, Maria and Jonsson, Tomas and Ebenman, Bo},
journal={Oikos},
volume={120},
number={4},
pages={510--519},
year={2011},
publisher={Wiley Online Library}
}
@phdthesis{berg2013community,
title={Community Robustness Analysis: Theoretical Approaches to Identifying Keystone Structures in Ecological Communities},
author={Berg, Sofia},
year={2013},
school={Link{\"o}ping}
}
@article{liu2011controllability,
title={Controllability of complex networks},
author={Liu, Yang-Yu and Slotine, Jean-Jacques and Barab{\'a}si, Albert-L{\'a}szl{\'o}},
journal={Nature},
volume={473},
number={7346},
pages={167--173},
year={2011},
publisher={Nature Publishing Group}
}
@article{neubert1997alternatives,
title={Alternatives to resilience for measuring the responses of ecological systems to perturbations},
author={Neubert, Michael G and Caswell, Hal},
journal={Ecology},
volume={78},
number={3},
pages={653--665},
year={1997},
publisher={Eco Soc America}
}
@article{boit2012mechanistic,
title={Mechanistic theory and modelling of complex food-web dynamics in Lake Constance},
author={Boit, Alice and Martinez, Neo D and Williams, Richard J and Gaedke, Ursula},
journal={Ecology letters},
volume={15},
number={6},
pages={594--602},
year={2012},
publisher={Wiley Online Library}
}
@book{sole2006self,
title={Self-Organization in Complex Ecosystems.(MPB-42)},
author={Sol{\'e}, Ricard V and Bascompte, Jordi},
volume={42},
year={2006},
publisher={Princeton University Press}
}
@article{mouquet2012ecophylogenetics,
title={Ecophylogenetics: advances and perspectives},
author={Mouquet, Nicolas and Devictor, Vincent and Meynard, Christine N and Munoz, Fran{\c{c}}ois and Bersier, Louis-F{\'e}lix and Chave, J{\'e}r{\^o}me and Couteron, Pierre and Dalecky, Ambroise and Fontaine, Colin and Gravel, Dominique and others},
journal={Biological reviews},
volume={87},
number={4},
pages={769--785},
year={2012},
publisher={Wiley Online Library}
}
@article{gravel2010experimental,
title={Experimental niche evolution alters the strength of the diversity-productivity relationship},
author={Gravel, Dominique and Bell, Thomas and Barbera, Claire and Bouvier, Thierry and Pommier, Thomas and Venail, Patrick and Mouquet, Nicolas},
journal={Nature},
volume={469},
number={7328},
pages={89--92},
year={2010},
publisher={Nature Publishing Group}
}
@article{bascompte2009disentangling,
title={Disentangling the web of life},
author={Bascompte, Jordi and others},
journal={Science},
volume={325},
number={5939},
pages={416},
year={2009}
}
@article{ingram2012should,
title={When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model},
author={Ingram, T and Harmon, LJ and Shurin, JB},
journal={Journal of Evolutionary Biology},
volume={25},
number={9},
pages={1902--1910},
year={2012},
publisher={Wiley Online Library}
}
@article{williams2010probabilistic,
title={The probabilistic niche model reveals the niche structure and role of body size in a complex food web},
author={Williams, Richard J and Anandanadesan, Ananthi and Purves, Drew},
journal={PloS one},
volume={5},
number={8},
pages={e12092},
year={2010},
publisher={Public Library of Science}
}
@article{yoshida_relationship_2008,
title = {The relationship between the duration of food web evolution and the vulnerability to biological invasion},
volume = {5},
issn = {1476-{945X}},
shorttitle = {Current Food-Web Theory},
url = {http://www.sciencedirect.com/science/article/pii/S1476945X08000081},
doi = {10.1016/j.ecocom.2008.02.002},
abstract = {I conducted computer simulations of food web evolution and investigated the relationship between the duration of food web evolution and the vulnerability to biological invasion. Model food webs without evolution consisted of animal species with a limited number of prey species and producer species with small intrinsic growth rates. Because these species were not resistant to predation pressure, model food webs without evolution were vulnerable to invasion of powerful omnivores, which had a wide range of feeding preference and a high ecological efficiency. In model food webs without evolution, the number of animal species depending on producer species was small. Therefore, if a producer species invaded and disturbed the base of such food webs, few animal species became extinct. However, model food webs with a long time evolution had a structure that a small number of producer species supported a large number of animal species. When a producer species invaded and disturbed the base of such food webs in this state, many species became extinct by an indirect effect. The mean number of prey species of animal species and the mean intrinsic growth rate of producer species increased rapidly in the early stage of evolution. Therefore, in the early stage of food web evolution, food webs were temporarily resistant to invasion of powerful omnivores. However, this resistibility was not maintained for a long time. The result of this study strongly suggests that food webs change with time, and consequently the vulnerability to invasion changes with time.},
number = {2},
urldate = {2013-01-23},
journal = {Ecological Complexity},
author = {Yoshida, Katsuhiko},
month = jun,
year = {2008},
keywords = {Biological invasion, Computer simulation, Food web evolution, Food web structure, Vulnerability to biological invasion},
pages = {86--98},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/9DI7QCS9/Yoshida - 2008 - The relationship between the duration of food web .pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/TU5DN5J7/S1476945X08000081.html:text/html}
},
@article{rossberg_top-down_2008,
title = {{THE} {TOP-DOWN} {MECHANISM} {FOR} {BODY-MASS–ABUNDANCE} {SCALING}},
volume = {89},
issn = {0012-9658},
url = {http://www.esajournals.org/doi/abs/10.1890/07-0124.1},
doi = {10.1890/07-0124.1},
abstract = {Scaling relationships between mean body masses and abundances of species in multitrophic communities continue to be a subject of intense research and debate. The top-down mechanism explored in this paper explains the frequently observed inverse linear relationship between body mass and abundance (i.e., constant biomass) in terms of a balancing of resource biomasses by behaviorally and evolutionarily adapting foragers, and the evolutionary response of resources to this foraging pressure. The mechanism is tested using an allometric, multitrophic community model with a complex food web structure. It is a statistical model describing the evolutionary and population dynamics of tens to hundreds of species in a uniform way. Particularities of the model are the detailed representation of the evolution and interaction of trophic traits to reproduce topological food web patterns, prey switching behavior modeled after experimental observations, and the evolutionary adaptation of attack rates. Model structure and design are discussed. For model states comparable to natural communities, we find that (1) the body-mass–abundance scaling does not depend on the allometric scaling exponent of physiological rates in the form expected from the energetic equivalence rule or other bottom-up theories; (2) the scaling exponent of abundance as a function of body mass is approximately −1, independent of the allometric exponent for physiological rates assumed; (3) removal of top-down control destroys this pattern, and energetic equivalence is recovered. We conclude that the top-down mechanism is active in the model, and that it is a viable alternative to bottom-up mechanisms for controlling body-mass–abundance relations in natural communities.},
number = {2},
urldate = {2013-01-23},
journal = {Ecology},
author = {Rossberg, A. G. and Ishii, R. and Amemiya, T. and Itoh, K.},
month = feb,
year = {2008},
keywords = {abundance, allometric scaling, body mass, community models, food webs},
pages = {567--580},
file = {ESA PDF fulltext:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/BXMF3BP8/Rossberg et al. - 2008 - THE TOP-DOWN MECHANISM FOR BODY-MASS–ABUNDANCE SCA.pdf:application/pdf;ESA Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/XZRZ6HC5/showCitFormats.html:text/html}
},
@article{roopnarine_networks_2010,
title = {Networks, extinction, and palecommunity food webs},
url = {http://zeus.calacademy.org/roopnarine/Selected_Publications/Roopnarine_10.pdf},
urldate = {2013-01-18},
journal = {Quantitative methods in paleobiology},
author = {Roopnarine, P. D.},
year = {2010},
pages = {143–161},
file = {Roopnarine_10.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/Q5WAAC36/Roopnarine_10.pdf:application/pdf}
},
@article{drossel_influence_2000,
title = {The Influence of Predator-Prey Population Dynamics on the Long-term Evolution of Food Web Structure},
url = {http://arxiv.org/abs/nlin/0002032},
abstract = {We develop a set of equations to describe the population dynamics of many interacting species in food webs. Predator-prey interactions are non-linear, and are based on ratio-dependent functional responses. The equations account for competition for resources between members of the same species, and between members of different species. Predators divide their total hunting/foraging effort between the available prey species according to an evolutionarily stable strategy ({ESS).} The {ESS} foraging behaviour does not correspond to the predictions of optimal foraging theory. We use the population dynamics equations in simulations of the Webworld model of evolving ecosystems. New species are added to an existing food web due to speciation events, whilst species become extinct due to coevolution and competition. We study the dynamics of species-diversity in Webworld on a macro-evolutionary timescale. Coevolutionary interactions are strong enough to cause continuous overturn of species, in contrast to our previous Webworld simulations with simpler population dynamics. Although there are significant fluctuations in species diversity because of speciation and extinction, very large scale extinction avalanches appear to be absent from the dynamics, and we find no evidence for self-organised criticality.},
urldate = {2013-01-22},
journal = {{arXiv:nlin/0002032}},
author = {Drossel, Barbara and Higgs, Paul G. and {McKane}, Alan J.},
month = feb,
year = {2000},
keywords = {Nonlinear Sciences - Adaptation and Self-Organizing Systems, Quantitative Biology},
file = {arXiv.org Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/MHRHX3ES/0002032.html:text/html;nlin/0002032 PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/BHRKI7RU/Drossel et al. - 2000 - The Influence of Predator-Prey Population Dynamics.pdf:application/pdf}
},
@misc{stouffer_ideas_2009,
type = {Capítulo de libro},
title = {Ideas for moving beyond structure to dynamics of ecological networks},
url = {http://digital.csic.es/handle/10261/51986},
language = {eng},
urldate = {2013-01-22},
author = {Stouffer, Daniel B. and Fortuna, Miguel A. and Bascompte, Jordi},
year = {2009},
note = {Peer reviewed},
howpublished = {http://digital.csic.es/handle/10261/51986},
file = {Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/22AUFIAM/51986.html:text/html}
},
@article{quince_topological_2005,
title = {Topological structure and interaction strengths in model food webs},
volume = {187},
issn = {0304-3800},
url = {http://www.sciencedirect.com/science/article/pii/S0304380005001031},
doi = {10.1016/j.ecolmodel.2004.12.018},
abstract = {We report the results of carrying out a large number of simulations on a coevolutionary model of multispecies communities. A wide range of parameter values were investigated which allowed a rather complete picture of the change in behaviour of the model as these parameters were varied to be built up. Our main interest was in the nature of the community food webs constructed via the simulations. We identify the range of parameter values which give rise to realistic food webs and give arguments which allow some of the structure which is found to be understood in an intuitive way. Since the webs are evolved according to the rules of the model, the strengths of the predator–prey links are not determined a priori, and emerge from the process of constructing the web. We measure the distribution of these link strengths, and find that there are a large number of weak links, in agreement with recent suggestions. We also review some of the data on food webs available in the literature, and make some tentative comparisons with our results. The difficulties of making such comparisons and the possible future developments of the model are also briefly discussed.},
number = {4},
urldate = {2013-01-22},
journal = {Ecological Modelling},
author = {Quince, Christopher and Higgs, Paul G. and {McKane}, Alan J.},
month = oct,
year = {2005},
keywords = {Coevolutionary model, food webs, Interaction strengths, Multispecies communities, Weak links},
pages = {389--412},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/U8MTQW2W/Quince et al. - 2005 - Topological structure and interaction strengths in.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/QTCPWJT3/S0304380005001031.html:text/html}
},
@article{allesina_network_2008,
title = {Network structure, predator–prey modules, and stability in large food webs},
volume = {1},
issn = {1874-1738, 1874-1746},
url = {http://link.springer.com/article/10.1007/s12080-007-0007-8},
doi = {10.1007/s12080-007-0007-8},
abstract = {Large, complex networks of ecological interactions with random structure tend invariably to instability. This mathematical relationship between complexity and local stability ignited a debate that has populated ecological literature for more than three decades. Here we show that, when species interact as predators and prey, systems as complex as the ones observed in nature can still be stable. Moreover, stability is highly robust to perturbations of interaction strength, and is largely a property of structure driven by predator–prey loops with the stability of these small modules cascading into that of the whole network. These results apply to empirical food webs and models that mimic the structure of natural systems as well. These findings are also robust to the inclusion of other types of ecological links, such as mutualism and interference competition, as long as consumer–resource interactions predominate. These considerations underscore the influence of food web structure on ecological dynamics and challenge the current view of interaction strength and long cycles as main drivers of stability in natural communities.},
language = {en},
number = {1},
urldate = {2013-01-22},
journal = {Theoretical Ecology},
author = {Allesina, Stefano and Pascual, Mercedes},
month = mar,
year = {2008},
keywords = {Complexity/stability, food webs, Plant Sciences, Predator–prey, Sign-stability, Theoretical {Ecology/Statistics}, Weak interactions, Zoology},
pages = {55--64},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/36WF8Q8U/Allesina and Pascual - 2008 - Network structure, predator–prey modules, and stab.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/EFTRUZFS/10.html:text/html}
},
@article{mullon_neats:_2009,
title = {{NEATS:} A Network Economics Approach to Trophic Systems},
volume = {220},
issn = {0304-3800},
shorttitle = {Selected Papers from the Sixth European Conference on Ecological Modelling - {ECEM} '07, on Challenges for ecological modelling in a changing world: Global Changes, Sustainability and Ecosystem Based Management, November 27-30, 2007, Trieste, Italy},
url = {http://www.sciencedirect.com/science/article/pii/S0304380009000891},
doi = {10.1016/j.ecolmodel.2009.02.008},
abstract = {The main principle of the economic approach to a trophic system we propose here lies in assuming that there is a transfer of food along a path between a prey and a predator if, for the predator, the benefits are greater than costs of predation on this path. Conversely, if the costs exceed the benefits, there are no flows. This trade-off, considered all along the food chains of an ecosystem, together with ecological processes (assimilation, somatic maintenance) results in a model coupling mass balance equations (biological constraints) and complementarity principles (Walras’ law). Here is the core of the Network Economics Approach to Trophic Systems ({NEATS).} We illustrate with simple examples of ecosystems how these principles result in algebraic equations which can be analyzed mathematically and solved numerically. We show, in a more sophisticated example of an input/output trophic network, that they result in “affine variational inequalities”, whose solutions can be estimated. We make explicit how the approach can be applied to address ecological questions, concerning differences of productivity, causes of biological diversity, or the nature of controls in marine ecosystems.},
number = {21},
urldate = {2013-01-22},
journal = {Ecological Modelling},
author = {Mullon, Christian and Shin, Yunne and Cury, Philippe},
month = nov,
year = {2009},
keywords = {Economic equilibrium, food web, Marine ecosystem, Variational inequality},
pages = {3033--3045},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/SIH4WRS8/Mullon et al. - 2009 - NEATS A Network Economics Approach to Trophic Sys.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/6643JMHE/S0304380009000891.html:text/html}
},
@article{nehring_theory_2002,
title = {A Theory of Diversity},
volume = {70},
copyright = {The Econometric Society 2002},
issn = {1468-0262},
url = {http://onlinelibrary.wiley.com/doi/10.1111/1468-0262.00321/abstract},
doi = {10.1111/1468-0262.00321},
abstract = {How can diversity be measured? What does it mean to value biodiversity? Can we assist Noah in constructing his preferences? To address these questions, we propose a multi-attribute approach under which the diversity of a set of species is the sum of the values of all attributes possessed by some species in the set. We develop the basic intuitions and requirements for a theory of diversity and show that the multi-attribute approach satisfies them in a flexible yet tractable {manner.A} natural starting point is to think of the diversity of a set as an aggregate of the pairwise dissimilarities between its elements. The multi-attribute framework allows one to make this program formally precise. It is shown that the program can be realized if and only if the family of relevant attributes is well-ordered (“acyclic”). Moreover, there is a unique functional form aggregating dissimilarity into diversity, the length of a minimum spanning tree. Examples are taxonomic hierarchies and lines representing uni-dimensional qualities. In multi-dimensional settings, pairwise dissimilarity information among elements is insufficient to determine their diversity. By consequence, the qualitative and quantitative behavior of diversity differs fundamentally.},
language = {en},
number = {3},
urldate = {2013-01-22},
journal = {Econometrica},
author = {Nehring, Klaus and Puppe, Clemens},
year = {2002},
keywords = {conjugate Moebius inversion, diversity, endangered species, similarity},
pages = {1155–1198},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/PUS9CGSW/Nehring and Puppe - 2002 - A Theory of Diversity.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/VXUZEDTT/abstract.html:text/html}
},
@article{caldarelli_self-organized_2008,
title = {A self-organized model for network evolution},
volume = {64},
issn = {1434-6028, 1434-6036},
url = {http://link.springer.com/article/10.1140/epjb/e2008-00243-5},
doi = {10.1140/epjb/e2008-00243-5},
abstract = {Here we provide a detailed analysis, along with some extensions and additonal investigations, of a recently proposed [1] self-organized model for the evolution of complex networks. Vertices of the network are characterized by a fitness variable evolving through an extremal dynamics process, as in the Bak-Sneppen [2] model representing a prototype of Self-Organized Criticality. The network topology is in turn shaped by the fitness variable itself, as in the fitness network model [3]. The system self-organizes to a nontrivial state, characterized by a power-law decay of dynamical and topological quantities above a critical threshold. The interplay between topology and dynamics in the system is the key ingredient leading to an unexpected behaviour of these quantities.},
language = {en},
number = {3-4},
urldate = {2013-01-22},
journal = {The European Physical Journal B},
author = {Caldarelli, G. and Capocci, A. and Garlaschelli, D.},
month = aug,
year = {2008},
keywords = {05.65.+b Self-organized systems, {89.75.Hc} Networks and genealogical trees, Complexity, Condensed Matter, Fluids, Physics, general, Solid State Physics and Spectroscopy, Superconductivity, Superfluidity, Quantum Fluids},
pages = {585--591},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/CT4QPD8T/Caldarelli et al. - 2008 - A self-organized model for network evolution.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/EIHHJQKE/10.html:text/html}
},
@article{krasnov_phylogenetic_2012,
title = {Phylogenetic Signal in Module Composition and Species Connectivity in Compartmentalized Host-Parasite Networks.},
volume = {179},
url = {http://www.otago.ac.nz/parasitegroup/PDF%20papers/Krasnovetal2012-AmNat.pdf},
number = {4},
urldate = {2013-01-22},
journal = {American Naturalist},
author = {Krasnov, B. R. and Fortuna, M. A. and Mouillot, D. and Khokhlova, I. S. and Shenbrot, G. I. and Poulin, R.},
year = {2012},
pages = {501},
file = {Krasnovetal2012-AmNat.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/K9AEMI74/Krasnovetal2012-AmNat.pdf:application/pdf}
},
@article{jensen_emergence_2008,
title = {Emergence of network structure in models of collective evolution and evolutionary dynamics},
volume = {464},
issn = {1364-5021, 1471-2946},
url = {http://rspa.royalsocietypublishing.org/content/464/2096/2207},
doi = {10.1098/rspa.2008.0032},
abstract = {We consider an evolving network of a fixed number of nodes. The allocation of edges is a dynamical stochastic process inspired by biological reproduction dynamics, namely by deleting and duplicating existing nodes and their edges. The properties of the degree distribution in the stationary state is analysed by use of the {Fokker–Planck} equation. For a broad range of parameters, exponential degree distributions are observed. The mechanism responsible for this behaviour is illuminated by use of a simple mean field equation and reproduced by the {Fokker–Planck} equation. The latter is treated exactly, except for an approximate treatment of the degree–degree correlations. In the limit of 0 mutations, the degree distribution becomes a power law with exponent 1.},
language = {en},
number = {2096},
urldate = {2013-01-23},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science},
author = {Jensen, Henrik Jeldtoft},
month = aug,
year = {2008},
keywords = {Degree distribution, dynamics, evolution, Networks},
pages = {2207--2217},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/98NG3TNA/Jensen - 2008 - Emergence of network structure in models of collec.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/GJ8FTUX9/2207.html:text/html}
},
@article{may1971stability,
title={Stability in multispecies community models},
author={May, Robert M},
journal={Mathematical Biosciences},
volume={12},
number={1},
pages={59--79},
year={1971},
publisher={Elsevier}
}
@article{may1972will,
title={Will a large complex system be stable?},
author={May, Robert M},
journal={Nature},
volume={238},
pages={413--414},
year={1972}
}
@article{camacho_quantitative_2007,
title = {Quantitative analysis of the local structure of food webs},
volume = {246},
issn = {0022-5193},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2128744/},
doi = {10.1016/j.jtbi.2006.12.036},
abstract = {We analyze the local structure of model and empirical food webs through the statistics of three-node subgraphs. We study analytically and numerically the number of appearances of each subgraph for a simple model of food web topology, the so-called generalized cascade model, and compare them with 17 empirical community food webs from a variety of environments, including aquatic, estuarine, and terrestrial ecosystems. We obtain analytical expressions for the probability of appearances of each subgraph in the model, and also for randomizations of the model that preserve species' numbers of prey and number of predators; their difference allows us to quantify which subgraphs are over- or under-represented in both the model and the empirical food webs. We find agreement between the model predictions and the empirical results. These results indicate that simple models such as the generalized cascade can provide a good description not only of the global topology of food webs, as recently shown, but also of its local structure.},
number = {2},
urldate = {2013-01-22},
journal = {Journal of theoretical biology},
author = {Camacho, J. and Stouffer, {D.B.} and Amaral, {L.A.N.}},
month = may,
year = {2007},
note = {{PMID:} 17292921
{PMCID:} {PMC2128744}},
pages = {260--268},
file = {PubMed Central Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/F5HKBIRX/Camacho et al. - 2007 - Quantitative analysis of the local structure of fo.pdf:application/pdf}
},
@article{miklos_randomization_2004,
title = {Randomization of Presence-Absence Matrices: Comments and New Algorithms},
volume = {85},
copyright = {Copyright © 2004 Ecological Society of America},
issn = {0012-9658},
shorttitle = {Randomization of Presence-Absence Matrices},
url = {http://www.jstor.org/stable/3450469},
doi = {10.2307/3450469},
abstract = {Randomization of presence-absence data matrices with fixed row and column totals is an important tool in ecological research wherever the significance of data-based statistics (e.g., species association measures) is to be evaluated. In the current literature of numerical ecology, however, there has been no algorithm that randomizes moderately large matrices in short time such that equidistribution of results is guaranteed. We show that a simple modification of the swap algorithm, called here the "trial-swap method," satisfies the requirement for equidistribution. Since this is relatively slow, we suggest two fast algorithms that, combined with the trial-swap method, produce all possible results with equal chance. The three procedures are illustrated using actual examples taken from bird biogeography and vegetation ecology.},
number = {1},
urldate = {2013-01-22},
journal = {Ecology},
author = {Miklós, I. and Podani, J.},
month = jan,
year = {2004},
note = {{ArticleType:} research-article / Full publication date: Jan., 2004 / Copyright © 2004 Ecological Society of America},
pages = {86--92},
file = {JSTOR Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/XIZRXMWV/Miklós and Podani - 2004 - Randomization of Presence-Absence Matrices Commen.pdf:application/pdf}
},
@article{nagurney_dynamics_2012,
title = {Dynamics and equilibria of ecological predator–prey networks as nature’s supply chains},
volume = {48},
issn = {1366-5545},
shorttitle = {Select Papers from the 19th International Symposium on Transportation and Traffic Theory},
url = {http://www.sciencedirect.com/science/article/pii/S1366554511001025},
doi = {10.1016/j.tre.2011.07.007},
abstract = {In this paper, we develop a dynamic network model of ecological food webs and prove that the set of stationary points of the projected dynamical system coincides with the set of solutions of a variational inequality governing the equilibrium of predator–prey networks. We also establish the equivalence between the ecological models and supply chain network equilibrium models and highlight the connections to spatial price equilibrium problems. We propose an algorithmic scheme, provide convergence results, and apply it to a food web drawn from a fisheries application. This paper is a contribution to the interdisciplinary supply chain network literature.},
number = {1},
urldate = {2013-01-22},
journal = {Transportation Research Part E: Logistics and Transportation Review},
author = {Nagurney, Anna and Nagurney, Ladimer S.},
month = jan,
year = {2012},
keywords = {Fisheries, food webs, Predator–prey models, Projected dynamical systems, Supply chains, Transportation and logistics, Variational inequalities},
pages = {89--99},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/WHHPSJW5/Nagurney and Nagurney - 2012 - Dynamics and equilibria of ecological predator–pre.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/GSN4IUJP/S1366554511001025.html:text/html}
},
@article{allesina_food_2009,
title = {Food web models: a plea for groups},
volume = {12},
copyright = {© 2009 Blackwell Publishing {Ltd/CNRS}},
issn = {1461-0248},
shorttitle = {Food web models},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01321.x/abstract},
doi = {10.1111/j.1461-0248.2009.01321.x},
abstract = {The concept of a group is ubiquitous in biology. It underlies classifications in evolution and ecology, including those used to describe phylogenetic levels, the habitat and functional roles of organisms in ecosystems. Surprisingly, this concept is not explicitly included in simple models for the structure of food webs, the ecological networks formed by consumer–resource interactions. We present here the simplest possible model based on groups, and show that it performs substantially better than current models at predicting the structure of large food webs. Our group-based model can be applied to different types of biological and non-biological networks, and for the first time merges in the same framework two important notions in network theory: that of compartments (sets of highly interacting nodes) and that of roles (sets of nodes that have similar interaction patterns). This model provides a basis to examine the significance of groups in biological networks and to develop more accurate models for ecological network structure. It is especially relevant at a time when a new generation of empirical data is providing increasingly large food webs.},
language = {en},
number = {7},
urldate = {2013-01-23},
journal = {Ecology Letters},
author = {Allesina, Stefano and Pascual, Mercedes},
year = {2009},
keywords = {Akaike information criterion, clustering algorithm, compartment, Connectance, food web model, group, likelihood, model selection, species richness, trophic role, trophospecies},
pages = {652–662},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/Z3H6F8CR/Allesina and Pascual - 2009 - Food web models a plea for groups.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/X5X49XSC/abstract.html:text/html}
},
@article{fortuna_nestedness_2010,
title = {Nestedness versus modularity in ecological networks: two sides of the same coin?},
volume = {79},
issn = {0021-8790},
shorttitle = {Nestedness versus modularity in ecological networks},
doi = {10.1111/j.1365-2656.2010.01688.x},
abstract = {P{\textgreater}1. Understanding the structure of ecological networks is a crucial task for interpreting community and ecosystem responses to global change. 2. Despite the recent interest in this subject, almost all studies have focused exclusively on one specific network property. The question remains as to what extent different network properties are related and how understanding this relationship can advance our comprehension of the mechanisms behind these patterns. 3. Here, we analysed the relationship between nestedness and modularity, two frequently studied network properties, for a large data set of 95 ecological communities including both plant-animal mutualistic and host-parasite networks. 4. We found that the correlation between nestedness and modularity for a population of random matrices generated from the real communities decreases significantly in magnitude and sign with increasing connectance independent of the network type. At low connectivities, networks that are highly nested also tend to be highly modular; the reverse happens at high connectivities. 5. The above result is qualitatively robust when different null models are used to infer network structure, but, at a finer scale, quantitative differences exist. We observed an important interaction between the network structure pattern and the null model used to detect it. 6. A better understanding of the relationship between nestedness and modularity is important given their potential implications on the dynamics and stability of ecological communities.},
language = {English},
number = {4},
journal = {Journal of Animal Ecology},
author = {Fortuna, Miguel A. and Stouffer, Daniel B. and Olesen, Jens M. and Jordano, Pedro and Mouillot, David and Krasnov, Boris R. and Poulin, Robert and Bascompte, Jordi},
month = jul,
year = {2010},
keywords = {algorithms, biodiversity, coevolutionary networks, complex networks, food webs, food-web structure, host-parasite, mutualistic networks, null model analysis, plant-pollinator, plant-seed disperser, pollination networks, presence-absence matrices, specialization, species cooccurrences},
pages = {811--817},
file = {ISI Web of Knowledge Record:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/75TJJHN2/full_record.html:text/html}
},
@article{dunne_compilation_2008,
title = {Compilation and network analyses of Cambrian food webs},
volume = {6},
url = {http://dx.plos.org/10.1371/journal.pbio.0060102},
number = {4},
urldate = {2013-01-22},
journal = {{PLoS} biology},
author = {Dunne, J. A. and Williams, R. J. and Martinez, N. D. and Wood, R. A. and Erwin, D. H.},
year = {2008},
pages = {e102},
file = {Dunne_2008_PLOSbiology.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/D3TKUWQZ/Dunne_2008_PLOSbiology.pdf:application/pdf}
},
@article{bascompte_assembly_2009,
title = {The assembly and disassembly of ecological networks},
volume = {364},
issn = {0962-8436},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685423/},
doi = {10.1098/rstb.2008.0226},
abstract = {Global change has created a severe biodiversity crisis. Species are driven extinct at an increasing rate, and this has the potential to cause further coextinction cascades. The rate and shape of these coextinction cascades depend very much on the structure of the networks of interactions across species. Understanding network structure and how it relates to network disassembly, therefore, is a priority for system-level conservation biology. This process of network collapse may indeed be related to the process of network build-up, although very little is known about both processes and even less about their relationship. Here we review recent work that provides some preliminary answers to these questions. First, we focus on network assembly by emphasizing temporal processes at the species level, as well as the structural building blocks of complex ecological networks. Second, we focus on network disassembly as a consequence of species extinctions or habitat loss. We conclude by emphasizing some general rules of thumb that can help in building a comprehensive framework to understand the responses of ecological networks to global change.},
number = {1524},
urldate = {2013-01-22},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
author = {Bascompte, Jordi and Stouffer, Daniel B.},
month = jun,
year = {2009},
note = {{PMID:} 19451127
{PMCID:} {PMC2685423}},
pages = {1781--1787},
file = {PubMed Central Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/97ZDKNQQ/Bascompte and Stouffer - 2009 - The assembly and disassembly of ecological network.pdf:application/pdf}
},
@article{plitzko_complexitystability_2012,
title = {Complexity–stability relations in generalized food-web models with realistic parameters},
volume = {306},
issn = {0022-5193},
url = {http://www.sciencedirect.com/science/article/pii/S0022519312001816},
doi = {10.1016/j.jtbi.2012.04.008},
abstract = {We investigate the relation between complexity and stability in model food webs by evaluating the local stability of fixed points of the population dynamics using the recently developed method of generalized modeling. We first determine general conditions that lead to positive complexity–stability relations. These include (1) high resource abundance and (2) strong density-dependent mortality effects that limit consumer populations. The parameters that constitute a generalized model have clear biological meanings. In this work, emphasis is placed on using realistic values for these generalized parameters. They are derived from conventional ordinary differential equations which are commonly used to describe population dynamics and for which empirical parameter estimates exist. We find that the empirically supported generalized parameters fall in regions of the parameter space that allow for a positive relation between food-web complexity and stability.},
number = {0},
urldate = {2013-01-24},
journal = {Journal of Theoretical Biology},
author = {Plitzko, Sebastian J. and Drossel, Barbara and Guill, Christian},
month = aug,
year = {2012},
keywords = {Density-dependent mortality, Functional response, Linear stability, Population Dynamics},
pages = {7--14},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/V2WQXQAZ/Plitzko et al. - 2012 - Complexity–stability relations in generalized food.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/K7N47JUZ/S0022519312001816.html:text/html}
},
@article{thompson_food_2012,
title = {Food webs: reconciling the structure and function of biodiversity},
volume = {27},
issn = {0169-5347},
shorttitle = {Food webs},
url = {http://www.sciencedirect.com/science/article/pii/S0169534712002005},
doi = {10.1016/j.tree.2012.08.005},
abstract = {The global biodiversity crisis concerns not only unprecedented loss of species within communities, but also related consequences for ecosystem function. Community ecology focuses on patterns of species richness and community composition, whereas ecosystem ecology focuses on fluxes of energy and materials. Food webs provide a quantitative framework to combine these approaches and unify the study of biodiversity and ecosystem function. We summarise the progression of food-web ecology and the challenges in using the food-web approach. We identify five areas of research where these advances can continue, and be applied to global challenges. Finally, we describe what data are needed in the next generation of food-web studies to reconcile the structure and function of biodiversity.},
number = {12},
urldate = {2013-01-22},
journal = {Trends in Ecology \$0 Evolution},
author = {Thompson, Ross M. and Brose, Ulrich and Dunne, Jennifer A. and Hall Jr., Robert O. and Hladyz, Sally and Kitching, Roger L. and Martinez, Neo D. and Rantala, Heidi and Romanuk, Tamara N. and Stouffer, Daniel B. and Tylianakis, Jason M.},
month = dec,
year = {2012},
pages = {689--697},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/AR2X2VPT/Thompson et al. - 2012 - Food webs reconciling the structure and function .pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/9KUAK3PA/S0169534712002005.html:text/html;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/8RR32SZH/S0169534712002005.html:text/html}
},
@article{ellison_predicting_2012,
title = {Predicting Food-Web Structure With Metacommunity Models},
issn = {0030-1299},
url = {http://dash.harvard.edu/handle/1/9886299},
abstract = {The metacommunity framework explores the relative influence of local and regional-scale processes in generating diversity patterns across the landscape. Metacommunity models and empirical studies have focused mostly on assemblages of competing organisms within a single trophic level. Studies of multi-trophic metacommunities are predominantly restricted to simplified trophic motifs and rarely consider entire food webs. We tested the ability of the patch-dynamics, species-sorting, mass-effects, and neutral metacommunity models, as well as three hybrid models, to reproduce empirical patterns of food web structure and composition in the complex aquatic food web found in the northern pitcher plant, Sarracenia purpurea. We used empirical data to determine regional species pools and estimate dispersal probabilities, simulated local food-web dynamics, dispersed species from regional pools into local food webs at rates based on the assumptions of each metacommunity model, and tested their relative fits to empirical data on food-web structure. The species-sorting and patch-dynamics models most accurately reproduced nine food web properties, suggesting that local-scale interactions were important in structuring Sarracenia food webs. However, differences in dispersal abilities were also important in models that accurately reproduced empirical food web properties. Although the models were tested using pitcher-plant food webs, the approach we have developed can be applied to any well-resolved food web for which data are available from multiple locations.},
language = {{en\$0US}},
urldate = {2013-01-22},
author = {Ellison, Aaron M. and Baiser, Benjamin H. and Gotelli, Nicholas and Buckley, Hannah L.},
year = {2012},
note = {Organismic and Evolutionary Biology},
keywords = {disperal, food web, metacommunity, patch dynamics, pitcher plant, Sarracenia purpurea, species sorting},
file = {Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/CA9T3AWI/9886299.html:text/html}
},
@article{palamara_population_2011,
title = {{POPULATION} {DYNAMICS} {ON} {COMPLEX} {FOOD} {WEBS}},
volume = {14},
issn = {0219-5259, 1793-6802},
url = {http://www.worldscientific.com/doi/abs/10.1142/S0219525911003116},
doi = {10.1142/S0219525911003116},
number = {04},
urldate = {2013-01-22},
journal = {Advances in Complex Systems},
author = {Palamara, Gian Marco and Zlatić, Vinko and Scala, Antonio and Caldarelli, Guido},
month = aug,
year = {2011},
pages = {635--647},
file = {POPULATION DYNAMICS ON COMPLEX FOOD WEBS : Advances in Complex Systems: Vol. 14, No. 04 (World Scientific):/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/CBGS9IAM/S0219525911003116.html:text/html}
},
@article{laird_correlation_2007,
title = {Correlation, selection and the evolution of species networks},
volume = {209},
issn = {03043800},
doi = {10.1016/j.ecolmodel.2007.06.016},
abstract = {We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction networks with exponential degree distributions and an inverse dependence between connectance and species richness. We use a simplified network evolution model to demonstrate that the observed degree distributions can occur as a consequence of partial correlations in the inheritance process. Further to this, in the limit of low connectance and maximal correlation, distributions of power-law form, P (k) ∝ 1 / k, can be achieved. We also show that a hyperbolic relationship between connectance and species richness, C ∼ 1 / D can arise as a consequence of probabilistic constraints on the evolutionary search process. © 2007 Elsevier {B.V.} All rights reserved.},
language = {English},
number = {2-4},
journal = {Ecological Modelling},
author = {Laird, S. and Jensen, {H.J.}},
year = {2007},
keywords = {Connectance-species relationship, Degree distribution, Evolution and adaptation, Species network},
pages = {149--156}
},
@article{garlaschelli_self-organized_2007,
title = {Self-organized network evolution coupled to extremal dynamics},
volume = {3},
copyright = {© 2007 Nature Publishing Group},
issn = {1745-2473},
url = {http://www.nature.com/nphys/journal/v3/n11/full/nphys729.html},
doi = {10.1038/nphys729},
abstract = {The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the dynamics of the {Bak–Sneppen} evolution model with the rules of the so-called fitness network model for establishing the topology of a network; each vertex is assigned a 'fitness', and the vertex with minimum fitness and its neighbours are updated in each iteration. At the same time, the links between the updated vertices and all other vertices are drawn anew with a fitness-dependent connection probability. We show analytically and numerically that the system self-organizes to a non-trivial state that differs from what is obtained when the two processes are decoupled. A power-law decay of dynamical and topological quantities above a threshold emerges spontaneously, as well as a feedback between different dynamical regimes and the underlying correlation and percolation properties of the network.},
language = {en},
number = {11},
urldate = {2013-01-22},
journal = {Nature Physics},
author = {Garlaschelli, Diego and Capocci, Andrea and Caldarelli, Guido},
year = {2007},
pages = {813--817}
},
@article{fukami_productivitybiodiversity_2003,
title = {Productivity–biodiversity relationships depend on the history of community assembly},
volume = {424},
copyright = {© 2003 Nature Publishing Group},
issn = {0028-0836},
url = {http://www.nature.com/nature/journal/v424/n6947/full/nature01785.html},
doi = {10.1038/nature01785},
abstract = {Identification of the causes of productivity–species diversity relationships remains a central topic of ecological research. Different relations have been attributed to the influence of disturbance, consumers, niche specialization and spatial scale. One unexplored cause is the history of community assembly, the partly stochastic sequential arrival of species from a regional pool of potential community members. The sequence of species arrival can greatly affect community structure. If assembly sequence interacts with productivity to influence diversity, different sequences can contribute to variation in productivity–diversity relationships. Here we report a test of this hypothesis by assembling aquatic microbial communities at five productivity levels using four assembly sequences. About 30 generations after assembly, productivity–diversity relationships took various forms, including a positive, a hump-shaped, a U-shaped and a non-significant pattern, depending on assembly sequence. This variation resulted from idiosyncratic joint effects of assembly sequence, productivity and species identity on species abundances. We suggest that the history of community assembly should be added to the growing list of factors that influence productivity–biodiversity patterns.},
language = {en},
number = {6947},
urldate = {2013-01-18},
journal = {Nature},
author = {Fukami, Tadashi and Morin, Peter J.},
month = jul,
year = {2003},
keywords = {astronomy, astrophysics, biochemistry, bioinformatics, biology, biotechnology, cancer, cell cycle, cell signalling, climate change, computational biology, development, developmental biology, {DNA}, drug discovery, earth science, ecology, environmental science, evolution, evolutionary biology, functional genomics, genetics, genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, physics, proteomics, quantum physics, {RNA}, science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
pages = {423--426},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/V33SICMT/Fukami and Morin - 2003 - Productivity–biodiversity relationships depend on .pdf:application/pdf}
},
@article{guimera_origin_2010,
title = {Origin of compartmentalization in food webs},
volume = {91},
url = {http://www.esajournals.org/doi/pdf/10.1890/09-1175.1},
number = {10},
urldate = {2013-01-22},
journal = {Ecology},
author = {Guimera, R. and Stouffer, D. B. and Sales-Pardo, M. and Leicht, E. A. and Newman, M. E. J. and Amaral, L. A. N.},
year = {2010},
pages = {2941–2951},
file = {09-1175.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/TX822V5Z/09-1175.pdf:application/pdf}
},
@article{rossberg_partwhole_2008,
title = {Part–whole relations between food webs and the validity of local food-web descriptions},
volume = {5},
issn = {1476-{945X}},
shorttitle = {Current Food-Web Theory},
url = {http://www.sciencedirect.com/science/article/pii/S1476945X0800010X},
doi = {10.1016/j.ecocom.2008.02.003},
abstract = {This work analyzes the relationship between large food webs describing potential feeding relations between species and smaller sub-webs thereof describing relations actually realized in local communities of various sizes. Special attention is given to the relationships between patterns of phylogenetic correlations encountered in large webs and sub-webs. Based on the current theory of food-web topology as implemented in the matching model, it is shown that food webs are scale invariant in the following sense: given a large web described by the model, a smaller, randomly sampled sub-web thereof is described by the model as well. A stochastic analysis of model steady states reveals that such a change in scale goes along with a re-normalization of model parameters. Explicit formulae for the re-normalized parameters are derived. Thus, the topology of food webs at all scales follows the same patterns, and these can be revealed by data and models referring to the local scale alone. As a by-product of the theory, a fast algorithm is derived which yields sample food webs from the exact steady state of the matching model for a high-dimensional trophic niche space in finite time.},
number = {2},
urldate = {2013-01-23},
journal = {Ecological Complexity},
author = {Rossberg, {A.G.}},
month = jun,
year = {2008},
keywords = {Coalescence, evolution, food webs, Networks, Spatial scale},
pages = {121--131},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/UITRWTAJ/Rossberg - 2008 - Part–whole relations between food webs and the val.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/ZD9JWHRV/S1476945X0800010X.html:text/html}
},
@article{cannon_diversification_2010,
title = {Diversification in Simulated Food Webs: The Role of Closed Motifs},
shorttitle = {Diversification in Simulated Food Webs},
url = {http://tuvalu.santafe.edu/events/workshops/images/c/c0/Foodnet.pdf},
urldate = {2013-01-22},
author = {Cannon, J. and Fay, G. and Hein, A. and Weinberger, V.},
year = {2010},
file = {Foodnet.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/IEWW5QVT/Foodnet.pdf:application/pdf}
},
@book{pascual_ecological_2005,
title = {Ecological Networks: Linking Structure to Dynamics in Food Webs},
isbn = {9780199884919},
shorttitle = {Ecological Networks},
abstract = {This book is based on proceedings from a February 2004 Santa Fe Institute workshop. Its contributing chapter authors treat the ecology of predator-prey interactions and food web theory, structure, and dynamics, joining researchers who also work on complex systems and on large nonlinear networks from the points of view of other sub-fields within ecology. Food webs play a central role in the debates on the role of complexity in stability, persistence, and resilience. Better empirical data and the exploding interest in the subject of networks across social, physical, and natural sciences prompted creation of this volume. The book explores the boundaries of what is known of the relationship between structure and dynamics in ecological networks and defines directions for future developments in this field.},
language = {en},
publisher = {Oxford University Press},
author = {Pascual, Mercedes and Dunne, Jennifer A.},
month = nov,
year = {2005},
keywords = {Science / Environmental Science, Science / Life Sciences / Ecology}
},
@article{rossberg_how_2010,
title = {How trophic interaction strength depends on traits},
volume = {3},
issn = {1874-1738, 1874-1746},
url = {http://link.springer.com/article/10.1007/s12080-009-0049-1},
doi = {10.1007/s12080-009-0049-1},
abstract = {A key problem in community ecology is to understand how individual-level traits give rise to population-level trophic interactions. Here, we propose a synthetic framework based on ecological considerations to address this question systematically. We derive a general functional form for the dependence of trophic interaction coefficients on trophically relevant quantitative traits of consumers and resources. The derived expression encompasses—and thus allows a unified comparison of—several functional forms previously proposed in the literature. Furthermore, we show how a community’s, potentially low-dimens ional, effective trophic niche space is related to its higher-dimensional phenotypic trait space. In this manner, we give ecological meaning to the notion of the “dimensionality of trophic niche space.” Our framework implies a method for directly measuring this dimensionality. We suggest a procedure for estimating the relevant parameters from empirical data and for verifying that such data matches the assumptions underlying our derivation.},
language = {en},
number = {1},
urldate = {2013-01-23},
journal = {Theoretical Ecology},
author = {Rossberg, A. G. and Brännström, Å and Dieckmann, U.},
month = feb,
year = {2010},
keywords = {evolution, food webs, interaction strength, Niche space, Plant Sciences, Theoretical {Ecology/Statistics}, Zoology},
pages = {13--24},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/VXF73T8H/Rossberg et al. - 2010 - How trophic interaction strength depends on traits.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/WH3GKC9A/10.html:text/html}
},
@article{ives_phylogenetic_2006,
title = {Phylogenetic Analysis of Trophic Associations.},
volume = {168},
copyright = {Copyright © 2006 The University of Chicago},
issn = {0003-0147},
url = {http://www.jstor.org/stable/10.1086/505157},
doi = {10.1086/505157},
abstract = {Abstract: Ecologists frequently collect data on the patterns of association between adjacent trophic levels in the form of binary or quantitative food webs. Here, we develop statistical methods to estimate the roles of consumer and resource phylogenies in explaining patterns of consumer‐resource association. We use these methods to ask whether closely related consumer species are more likely to attack the same resource species and whether closely related resource species are more likely to be attacked by the same consumer species. We then show how to use estimates of phylogenetic signals to predict novel consumer‐resource associations solely from the phylogenetic position of species for which no other (or only partial) data are available. Finally, we show how to combine phylogenetic information with information about species’ ecological characteristics and life‐history traits to estimate the effects of species traits on consumer‐resource associations while accounting for phylogenies. We illustrate these techniques using a food web comprising species of parasitoids, leaf‐mining moths, and their host plants.},
number = {1},
urldate = {2013-01-23},
journal = {The American Naturalist},
author = {Ives, A. R. and Godfray, H. C. J.},
month = jul,
year = {2006},
note = {{ArticleType:} research-article / Full publication date: July 2006 / Copyright © 2006 The University of Chicago},
pages = {E1--E14},
file = {JSTOR Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/VAM83TF3/Ives and Godfray - 2006 - Phylogenetic Analysis of Trophic Associations..pdf:application/pdf}
},
@article{bascompte_disentangling_2009,
title = {Disentangling the Web of Life},
volume = {325},
issn = {0036-8075, 1095-9203},
url = {http://www.sciencemag.org/content/325/5939/416},
doi = {10.1126/science.1170749},
abstract = {Biodiversity research typically focuses on species richness and has often neglected interactions, either by assuming that such interactions are homogeneously distributed or by addressing only the interactions between a pair of species or a few species at a time. In contrast, a network approach provides a powerful representation of the ecological interactions among species and highlights their global interdependence. Understanding how the responses of pairwise interactions scale to entire assemblages remains one of the great challenges that must be met as society faces global ecosystem change.},
language = {en},
number = {5939},
urldate = {2013-01-22},
journal = {Science},
author = {Bascompte, Jordi},
month = jul,
year = {2009},
pages = {416--419},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/6UTB9B8F/Bascompte - 2009 - Disentangling the Web of Life.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/MZUNMJIZ/416.html:text/html}
},
@article{laird_tangled_2006,
title = {The Tangled Nature model with inheritance and constraint: Evolutionary ecology restricted by a conserved resource},
volume = {3},
issn = {1476-{945X}},
shorttitle = {The Tangled Nature model with inheritance and constraint},
url = {http://www.sciencedirect.com/science/article/pii/S1476945X06000468},
doi = {10.1016/j.ecocom.2006.06.001},
abstract = {We study a version of the Tangled Nature model of evolutionary ecology redefined in a phenotype space where mutants have properties correlated to their parents. The model has individual-based dynamics whilst incorporating species scale competitive constraints and a system scale resource constraint. Multiple species arise that coexist in a species interaction network with evolving global properties. Both the mean interaction strength and the network connectance increase relative to the null system as mutualism becomes more extensive. From a study of the dependence of average degree on the resource level we extract the diversity-connectance relationship which conforms to the hyperbolic form seen in field data. This is adjudged to arise as a consequence of the evolutionary pressure to achieve positive interactions. The network degree distributions conform more strongly to exponential than to the null binomial distributions in all cases. This effect is believed to be caused by correlations in the reproductive process. We also study how resource availability influences the phenotypical lifetime distribution which is approximately of power law form. We observe that the mean lifetime is inversely related to the resource level.},
number = {3},
urldate = {2013-01-23},
journal = {Ecological Complexity},
author = {Laird, Simon and Jensen, Henrik Jeldtoft},
month = sep,
year = {2006},
keywords = {Bio-diversity, Connectance, Evolutionary ecology, Resource constraint, Species degree distribution, Species lifetimes},
pages = {253--262},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/GTQ2V5BF/Laird and Jensen - 2006 - The Tangled Nature model with inheritance and cons.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/4B8ER38H/S1476945X06000468.html:text/html}
},
@article{takahashi_cyclic_2011,
title = {Cyclic transitions in simulated food-web evolution},
volume = {6},
issn = {1742-9145},
url = {http://www.tandfonline.com/doi/abs/10.1080/17429145.2011.552794},
doi = {10.1080/17429145.2011.552794},
abstract = {Abstract Eco-evolutionary food-web models help elucidate the processes responsible for the emergence and maintenance of complex community structures. Using an individual-based model of evolving trophic and competitive interactions, we highlight a pattern of community macroevolution involving two meta-stable states, corresponding to a plant–herbivore community and a plant community, respectively. On the evolutionary timescale, our model exhibits cyclic transitions between these alternative community states. The model also helps understand the eco-evolutionary mechanisms underlying these recurrent rapid transitions, which end intermittent periods of near-stasis or punctuated equilibrium.},
number = {2-3},
urldate = {2013-01-24},
journal = {Journal of Plant Interactions},
author = {Takahashi, Daisuke and Brännström, Åke and Mazzucco, Rupert and Yamauchi, Atsushi and Dieckmann, Ulf},
year = {2011},
pages = {181--182},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/4KTPSC8U/Takahashi et al. - 2011 - Cyclic transitions in simulated food-web evolution.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/V8P8H6DG/17429145.2011.html:text/html}
},
@article{roopnarine_red_2012,
title = {Red queen for a day: models of symmetry and selection in paleoecology},
volume = {26},
issn = {0269-7653, 1573-8477},
shorttitle = {Red queen for a day},
url = {http://link.springer.com/article/10.1007/s10682-011-9494-6},
doi = {10.1007/s10682-011-9494-6},
abstract = {The Unified Theory of Biodiversity ({UNTB)}, the Red Queen’s Hypothesis ({RQH)}, and the Cascading Extinctions on Graphs hypothesis ({CEG)} are explored as members of a spectrum describing the ecological partitioning of species richness. All are models of historical biodiversity, but fare differently in explaining observed features of Phanerozoic biodiversity. The models treat species as symmetric, asymmetric, or partially symmetric respectively. Symmetry in the {UNTB} is broken by the generation and selection of variation of ecological performance, while the robustness and hence longevity of {RQ} communities are subject to selection. The {CEG} model reconciles some of the differences, demonstrating the importance of functional partitioning to both species evolution and selection at the community level. It is concluded that the {UNTB} explains communities partially on the shortest of evolutionary time scales, while {RQ} communities would be, at best, geologically ephemeral yet conditionally important.},
language = {en},
number = {1},
urldate = {2013-01-18},
journal = {Evolutionary Ecology},
author = {Roopnarine, Peter},
month = jan,
year = {2012},
keywords = {{CEG}, Community selection, evolutionary biology, food webs, Human Genetics, Neutral theory, Phanerozoic diversity, Plant Sciences, Red queen},
pages = {1--10},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/JUB3BQSA/Roopnarine - 2012 - Red queen for a day models of symmetry and select.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/4V32BUVX/10.html:text/html}
},
@article{naisbit_phylogeny_2012,
title = {Phylogeny versus body size as determinants of food web structure},
volume = {279},
issn = {0962-8452, 1471-2954},
url = {http://rspb.royalsocietypublishing.org/content/279/1741/3291},
doi = {10.1098/rspb.2012.0327},
abstract = {Food webs are the complex networks of trophic interactions that stoke the metabolic fires of life. To understand what structures these interactions in natural communities, ecologists have developed simple models to capture their main architectural features. However, apparently realistic food webs can be generated by models invoking either predator–prey body-size hierarchies or evolutionary constraints as structuring mechanisms. As a result, this approach has not conclusively revealed which factors are the most important. Here we cut to the heart of this debate by directly comparing the influence of phylogeny and body size on food web architecture. Using data from 13 food webs compiled by direct observation, we confirm the importance of both factors. Nevertheless, phylogeny dominates in most networks. Moreover, path analysis reveals that the size-independent direct effect of phylogeny on trophic structure typically outweighs the indirect effect that could be captured by considering body size alone. Furthermore, the phylogenetic signal is asymmetric: closely related species overlap in their set of consumers far more than in their set of resources. This is at odds with several food web models, which take only the view-point of consumers when assigning interactions. The echo of evolutionary history clearly resonates through current food webs, with implications for our theoretical models and conservation priorities.},
language = {en},
number = {1741},
urldate = {2013-01-18},
journal = {Proceedings of the Royal Society B: Biological Sciences},
author = {Naisbit, Russell E. and Rohr, Rudolf P. and Rossberg, Axel G. and Kehrli, Patrik and Bersier, Louis-Félix},
month = aug,
year = {2012},
keywords = {body mass, ecological network, food web, path analysis, phylogenetic constraints, trophic structure},
pages = {3291--3297},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/T5JUKSC9/Naisbit et al. - 2012 - Phylogeny versus body size as determinants of food.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/G667EQXZ/3291.html:text/html}
},
@article{roopnarine_detailed_2013,
title = {Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica},
volume = {2013},
issn = {2090-9322},
shorttitle = {Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems},
url = {http://www.datasets.com/journals/ecology/2013/857470/},
doi = {10.7167/2013/857470},
urldate = {2013-01-18},
journal = {Dataset Papers in Ecology},
author = {Roopnarine, Peter D. and Hertog, Rachel},
year = {2013},
pages = {1--9},
file = {Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/9JWTDTJ7/857470.html:application/xhtml+xml}
},
@article{alarcon_spreading_2009,
title = {Spreading on a complex network avoiding certain motifs},
url = {http://arxiv.org/abs/0903.1199},
abstract = {Spreading of either information or matter can often be treated as a network problem. It can be of great importance to be able to estimate the likelihood that spreading through a network reaches essentially the entire network while still not reaching certain sub-classes of the network. We show that excluding nodes and edges from the network has a subtle effect on the percolation. We study two specific examples of degree distributions (exponential and scale free) for which analytical solutions can be obtained. The two cases exhibit qualitatively different behavior.},
urldate = {2013-01-23},
journal = {{arXiv:0903.1199}},
author = {Alarcon, Tomas and Jensen, Henrik Jeldtoft},
month = mar,
year = {2009},
keywords = {Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Statistical Mechanics},
file = {0903.1199 PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/RVPCTZZT/Alarcon and Jensen - 2009 - Spreading on a complex network avoiding certain mo.pdf:application/pdf;arXiv.org Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/NUUR8UGN/0903.html:text/html}
},
@article{williams_maxent_2010,
year={2010},
issn={1874-1738},
journal={Theoretical Ecology},
volume={3},
issue={1},
doi={10.1007/s12080-009-0052-6},
title={Simple MaxEnt models explain food web degree distributions},
url={http://dx.doi.org/10.1007/s12080-009-0052-6},
publisher={Springer Netherlands},
keywords={Network; Resource distribution; Consumer distribution; Null model},
author={Williams, RichardJ.},
pages={45-52},
language={English}
}
@article{williams_simple_2000,
title = {Simple rules yield complex food webs},
volume = {404},
url = {http://userwww.sfsu.edu/~parker/bio840/pdfs/WilliamsMartinez2000.pdf},
number = {6774},
urldate = {2013-01-23},
journal = {Nature},
author = {Williams, R. J. and Martinez, N. D.},
year = {2000},
pages = {180–183},
file = {WilliamsMartinez2000.pdf:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/K7E4426C/WilliamsMartinez2000.pdf:application/pdf}
},
@article{caldarelli_modelling_1998,
title = {Modelling Coevolution in Multispecies Communities},
volume = {193},
issn = {0022-5193},
url = {http://www.sciencedirect.com/science/article/pii/S0022519398907068},
doi = {10.1006/jtbi.1998.0706},
abstract = {We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary time-scale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is than calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.},
number = {2},
urldate = {2013-01-23},
journal = {Journal of Theoretical Biology},
author = {Caldarelli, Guido and Higgs, Paul G. and {McKane}, Alan J.},
month = jul,
year = {1998},
pages = {345--358},
file = {ScienceDirect Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/HSX72T6X/Caldarelli et al. - 1998 - Modelling Coevolution in Multispecies Communities.pdf:application/pdf;ScienceDirect Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/TB2TX5HJ/S0022519398907068.html:text/html}
},
@article{blomberg_testing_2003,
title = {Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile},
volume = {57},
issn = {1558-5646},
shorttitle = {Testing for Phylogenetic Signal in Comparative Data},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2003.tb00285.x/abstract},
doi = {10.1111/j.0014-3820.2003.tb00285.x},
abstract = {Abstract The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal α= 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck ({OU)} model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate ({ACDC)} in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the {OU} (d) and {ACDC} (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92\$0 of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated {OU} (25\$0 of traits) and/or {ACDC} (40\$0) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.},
language = {en},
number = {4},
urldate = {2013-01-23},
journal = {Evolution},
author = {Blomberg, Simon P. and Garland, Theodore and Ives, Anthony R.},
year = {2003},
keywords = {Adaptation, behavior, body size, branch lengths, comparative method, Constraint, physiology},
pages = {717–745},
file = {Full Text PDF:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/QZBK3MGB/Blomberg et al. - 2003 - Testing for Phylogenetic Signal in Comparative Dat.pdf:application/pdf;Snapshot:/Users/biomathguest/Library/Application Support/Firefox/Profiles/87kwt7dm.default/zotero/storage/UHBQX9QM/abstract.html:text/html}
},
@article{bordewich_budgeted_2012,
title = {Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems},