Publications

2017

  • [DOI] Michalska-Smith, Matthew J., Elizabeth L. Sander, Mercedes Pascual, and Stefano Allesina. “Understanding the role of parasites in food webs using the group model.” Journal of animal ecology (2017).
    [Bibtex]
    @article{citeulike:14474671,
    author = {Michalska-Smith, Matthew J. and Sander, Elizabeth L. and Pascual, Mercedes and Allesina, Stefano},
    citeulike-article-id = {14474671},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/1365-2656.12782},
    day = {08},
    doi = {10.1111/1365-2656.12782},
    issn = {00218790},
    journal = {Journal of Animal Ecology},
    month = nov,
    posted-at = {2017-11-11 21:42:46},
    priority = {2},
    title = {Understanding the role of parasites in food webs using the group model},
    url = {http://dx.doi.org/10.1111/1365-2656.12782},
    year = {2017}
    }
  • [DOI] Barabás, György, Matthew J. Michalska-Smith, and Stefano Allesina. “Self-regulation and the stability of large ecological networks.” Nature ecology & evolution (2017).
    [Bibtex]
    @article{citeulike:14463476,
    author = {Barab\'{a}s, Gy\"{o}rgy and Michalska-Smith, Matthew J. and Allesina, Stefano},
    citeulike-article-id = {14463476},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/s41559-017-0357-6},
    day = {23},
    doi = {10.1038/s41559-017-0357-6},
    issn = {2397-334X},
    journal = {Nature Ecology \& Evolution},
    month = oct,
    posted-at = {2017-10-24 14:24:05},
    priority = {2},
    title = {Self-regulation and the stability of large ecological networks},
    url = {http://dx.doi.org/10.1038/s41559-017-0357-6},
    year = {2017}
    }
  • [DOI] Sander, Elizabeth L., Timothy J. Wootton, and Stefano Allesina. “Ecological network inference from Long-Term Presence-Absence data.” Scientific reports 7.1 (2017).
    [Bibtex]
    @article{citeulike:14413500,
    author = {Sander, Elizabeth L. and Wootton, J. Timothy and Allesina, Stefano},
    citeulike-article-id = {14413500},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/s41598-017-07009-x},
    day = {2},
    doi = {10.1038/s41598-017-07009-x},
    issn = {2045-2322},
    journal = {Scientific Reports},
    month = aug,
    number = {1},
    posted-at = {2017-08-13 08:50:14},
    priority = {2},
    title = {Ecological Network Inference From {Long-Term} {Presence-Absence} Data},
    url = {http://dx.doi.org/10.1038/s41598-017-07009-x},
    volume = {7},
    year = {2017}
    }
  • [DOI] Grilli, Jacopo, Gyorgy Barabas, Matthew J. Michalska-Smith, and Stefano Allesina. “Higher-order interactions stabilize dynamics in competitive network models.” Nature AOP.7666 (2017): 210-213.
    [Bibtex]
    @article{citeulike:14399737,
    author = {Grilli, Jacopo and Barabas, Gyorgy and Michalska-Smith, Matthew J. and Allesina, Stefano},
    citeulike-article-id = {14399737},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature23273},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature23273},
    day = {26},
    doi = {10.1038/nature23273},
    issn = {0028-0836},
    journal = {Nature},
    month = jul,
    number = {7666},
    pages = {210--213},
    posted-at = {2017-07-26 21:30:56},
    priority = {2},
    publisher = {Nature Research},
    title = {Higher-order interactions stabilize dynamics in competitive network models},
    url = {http://dx.doi.org/10.1038/nature23273},
    volume = {AOP},
    year = {2017}
    }
  • [DOI] Grilli, Jacopo and Stefano Allesina. “Last name analysis of mobility, gender imbalance, and nepotism across academic systems.” Proceedings of the national academy of sciences 114.29 (2017): 7600-7605.
    [Bibtex]
    @article{citeulike:14387571,
    author = {Grilli, Jacopo and Allesina, Stefano},
    citeulike-article-id = {14387571},
    citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1703513114},
    citeulike-linkout-1 = {http://www.pnas.org/content/early/2017/06/26/1703513114.abstract},
    citeulike-linkout-2 = {http://www.pnas.org/content/early/2017/06/26/1703513114.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/28673985},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=28673985},
    day = {18},
    doi = {10.1073/pnas.1703513114},
    issn = {1091-6490},
    journal = {Proceedings of the National Academy of Sciences},
    month = jul,
    number = {29},
    pages = {7600--7605},
    pmid = {28673985},
    posted-at = {2017-07-03 20:27:18},
    priority = {2},
    publisher = {National Academy of Sciences},
    title = {Last name analysis of mobility, gender imbalance, and nepotism across academic systems},
    url = {http://dx.doi.org/10.1073/pnas.1703513114},
    volume = {114},
    year = {2017}
    }
  • [DOI] Michalska-Smith, Matthew J. and Stefano Allesina. “And, not or: quality, quantity in scientific publishing.” Plos one 12.6 (2017): e0178074+.
    [Bibtex]
    @article{citeulike:14368282,
    abstract = {Scientists often perceive a trade-off between quantity and quality in scientific publishing: finite amounts of time and effort can be spent to produce few high-quality papers or subdivided to produce many papers of lower quality. Despite this perception, previous studies have indicated the opposite relationship, in which productivity (publishing more papers) is associated with increased paper quality (usually measured by citation accumulation). We examine this question in a novel way, comparing members of the National Academy of Sciences with themselves across years, and using a much larger dataset than previously analyzed. We find that a member's most highly cited paper in a given year has more citations in more productive years than in in less productive years. Their lowest cited paper each year, on the other hand, has fewer citations in more productive years. To disentangle the effect of the underlying distributions of citations and productivities, we repeat the analysis for hypothetical publication records generated by scrambling each author's citation counts among their publications. Surprisingly, these artificial histories re-create the above trends almost exactly. Put another way, the observed positive relationship between quantity and quality can be interpreted as a consequence of randomly drawing citation counts for each publication: more productive years yield higher-cited papers because they have more chances to draw a large value. This suggests that citation counts, and the rewards that have come to be associated with them, may be more stochastic than previously appreciated.},
    author = {Michalska-Smith, Matthew J. and Allesina, Stefano},
    citeulike-article-id = {14368282},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0178074},
    day = {1},
    doi = {10.1371/journal.pone.0178074},
    journal = {PLOS ONE},
    month = jun,
    number = {6},
    pages = {e0178074+},
    posted-at = {2017-06-05 21:39:37},
    priority = {2},
    publisher = {Public Library of Science},
    title = {And, not or: Quality, quantity in scientific publishing},
    url = {http://dx.doi.org/10.1371/journal.pone.0178074},
    volume = {12},
    year = {2017}
    }
  • [DOI] Levine, Jonathan M., Jordi Bascompte, Peter B. Adler, and Stefano Allesina. “Beyond pairwise mechanisms of species coexistence in complex communities.” Nature 546.7656 (2017): 56-64.
    [Bibtex]
    @article{citeulike:14366345,
    author = {Levine, Jonathan M. and Bascompte, Jordi and Adler, Peter B. and Allesina, Stefano},
    citeulike-article-id = {14366345},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature22898},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature22898},
    day = {31},
    doi = {10.1038/nature22898},
    issn = {0028-0836},
    journal = {Nature},
    month = may,
    number = {7656},
    pages = {56--64},
    posted-at = {2017-06-01 14:46:44},
    priority = {2},
    publisher = {Nature Research},
    title = {Beyond pairwise mechanisms of species coexistence in complex communities},
    url = {http://dx.doi.org/10.1038/nature22898},
    volume = {546},
    year = {2017}
    }
  • [DOI] Grilli, Jacopo, Matteo Adorisio, Samir Suweis, György Barabás, Jayanth R. Banavar, Stefano Allesina, and Amos Maritan. “Feasibility and coexistence of large ecological communities.” Nature communications 8 (2017).
    [Bibtex]
    @article{citeulike:14287119,
    author = {Grilli, Jacopo and Adorisio, Matteo and Suweis, Samir and Barab\'{a}s, Gy\"{o}rgy and Banavar, Jayanth R. and Allesina, Stefano and Maritan, Amos},
    citeulike-article-id = {14287119},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms14389},
    day = {24},
    doi = {10.1038/ncomms14389},
    issn = {2041-1723},
    journal = {Nature Communications},
    month = feb,
    posted-at = {2017-02-24 16:37:54},
    priority = {2},
    title = {Feasibility and coexistence of large ecological communities},
    url = {http://dx.doi.org/10.1038/ncomms14389},
    volume = {8},
    year = {2017}
    }
  • [DOI] Dee, Laura E., Stefano Allesina, Aletta Bonn, Anna Eklöf, Steven D. Gaines, Jes Hines, Ute Jacob, Eve McDonald-Madden, Hugh Possingham, Matthias Schröter, and Ross M. Thompson. “Operationalizing network theory for ecosystem service assessments.” Trends in ecology & evolution 32.2 (2017): 118-130.
    [Bibtex]
    @article{citeulike:14287117,
    author = {Dee, Laura E. and Allesina, Stefano and Bonn, Aletta and Ekl\"{o}f, Anna and Gaines, Steven D. and Hines, Jes and Jacob, Ute and McDonald-Madden, Eve and Possingham, Hugh and Schr\"{o}ter, Matthias and Thompson, Ross M.},
    citeulike-article-id = {14287117},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tree.2016.10.011},
    doi = {10.1016/j.tree.2016.10.011},
    issn = {01695347},
    journal = {Trends in Ecology \& Evolution},
    month = feb,
    number = {2},
    pages = {118--130},
    posted-at = {2017-02-24 16:35:38},
    priority = {2},
    title = {Operationalizing Network Theory for Ecosystem Service Assessments},
    url = {http://dx.doi.org/10.1016/j.tree.2016.10.011},
    volume = {32},
    year = {2017}
    }

2016

  • [DOI] Grilli, Jacopo, Tim Rogers, and Stefano Allesina. “Modularity and stability in ecological communities.” Nature communications 7 (2016): 12031+.
    [Bibtex]
    @article{citeulike:14076907,
    author = {Grilli, Jacopo and Rogers, Tim and Allesina, Stefano},
    citeulike-article-id = {14076907},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms12031},
    day = {23},
    doi = {10.1038/ncomms12031},
    issn = {2041-1723},
    journal = {Nature Communications},
    month = jun,
    pages = {12031+},
    posted-at = {2016-06-25 00:31:04},
    priority = {2},
    title = {Modularity and stability in ecological communities},
    url = {http://dx.doi.org/10.1038/ncomms12031},
    volume = {7},
    year = {2016}
    }
  • [DOI] Barabás, György, Michalska-Smith, and Stefano Allesina. “The effect of intra- and interspecific competition on coexistence in multispecies communities.” The american naturalist 188.1 (2016): E1–E12.
    [Bibtex]
    @article{citeulike:14042124,
    abstract = {{AbstractFor} two competing species, intraspecific competition must exceed interspecific competition for coexistence. To generalize this well-known criterion to multiple competing species, one must take into account both the distribution of interaction strengths and community structure. Here we derive a multispecies generalization of the two-species rule in the context of symmetric {Lotka-Volterra} competition and obtain explicit stability conditions for random competitive communities. We then explore the influence of community structure on coexistence. Results show that both the most and least stabilized cases have striking global structures, with a nested pattern emerging in both cases. The distribution of intraspecific coefficients leading to the most and least stabilized communities also follows a predictable pattern that can be justified analytically. In addition, we show that the size of the parameter space allowing for feasible communities always increases with the strength of intraspecific effects in a characteristic way that is independent of the interspecific interaction structure. We conclude by discussing possible extensions of our results to nonsymmetric competition.},
    author = {Barab\'{a}s, Gy\"{o}rgy and Michalska-Smith and Allesina, Stefano},
    citeulike-article-id = {14042124},
    citeulike-linkout-0 = {http://dx.doi.org/10.1086/686901},
    citeulike-linkout-1 = {http://www.journals.uchicago.edu/doi/abs/10.1086/686901},
    day = {23},
    doi = {10.1086/686901},
    journal = {The American Naturalist},
    month = may,
    number = {1},
    pages = {E1--E12},
    posted-at = {2016-06-23 17:31:57},
    priority = {2},
    publisher = {The University of Chicago Press},
    title = {The Effect of Intra- and Interspecific Competition on Coexistence in Multispecies Communities},
    url = {http://dx.doi.org/10.1086/686901},
    volume = {188},
    year = {2016}
    }
  • [DOI] McCoy, Sophie J., Stefano Allesina, and Catherine A. Pfister. “Ocean acidification affects competition for space: projections of community structure using cellular automata.” Proc. r. soc. b 283.1826 (2016): 20152561+.
    [Bibtex]
    @article{citeulike:13948829,
    author = {McCoy, Sophie J. and Allesina, Stefano and Pfister, Catherine A.},
    citeulike-article-id = {13948829},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.2015.2561},
    citeulike-linkout-1 = {http://rspb.royalsocietypublishing.org/content/283/1826/20152561.abstract},
    citeulike-linkout-2 = {http://rspb.royalsocietypublishing.org/content/283/1826/20152561.full.pdf},
    day = {16},
    doi = {10.1098/rspb.2015.2561},
    issn = {1471-2954},
    journal = {Proc. R. Soc. B},
    month = mar,
    number = {1826},
    pages = {20152561+},
    posted-at = {2016-03-02 16:06:56},
    priority = {2},
    publisher = {The Royal Society},
    title = {Ocean acidification affects competition for space: projections of community structure using cellular automata},
    url = {http://dx.doi.org/10.1098/rspb.2015.2561},
    volume = {283},
    year = {2016}
    }
  • [DOI] Masco, Christina, Stefano Allesina, Daniel J. Mennill, and Stephen Pruett-Jones. “The song overlap null model generator (SONG): a new tool for distinguishing between random and non-random song overlap.” Bioacoustics 25.1 (2016): 29-40.
    [Bibtex]
    @article{citeulike:13911161,
    abstract = {{AbstractSong} overlapping, a behaviour in which an individual begins singing before its counterpart has completed its song, has been the subject of recent debate. Although many studies have suggested that song overlapping functions as a signal, the majority of these studies fail to address the possibility that overlapping is a chance occurrence. Part of the difficulty in determining whether overlap is intentional or accidental lies in the lack of compelling null models for estimating chance levels of song overlap. We have developed the Song Overlap Null model Generator ({SONG}), a software package for R. {SONG} uses resampling randomization to predict the expected amount of overlap due to chance, and is applicable to any system in which individuals engage in signalling interactions. To evaluate the effectiveness of {SONG}, we examined the overlapping behaviour of three avian species: black-capped chickadees (Poecile atricapillus), rufous-and-white wrens (Thryophilus rufalbus) and long-tailed manakins (Chiroxiphia linearis). Our analyses revealed that black-capped chickadees avoided overlapping the songs of playback-simulated intruders, duetting wrens overlapped the songs of their mates and manakins avoided overlapping the duets of their neighbours. We believe that {SONG} will prove to be a valuable tool for understanding signal timing in songbirds as well as other taxa.},
    author = {Masco, Christina and Allesina, Stefano and Mennill, Daniel J. and Pruett-Jones, Stephen},
    citeulike-article-id = {13911161},
    citeulike-linkout-0 = {http://dx.doi.org/10.1080/09524622.2015.1079734},
    citeulike-linkout-1 = {http://www.tandfonline.com/doi/abs/10.1080/09524622.2015.1079734},
    day = {2},
    doi = {10.1080/09524622.2015.1079734},
    journal = {Bioacoustics},
    month = jan,
    number = {1},
    pages = {29--40},
    posted-at = {2016-01-17 20:47:28},
    priority = {2},
    publisher = {Taylor \& Francis},
    title = {The Song Overlap Null model Generator ({SONG}): a new tool for distinguishing between random and non-random song overlap},
    url = {http://dx.doi.org/10.1080/09524622.2015.1079734},
    volume = {25},
    year = {2016}
    }

2015

  • [DOI] Suweis, Samir, Jacopo Grilli, Jayanth R. Banavar, Stefano Allesina, and Amos Maritan. “Effect of localization on the stability of mutualistic ecological networks.” Nature communications 6 (2015): 10179+.
    [Bibtex]
    @article{citeulike:13888006,
    author = {Suweis, Samir and Grilli, Jacopo and Banavar, Jayanth R. and Allesina, Stefano and Maritan, Amos},
    citeulike-article-id = {13888006},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms10179},
    day = {17},
    doi = {10.1038/ncomms10179},
    issn = {2041-1723},
    journal = {Nature Communications},
    month = dec,
    pages = {10179+},
    posted-at = {2015-12-20 22:12:47},
    priority = {2},
    title = {Effect of localization on the stability of mutualistic ecological networks},
    url = {http://dx.doi.org/10.1038/ncomms10179},
    volume = {6},
    year = {2015}
    }
  • [DOI] Borrelli, Jonathan J., Stefano Allesina, Priyanga Amarasekare, Roger Arditi, Ivan Chase, John Damuth, Robert D. Holt, Dmitrii O. Logofet, Mark Novak, Rudolf P. Rohr, Axel G. Rossberg, Matthew Spencer, Khai J. Tran, and Lev R. Ginzburg. “Selection on stability across ecological scales.” Trends in Ecology & Evolution 30.7 (2015): 417-425.
    [Bibtex]
    @article{citeulike:13696381,
    author = {Borrelli, Jonathan J. and Allesina, Stefano and Amarasekare, Priyanga and Arditi, Roger and Chase, Ivan and Damuth, John and Holt, Robert D. and Logofet, Dmitrii O. and Novak, Mark and Rohr, Rudolf P. and Rossberg, Axel G. and Spencer, Matthew and Tran, J. Khai and Ginzburg, Lev R.},
    citeulike-article-id = {13696381},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.tree.2015.05.001},
    doi = {10.1016/j.tree.2015.05.001},
    issn = {01695347},
    journal = {Trends in {E}cology \& {E}volution},
    month = jul,
    number = {7},
    pages = {417--425},
    posted-at = {2015-08-06 16:11:52},
    priority = {2},
    title = {Selection on stability across ecological scales},
    url = {http://dx.doi.org/10.1016/j.tree.2015.05.001},
    volume = {30},
    year = {2015}
    }
  • [DOI] Allesina, Stefano, Jacopo Grilli, György Barabás, Si Tang, Johnatan Aljadeff, and Amos Maritan. “Predicting the stability of large structured food webs.” Nature Communications 6 (2015): 7842+.
    [Bibtex]
    @article{citeulike:13696380,
    author = {Allesina, Stefano and Grilli, Jacopo and Barab\'{a}s, Gy\"{o}rgy and Tang, Si and Aljadeff, Johnatan and Maritan, Amos},
    citeulike-article-id = {13696380},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms8842},
    day = {22},
    doi = {10.1038/ncomms8842},
    issn = {2041-1723},
    journal = {Nature {C}ommunications},
    month = jul,
    pages = {7842+},
    posted-at = {2015-08-06 16:10:43},
    priority = {2},
    title = {Predicting the stability of large structured food webs},
    url = {http://dx.doi.org/10.1038/ncomms8842},
    volume = {6},
    year = {2015}
    }
  • [DOI] Sander, Elizabeth L., Timothy J. Wootton, and Stefano Allesina. “What can interaction webs tell us about species roles?.” Plos Comput Biol 11.7 (2015): e1004330+.
    [Bibtex]
    @article{citeulike:13696378,
    abstract = {The group model is a useful tool to understand broad-scale patterns of interaction in a network, but it has previously been limited in use to food webs, which contain only predator-prey interactions. Natural populations interact with each other in a variety of ways and, although most published ecological networks only include information about a single interaction type (e.g., feeding, pollination), ecologists are beginning to consider networks which combine multiple interaction types. Here we extend the group model to signed directed networks such as ecological interaction webs. As a specific application of this method, we examine the effects of including or excluding specific interaction types on our understanding of species roles in ecological networks. We consider all three currently available interaction webs, two of which are extended plant-mutualist networks with herbivores and parasitoids added, and one of which is an extended intertidal food web with interactions of all possible sign structures (+/+, -/0, etc.). Species in the extended food web grouped similarly with all interactions, only trophic links, and only nontrophic links. However, removing mutualism or herbivory had a much larger effect in the extended plant-pollinator webs. Species removal even affected groups that were not directly connected to those that were removed, as we found by excluding a small number of parasitoids. These results suggest that including additional species in the network provides far more information than additional interactions for this aspect of network structure. Our methods provide a useful framework for simplifying networks to their essential structure, allowing us to identify generalities in network structure and better understand the roles species play in their communities. Ecological interactions are highly diverse even when considering a single species: the species might feed on a first, disperse the seeds of a second, and pollinate a third. Here we extend the group model, a method for identifying broad patterns of interaction across a food web, to networks which contain multiple types of interactions. Using this new method, we ask whether the traditional approach of building a network for each type of interaction (food webs for consumption, pollination webs, seed-dispersal webs, host-parasite webs) can be improved by merging all interaction types in a single network. In particular, we test whether combining different interaction types leads to a better definition of the roles species play in ecological communities. We find that, although having more information necessarily leads to better results, the improvement is only incremental if the linked species remain unchanged. However, including a new interaction type that attaches new species to the network substantially improves performance. This method provides insight into possible implications of merging different types of interactions and allows for the study of coarse-grained structure in any signed network, including ecological interaction webs, gene regulation networks, and social networks.},
    author = {Sander, Elizabeth L. and Wootton, J. Timothy and Allesina, Stefano},
    citeulike-article-id = {13696378},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1004330},
    day = {21},
    doi = {10.1371/journal.pcbi.1004330},
    journal = {PLoS {C}omput {B}iol},
    month = jul,
    number = {7},
    pages = {e1004330+},
    posted-at = {2015-08-06 16:09:37},
    priority = {2},
    publisher = {Public Library of Science},
    title = {What Can Interaction Webs Tell Us About Species Roles?},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1004330},
    volume = {11},
    year = {2015}
    }
  • [DOI] Barabás, György and Stefano Allesina. “Predicting global community properties from uncertain estimates of interaction strengths.” Journal of The Royal Society Interface 12.109 (2015): 20150218+.
    [Bibtex]
    @article{citeulike:13696376,
    author = {Barab\'{a}s, Gy\"{o}rgy and Allesina, Stefano},
    citeulike-article-id = {13696376},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rsif.2015.0218},
    citeulike-linkout-1 = {http://rsif.royalsocietypublishing.org/content/12/109/20150218.abstract},
    citeulike-linkout-2 = {http://rsif.royalsocietypublishing.org/content/12/109/20150218.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/26246417},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=26246417},
    day = {06},
    doi = {10.1098/rsif.2015.0218},
    issn = {1742-5662},
    journal = {Journal of {T}he {R}oyal {S}ociety {I}nterface},
    month = aug,
    number = {109},
    pages = {20150218+},
    pmid = {26246417},
    posted-at = {2015-08-06 16:08:25},
    priority = {2},
    publisher = {The Royal Society},
    title = {Predicting global community properties from uncertain estimates of interaction strengths},
    url = {http://dx.doi.org/10.1098/rsif.2015.0218},
    volume = {12},
    year = {2015}
    }
  • [DOI] Grilli, Jacopo, György Barabás, and Stefano Allesina. “Metapopulation persistence in random fragmented landscapes.” PLoS Comput Biol 11.5 (2015): e1004251+.
    [Bibtex]
    @article{citeulike:13634679,
    abstract = {Habitat destruction and land use change are making the world in which natural populations live increasingly fragmented, often leading to local extinctions. Although local populations might undergo extinction, a metapopulation may still be viable as long as patches of suitable habitat are connected by dispersal, so that empty patches can be recolonized. Thus far, metapopulations models have either taken a mean-field approach, or have modeled empirically-based, realistic landscapes. Here we show that an intermediate level of complexity between these two extremes is to consider random landscapes, in which the patches of suitable habitat are randomly arranged in an area (or volume). Using methods borrowed from the mathematics of Random Geometric Graphs and Euclidean Random Matrices, we derive a simple, analytic criterion for the persistence of the metapopulation in random fragmented landscapes. Our results show how the density of patches, the variability in their value, the shape of the dispersal kernel, and the dimensionality of the landscape all contribute to determining the fate of the metapopulation. Using this framework, we derive sufficient conditions for the population to be spatially localized, such that spatially confined clusters of patches act as a source of dispersal for the whole landscape. Finally, we show that a regular arrangement of the patches is always detrimental for persistence, compared to the random arrangement of the patches. Given the strong parallel between metapopulation models and contact processes, our results are also applicable to models of disease spread on spatial networks. Like the hundreds of paintings of water lilies by Monet, any two landscapes in which a metapopulation dwells are different, as the size, shape and location of the patches of suitable habitat (the lilies), distributed over a inhospitable background (the water) vary among landscapes. Yet, as all the paintings depict the same pond in Giverny, different fragmented landscapes could have the same value to a metapopulation. Here we ask what are the key features we should measure to predict persistence of metapopulations inhabiting fragmented landscapes, and show that few quantities determine the fate of metapopulations—so that two very different-looking landscapes could lead to the same likelihood of persistence. We also show that regular arrangements of the patches in space are detrimental for persistence, and that the typical behavior of metapopulations close to extinction is to be mostly localized in a confined region of the landscape.},
    author = {Grilli, Jacopo and Barab\'{a}s, Gy\"{o}rgy and Allesina, Stefano},
    citeulike-article-id = {13634679},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1004251},
    day = {20},
    doi = {10.1371/journal.pcbi.1004251},
    journal = {P{L}o{S} {C}omput {B}iol},
    month = may,
    number = {5},
    pages = {e1004251+},
    posted-at = {2015-06-02 23:31:35},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Metapopulation Persistence in Random Fragmented Landscapes},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1004251},
    volume = {11},
    year = {2015}
    }
  • [DOI] Smith, Matthew J., Elizabeth Sander, György Barabás, and Stefano Allesina. “Stability and feedback levels in food web models.” Ecology letters 18.6 (2015): 593-595.
    [Bibtex]
    @article{citeulike:13611659,
    author = {Smith, Matthew J. and Sander, Elizabeth and Barab\'{a}s, Gy\"{o}rgy and Allesina, Stefano},
    citeulike-article-id = {13611659},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/ele.12416},
    doi = {10.1111/ele.12416},
    issn = {1461023X},
    journal = {Ecology Letters},
    month = jun,
    number = {6},
    pages = {593--595},
    posted-at = {2015-05-14 15:00:33},
    priority = {2},
    title = {Stability and feedback levels in food web models},
    url = {http://dx.doi.org/10.1111/ele.12416},
    volume = {18},
    year = {2015}
    }
  • [DOI] Weinberger, Cody J., James A. Evans, and Stefano Allesina. “Ten simple (empirical) rules for writing science.” PLoS Comput Biol 11.4 (2015): e1004205+.
    [Bibtex]
    @article{citeulike:13600042,
    author = {Weinberger, Cody J. and Evans, James A. and Allesina, Stefano},
    citeulike-article-id = {13600042},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1004205},
    day = {30},
    doi = {10.1371/journal.pcbi.1004205},
    journal = {P{L}o{S} {C}omput {B}iol},
    month = apr,
    number = {4},
    pages = {e1004205+},
    posted-at = {2015-04-30 21:55:31},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Ten Simple (Empirical) Rules for Writing Science},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1004205},
    volume = {11},
    year = {2015}
    }
  • [DOI] Allesina, Stefano and Si Tang. “The stability–complexity relationship at age 40: a random matrix perspective.” Population ecology 57.1 (2015): 63-75.
    [Bibtex]
    @article{citeulike:13577196,
    abstract = {Since the work of Robert May in 1972, the local asymptotic stability of large ecological systems has been a focus of theoretical ecology. Here we review May's work in the light of random matrix theory, the field of mathematics devoted to the study of large matrices whose coefficients are randomly sampled from distributions with given characteristics. We show how May's celebrated ” stability criterion” can be derived using random matrix theory, and how extensions of the so-called circular law for the limiting distribution of the eigenvalues of large random matrix can further our understanding of ecological systems. Our goal is to present the more technical material in an accessible way, and to provide pointers to the primary mathematical literature on this subject. We conclude by enumerating a number of challenges, whose solution is going to greatly improve our ability to predict the stability of large ecological networks.},
    author = {Allesina, Stefano and Tang, Si},
    booktitle = {Population Ecology},
    citeulike-article-id = {13577196},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10144-014-0471-0},
    citeulike-linkout-1 = {http://link.springer.com/article/10.1007/s10144-014-0471-0},
    doi = {10.1007/s10144-014-0471-0},
    journal = {Population Ecology},
    number = {1},
    pages = {63--75},
    posted-at = {2015-04-08 17:10:32},
    priority = {2},
    publisher = {Springer Japan},
    title = {The stability–complexity relationship at age 40: a random matrix perspective},
    url = {http://dx.doi.org/10.1007/s10144-014-0471-0},
    volume = {57},
    year = {2015}
    }

2014

  • [DOI] Smith, Matthew J., Cody Weinberger, Emilio M. Bruna, and Stefano Allesina. “The Scientific Impact of Nations: Journal Placement and Citation Performance.” PLoS ONE 9.10 (2014): e109195+.
    [Bibtex]
    @article{citeulike:13386151,
    abstract = {International collaboration is becoming increasingly important for the advancement of science. To gain a more precise understanding of how factors such as international collaboration influence publication success, we divide publication success into two categories: journal placement and citation performance. Analyzing all papers published between 1996 and 2012 in eight disciplines, we find that those with more countries in their affiliations performed better in both categories. Furthermore, specific countries vary in their effects both individually and in combination. Finally, we look at the relationship between national output (in papers published) and input (in citations received) over the 17 years, expanding upon prior depictions by also plotting an expected proportion of citations based on Journal Placement. Discrepancies between this expectation and the realized proportion of citations illuminate trends in performance, such as the decline of the Global North in response to rapidly developing countries, especially China. Yet, most countries' show little to no discrepancy, meaning that, in most cases, citation proportion can be predicted by Journal Placement alone. This reveals an extreme asymmetry between the opinions of a few reviewers and the degree to which paper acceptance and citation rates influence career advancement.},
    author = {Smith, Matthew J. and Weinberger, Cody and Bruna, Emilio M. and Allesina, Stefano},
    citeulike-article-id = {13386151},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0109195},
    day = {8},
    doi = {10.1371/journal.pone.0109195},
    journal = {{P}{L}o{S} {O}{N}{E}},
    month = oct,
    number = {10},
    pages = {e109195+},
    posted-at = {2014-10-08 20:28:48},
    priority = {2},
    publisher = {Public Library of Science},
    title = {The {S}cientific {I}mpact of {N}ations: {J}ournal {P}lacement and {C}itation {P}erformance},
    url = {http://dx.doi.org/10.1371/journal.pone.0109195},
    volume = {9},
    year = {2014}
    }
  • [DOI] Tang, Si and Stefano Allesina. “Reactivity and stability of large ecosystems.” Frontiers in ecology and evolution 2 (2014).
    [Bibtex]
    @article{citeulike:13364190,
    author = {Tang, Si and Allesina, Stefano},
    citeulike-article-id = {13364190},
    citeulike-linkout-0 = {http://dx.doi.org/10.3389/fevo.2014.00021},
    day = {04},
    doi = {10.3389/fevo.2014.00021},
    issn = {2296-701X},
    journal = {Frontiers in Ecology and Evolution},
    month = jun,
    posted-at = {2014-09-16 00:01:48},
    priority = {2},
    title = {Reactivity and stability of large ecosystems},
    url = {http://dx.doi.org/10.3389/fevo.2014.00021},
    volume = {2},
    year = {2014}
    }
  • [DOI] Staniczenko, Phillip P. A., Matthew J. Smith, and Stefano Allesina. “Selecting food web models using Normalized Maximum Likelihood.” Methods in ecology and evolution 5.6 (2014): 551-562.
    [Bibtex]
    @article{citeulike:13364189,
    author = {Staniczenko, Phillip P. A. and Smith, Matthew J. and Allesina, Stefano},
    citeulike-article-id = {13364189},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/2041-210x.12192},
    doi = {10.1111/2041-210x.12192},
    issn = {2041210X},
    journal = {Methods in Ecology and Evolution},
    month = jun,
    number = {6},
    pages = {551--562},
    posted-at = {2014-09-16 00:01:05},
    priority = {2},
    title = {Selecting food web models using {N}ormalized {M}aximum {L}ikelihood},
    url = {http://dx.doi.org/10.1111/2041-210x.12192},
    volume = {5},
    year = {2014}
    }
  • [DOI] Tang, Si, Samraat Pawar, and Stefano Allesina. “Correlation between interaction strengths drives stability in large ecological networks.” Ecology letters 17.9 (2014): 1094-1100.
    [Bibtex]
    @article{citeulike:13364187,
    author = {Tang, Si and Pawar, Samraat and Allesina, Stefano},
    citeulike-article-id = {13364187},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/ele.12312},
    doi = {10.1111/ele.12312},
    issn = {1461023X},
    journal = {Ecology Letters},
    month = jun,
    number = {9},
    pages = {1094--1100},
    posted-at = {2014-09-15 23:59:04},
    priority = {2},
    title = {Correlation between interaction strengths drives stability in large ecological networks},
    url = {http://dx.doi.org/10.1111/ele.12312},
    volume = {17},
    year = {2014}
    }
  • [DOI] Wolkovich, Elizabeth M., Stefano Allesina, Kathryn L. Cottingham, John C. Moore, Stuart A. Sandin, and Claire de Mazancourt. “Linking the green and brown worlds: the prevalence and effect of multi-channel feeding in food webs.” Ecology (2014): 140531172126004+.
    [Bibtex]
    @article{citeulike:13364186,
    author = {Wolkovich, Elizabeth M. and Allesina, Stefano and Cottingham, Kathryn L. and Moore, John C. and Sandin, Stuart A. and de Mazancourt, Claire},
    citeulike-article-id = {13364186},
    citeulike-linkout-0 = {http://dx.doi.org/10.1890/13-1721.1},
    day = {31},
    doi = {10.1890/13-1721.1},
    issn = {0012-9658},
    journal = {Ecology},
    month = may,
    pages = {140531172126004+},
    posted-at = {2014-09-15 23:58:12},
    priority = {2},
    title = {Linking the green and brown worlds: The prevalence and effect of multi-channel feeding in food webs},
    url = {http://dx.doi.org/10.1890/13-1721.1},
    year = {2014}
    }

2013

  • [DOI] Allesina, Stefano. “Food web stability, unapologetically — book review.” Ecology 94.9 (2013): 2112-2115.
    [Bibtex]
    @article{citeulike:13364200,
    author = {Allesina, Stefano},
    citeulike-article-id = {13364200},
    citeulike-linkout-0 = {http://dx.doi.org/10.1890/br13-48},
    doi = {10.1890/br13-48},
    issn = {0012-9658},
    journal = {Ecology},
    month = sep,
    number = {9},
    pages = {2112--2115},
    posted-at = {2014-09-16 00:20:13},
    priority = {2},
    title = {Food web stability, unapologetically -- Book Review},
    url = {http://dx.doi.org/10.1890/br13-48},
    volume = {94},
    year = {2013}
    }
  • [DOI] Parker, JohnN, Stefano Allesina, and ChristopherJ Lortie. “Characterizing a scientific elite (b): publication and citation patterns of the most highly cited scientists in environmental science and ecology.” Scientometrics 94.2 (2013): 469-480.
    [Bibtex]
    @article{citeulike:11560105,
    abstract = {Science is principally driven by the efforts of a vanishingly small fraction of researchers publishing the majority of scientific research and garnering the majority of citations. Despite this well-established trend, knowledge of exactly how many articles these researchers publish, how highly they are cited, and how they achieved their distinctive accomplishments is meager. This article examines the publication and citation patterns of the world's most highly cited environmental scientists and ecologists, inquiring into their levels of scientific productivity and visibility, examining relationships between scientific productivity and quality within their research programs, and considering how different publication strategies contribute to these distinctive successes. Generally speaking, highly cited researchers are also highly productive, publishing on average well over 100 articles each. Furthermore, articles published by this group are more highly cited on average than articles published in premier generalist journal like Nature and Science, and their citation to publication ratios are more equitably distributed than is typical. Research specialization and primacy of authorship are important determinants of citation frequency, while geographic differences and collaborative propensity matter less. The article closes with a set of suggestions for those wishing to increase the use of their research by the scientific community.},
    author = {Parker, JohnN and Allesina, Stefano and Lortie, ChristopherJ},
    booktitle = {Scientometrics},
    citeulike-article-id = {11560105},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11192-012-0859-6},
    citeulike-linkout-1 = {http://www.springerlink.com/content/954121516x52k221},
    citeulike-linkout-2 = {http://link.springer.com/article/10.1007/s11192-012-0859-6},
    day = {21},
    doi = {10.1007/s11192-012-0859-6},
    issn = {0138-9130},
    journal = {Scientometrics},
    month = oct,
    number = {2},
    pages = {469--480},
    posted-at = {2014-09-16 00:18:51},
    priority = {2},
    publisher = {Springer Netherlands},
    title = {Characterizing a scientific elite (B): publication and citation patterns of the most highly cited scientists in environmental science and ecology},
    url = {http://dx.doi.org/10.1007/s11192-012-0859-6},
    volume = {94},
    year = {2013}
    }
  • [DOI] Eklöf, Anna, Ute Jacob, Jason Kopp, Jordi Bosch, Rocío Castro-Urgal, Natacha P. Chacoff, Bo Dalsgaard, Claudio de Sassi, Mauro Galetti, Paulo R. Guimarães, Silvia B. Lomáscolo, Ana M. Martín González, Marco A. Pizo, Romina Rader, Anselm Rodrigo, Jason M. Tylianakis, Diego P. Vázquez, and Stefano Allesina. “The dimensionality of ecological networks.” Ecology letters 16.5 (2013): 577-583.
    [Bibtex]
    @article{citeulike:12077248,
    abstract = {How many dimensions (trait-axes) are required to predict whether two species interact? This unanswered question originated with the idea of ecological niches, and yet bears relevance today for understanding what determines network structure. Here, we analyse a set of 200 ecological networks, including food webs, antagonistic and mutualistic networks, and find that the number of dimensions needed to completely explain all interactions is small ( < 10), with model selection favouring less than five. Using 18 high-quality webs including several species traits, we identify which traits contribute the most to explaining network structure. We show that accounting for a few traits dramatically improves our understanding of the structure of ecological networks. Matching traits for resources and consumers, for example, fruit size and bill gape, are the most successful combinations. These results link ecologically important species attributes to large-scale community structure.},
    author = {Ekl\"{o}f, Anna and Jacob, Ute and Kopp, Jason and Bosch, Jordi and Castro-Urgal, Roc\'{\i}o and Chacoff, Natacha P. and Dalsgaard, Bo and de Sassi, Claudio and Galetti, Mauro and Guimar\~{a}es, Paulo R. and Lom\'{a}scolo, Silvia B. and Mart\'{\i}n Gonz\'{a}lez, Ana M. and Pizo, Marco A. and Rader, Romina and Rodrigo, Anselm and Tylianakis, Jason M. and V\'{a}zquez, Diego P. and Allesina, Stefano},
    citeulike-article-id = {12077248},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/ele.12081},
    day = {1},
    doi = {10.1111/ele.12081},
    issn = {1461023X},
    journal = {Ecology Letters},
    month = may,
    number = {5},
    pages = {577--583},
    posted-at = {2014-09-16 00:17:05},
    priority = {2},
    title = {The dimensionality of ecological networks},
    url = {http://dx.doi.org/10.1111/ele.12081},
    volume = {16},
    year = {2013}
    }
  • [DOI] Eklöf, Anna, Si Tang, and Stefano Allesina. “Secondary extinctions in food webs: a Bayesian network approach.” Methods in ecology and evolution 4.8 (2013): 760-770.
    [Bibtex]
    @article{citeulike:13364194,
    author = {Ekl\"{o}f, Anna and Tang, Si and Allesina, Stefano},
    citeulike-article-id = {13364194},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/2041-210x.12062},
    doi = {10.1111/2041-210x.12062},
    issn = {2041210X},
    journal = {Methods in Ecology and Evolution},
    month = aug,
    number = {8},
    pages = {760--770},
    posted-at = {2014-09-16 00:10:30},
    priority = {2},
    title = {Secondary extinctions in food webs: a {B}ayesian network approach},
    url = {http://dx.doi.org/10.1111/2041-210x.12062},
    volume = {4},
    year = {2013}
    }
  • [DOI] Staniczenko, Phillip P. A., Jason C. Kopp, and Stefano Allesina. “The ghost of nestedness in ecological networks.” Nature communications 4 (2013): 1391+.
    [Bibtex]
    @article{citeulike:13364193,
    author = {Staniczenko, Phillip P. A. and Kopp, Jason C. and Allesina, Stefano},
    citeulike-article-id = {13364193},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/ncomms2422},
    day = {22},
    doi = {10.1038/ncomms2422},
    issn = {2041-1723},
    journal = {Nature Communications},
    month = jan,
    pages = {1391+},
    posted-at = {2014-09-16 00:08:23},
    priority = {2},
    title = {The ghost of nestedness in ecological networks},
    url = {http://dx.doi.org/10.1038/ncomms2422},
    volume = {4},
    year = {2013}
    }
  • [DOI] Lortie, Christopher J., Stefano Allesina, Lonnie Aarssen, Olyana Grod, and Amber E. Budden. “With great power comes great responsibility: the importance of rejection, power, and editors in the practice of scientific publishing.” Plos one 8.12 (2013): e85382+.
    [Bibtex]
    @article{citeulike:12890659,
    abstract = {Peer review is an important element of scientific communication but deserves quantitative examination. We used data from the handling service manuscript Central for ten mid-tier ecology and evolution journals to test whether number of external reviews completed improved citation rates for all accepted manuscripts. Contrary to a previous study examining this issue using resubmission data as a proxy for reviews, we show that citation rates of manuscripts do not correlate with the number of individuals that provided reviews. Importantly, externally-reviewed papers do not outperform editor-only reviewed published papers in terms of visibility within a 5-year citation window. These findings suggest that in many instances editors can be all that is needed to review papers (or at least conduct the critical first review to assess general suitability) if the purpose of peer review is to primarily filter and that journals can consider reducing the number of referees associated with reviewing ecology and evolution papers.},
    author = {Lortie, Christopher J. and Allesina, Stefano and Aarssen, Lonnie and Grod, Olyana and Budden, Amber E.},
    citeulike-article-id = {12890659},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0085382},
    day = {30},
    doi = {10.1371/journal.pone.0085382},
    journal = {PLoS ONE},
    month = dec,
    number = {12},
    pages = {e85382+},
    posted-at = {2014-09-16 00:05:40},
    priority = {2},
    publisher = {Public Library of Science},
    title = {With Great Power Comes Great Responsibility: the Importance of Rejection, Power, and Editors in the Practice of Scientific Publishing},
    url = {http://dx.doi.org/10.1371/journal.pone.0085382},
    volume = {8},
    year = {2013}
    }

2012

  • [DOI] Melián, Carlos J., David Alonso, Stefano Allesina, Richard S. Condit, and Rampal S. Etienne. “Does sex speed up evolutionary rate and increase biodiversity?.” Plos comput biol 8.3 (2012): e1002414+.
    [Bibtex]
    @article{citeulike:13364252,
    abstract = {Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on {DNA} sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity. The role of sex in driving genetic variation and the speed at which new species emerge has been debated for over a century. There is experimental and theoretical evidence that sex increases genetic variation and the speed at which new species emerge, although evidence that sex reduces variation and slows the formation of new species also exists. Surprisingly, given the link between sex and genetic variation, little work has been done on the impact of sex on biodiversity. In the present theoretical study we show that a faster evolutionary rate can decrease the abundance of newly formed species and thus decrease long-term biodiversity. This leads to the paradoxical result that sexual reproduction can increase genetic variation but reduce species diversity. These results suggest that reducing the rate of appearance of genetic variation and the speed at which new species emerge may increase biodiversity in the long-term. This unexpected link between reproductive mode, the speed of evolution and biodiversity suggests that a high evolutionary rate may not be required to yield a large number of species in natural ecosystems.},
    author = {Meli\'{a}n, Carlos J. and Alonso, David and Allesina, Stefano and Condit, Richard S. and Etienne, Rampal S.},
    citeulike-article-id = {13364252},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1002414},
    day = {8},
    doi = {10.1371/journal.pcbi.1002414},
    journal = {PLoS Comput Biol},
    month = mar,
    number = {3},
    pages = {e1002414+},
    posted-at = {2014-09-16 02:50:44},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1002414},
    volume = {8},
    year = {2012}
    }
  • [DOI] Eklöf, Anna, Matthew R. Helmus, M. Moore, and Stefano Allesina. “Relevance of evolutionary history for food web structure.” Proceedings of the royal society b: biological sciences 279.1733 (2012): 1588-1596.
    [Bibtex]
    @article{citeulike:10034410,
    abstract = {Explaining the structure of ecosystems is one of the great challenges of ecology. Simple models for food web structure aim at disentangling the complexity of ecological interaction networks and detect the main forces that are responsible for their shape. Trophic interactions are influenced by species traits, which in turn are largely determined by evolutionary history. Closely related species are more likely to share similar traits, such as body size, feeding mode and habitat preference than distant ones. Here, we present a theoretical framework for analysing whether evolutionary history—represented by taxonomic classification—provides valuable information on food web structure. In doing so, we measure which taxonomic ranks better explain species interactions. Our analysis is based on partitioning of the species into taxonomic units. For each partition, we compute the likelihood that a probabilistic model for food web structure reproduces the data using this information. We find that taxonomic partitions produce significantly higher likelihoods than expected at random. Marginal likelihoods (Bayes factors) are used to perform model selection among taxonomic ranks. We show that food webs are best explained by the coarser taxonomic ranks (kingdom to class). Our methods provide a way to explicitly include evolutionary history in models for food web structure.},
    author = {Ekl\"{o}f, Anna and Helmus, Matthew R. and Moore, M. and Allesina, Stefano},
    citeulike-article-id = {10034410},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rspb.2011.2149},
    citeulike-linkout-1 = {http://rspb.royalsocietypublishing.org/content/279/1733/1588.abstract},
    citeulike-linkout-2 = {http://rspb.royalsocietypublishing.org/content/279/1733/1588.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/22090387},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=22090387},
    day = {22},
    doi = {10.1098/rspb.2011.2149},
    issn = {1471-2954},
    journal = {Proceedings of the Royal Society B: Biological Sciences},
    month = apr,
    number = {1733},
    pages = {1588--1596},
    pmid = {22090387},
    posted-at = {2014-09-16 02:48:22},
    priority = {2},
    publisher = {The Royal Society},
    title = {Relevance of evolutionary history for food web structure},
    url = {http://dx.doi.org/10.1098/rspb.2011.2149},
    volume = {279},
    year = {2012}
    }
  • [DOI] Lortie, Christopher J., Lonnie Aarssen, John N. Parker, and Stefano Allesina. “Good news for the people who love bad news: an analysis of the funding of the top 1\% most highly cited ecologists.” Oikos 121.7 (2012): 1005-1008.
    [Bibtex]
    @article{citeulike:12345555,
    abstract = {The most highly cited ecologists and environmental scientists provide both a benchmark and unique opportunity to consider the importance of research funding. Here, we use citation data and self-reported funding levels to assess the relative importance of various factors in shaping productivity and potential impact. The elite were senior Americans, well funded, with large labs. In contrast to Canadian {NSERC} grant holders (not in the top 1\%), citations per paper did not increase with higher levels of funding within the ecological elite. We propose that this is good news for several reasons. It suggests that the publications generated by the top ecologists and environmental scientists are subject to limitations, that higher volume of publications is always important, and that increased funding to ecologists in general can shift our discipline to wider research networks. As expected, collaboration was identified as an important factor for the elite, and hopefully, this serves as a positive incentive to funding agencies since it increases the visibility of their research.},
    author = {Lortie, Christopher J. and Aarssen, Lonnie and Parker, John N. and Allesina, Stefano},
    citeulike-article-id = {12345555},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1600-0706.2012.20109.x},
    day = {1},
    doi = {10.1111/j.1600-0706.2012.20109.x},
    issn = {00301299},
    journal = {Oikos},
    month = jul,
    number = {7},
    pages = {1005--1008},
    posted-at = {2014-09-16 02:43:36},
    priority = {2},
    publisher = {Blackwell Publishing Ltd},
    title = {Good news for the people who love bad news: an analysis of the funding of the top 1\% most highly cited ecologists},
    url = {http://dx.doi.org/10.1111/j.1600-0706.2012.20109.x},
    volume = {121},
    year = {2012}
    }
  • Allesina, Stefano. “Modeling peer review: an agent-based approach.” Ideas in ecology and evolution 5.2 (2012).
    [Bibtex]
    @article{citeulike:13364243,
    author = {Allesina, Stefano},
    citeulike-article-id = {13364243},
    citeulike-linkout-0 = {http://library.queensu.ca/ojs/index.php/IEE/article/view/4447},
    issn = {1918-3178},
    journal = {Ideas in Ecology and Evolution},
    number = {2},
    posted-at = {2014-09-16 02:42:42},
    priority = {2},
    title = {Modeling peer review: an agent-based approach},
    url = {http://library.queensu.ca/ojs/index.php/IEE/article/view/4447},
    volume = {5},
    year = {2012}
    }
  • [DOI] Allesina, Stefano and Si Tang. “Stability criteria for complex ecosystems.” Nature 483.7388 (2012): 205-208.
    [Bibtex]
    @article{citeulike:10373270,
    abstract = {Forty years ago, May proved that sufficiently large or complex ecological networks have a probability of persisting that is close to zero, contrary to previous expectations. May analysed large networks in which species interact at random. However, in natural systems pairs of species have well-defined interactions (for example predator\&\#19;prey, mutualistic or competitive). Here we extend May\&\#25;s results to these relationships and find remarkable differences between predator\&\#19;prey interactions, which are stabilizing, and mutualistic and competitive interactions, which are destabilizing. We provide analytic stability criteria for all cases. We use the criteria to prove that, counterintuitively, the probability of stability for predator\&\#19;prey networks decreases when a realistic food web structure is imposed or if there is a large preponderance of weak interactions. Similarly, stability is negatively affected by nestedness in bipartite mutualistic networks. These results are found by separating the contribution of network structure and interaction strengths to stability. Stable predator\&\#19;prey networks can be arbitrarily large and complex, provided that predator\&\#19;prey pairs are tightly coupled. The stability criteria are widely applicable, because they hold for any system of differential equations.},
    author = {Allesina, Stefano and Tang, Si},
    citeulike-article-id = {10373270},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature10832},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature10832},
    day = {19},
    doi = {10.1038/nature10832},
    issn = {0028-0836},
    journal = {Nature},
    month = feb,
    number = {7388},
    pages = {205--208},
    posted-at = {2014-09-16 02:40:57},
    priority = {2},
    publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    title = {Stability criteria for complex ecosystems},
    url = {http://dx.doi.org/10.1038/nature10832},
    volume = {483},
    year = {2012}
    }
  • [DOI] Allesina, Stefano. “Ecology: the more the merrier.” Nature 487.7406 (2012): 175-176.
    [Bibtex]
    @article{citeulike:10877988,
    abstract = {The 'nested' pattern of mutualistic interactions between plants and their pollinators is thought to promote species coexistence. But the key determinant may instead be the number of partners that species have. See Letter p.227},
    author = {Allesina, Stefano},
    citeulike-article-id = {10877988},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/487175a},
    day = {11},
    doi = {10.1038/487175a},
    issn = {0028-0836},
    journal = {Nature},
    month = jul,
    number = {7406},
    pages = {175--176},
    posted-at = {2014-09-16 02:40:41},
    priority = {2},
    publisher = {Nature Publishing Group},
    title = {Ecology: The more the merrier},
    url = {http://dx.doi.org/10.1038/487175a},
    volume = {487},
    year = {2012}
    }
  • [DOI] Acuna, Daniel E., Stefano Allesina, and Konrad P. Kording. “Future impact: predicting scientific success.” Nature 489.7415 (2012): 201-202.
    [Bibtex]
    @article{citeulike:11233918,
    author = {Acuna, Daniel E. and Allesina, Stefano and Kording, Konrad P.},
    citeulike-article-id = {11233918},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/489201a},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/489201a},
    day = {12},
    doi = {10.1038/489201a},
    issn = {0028-0836},
    journal = {Nature},
    month = sep,
    number = {7415},
    pages = {201--202},
    posted-at = {2014-09-16 02:38:55},
    priority = {2},
    publisher = {Nature Research},
    title = {Future impact: Predicting scientific success},
    url = {http://dx.doi.org/10.1038/489201a},
    volume = {489},
    year = {2012}
    }
  • [DOI] Bodini, Antonio, Cristina Bondavalli, and Stefano Allesina. “Cities as ecosystems: growth, development and implications for sustainability.” Ecological modelling 245 (2012): 185-198.
    [Bibtex]
    @article{citeulike:10532807,
    abstract = {Prescriptions for a more sustainable society are usually piecemeal. They are inspired by single issue criteria, no matter if sustainability is, rather, a whole system trait as it pertains to growth and development, that are overall system attributes. In this paper urban sustainability is discussed in a whole system perspective using the ecosystem approach as a framework. This required that urban systems were described as flow networks and investigated through ecological network analysis. Three cities are discussed as a case study and their network representation concerned water flows that were identified knowing water exchanges between city components (i.e. sectors of human activity). Network analysis yielded system level indices that condense the complexity of the flow structure (representing system's metabolism) in a few measures that provide information on how systems grow and develop; as such they allow to explore sustainability at the whole system scale. For every system the present network is compared with an alternative scenario envisioned considering policies that foster sustainability. The results show that although all the alternative scenarios would improve sustainability through reducing water consumption, effects at the whole system level may diverge from the expectation. Because system sustainability depends on the balance between organization of flows (order and coherence of flows) and flexibility (redundancy of connections), network reshaping may bring about a reduction in both these fundamental properties, with negative effects on system's propensity to be sustainable. System level indices are holistic measures that unveil the relation between internal processes and whole system performance. Understanding this relation is crucial because the former are the target of environmental policies but sustainability, the objective of such policies, is an overall system trait. \^{a}–º We explore growth and development of three urban systems as water flow networks. \^{a}–º Sustainability of the whole system is investigated while current approaches to it are piecemeal. \^{a}–º Actions directed to single-issue objectives may fail to foster the sustainability of the whole. \^{a}–º Sustainability depends on the system structure and how it changes upon management actions.},
    author = {Bodini, Antonio and Bondavalli, Cristina and Allesina, Stefano},
    citeulike-article-id = {10532807},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2012.02.022},
    doi = {10.1016/j.ecolmodel.2012.02.022},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = oct,
    pages = {185--198},
    posted-at = {2014-09-16 02:37:42},
    priority = {2},
    title = {Cities as ecosystems: Growth, development and implications for sustainability},
    url = {http://dx.doi.org/10.1016/j.ecolmodel.2012.02.022},
    volume = {245},
    year = {2012}
    }
  • [DOI] Bodini, Antonio, Cristina Bondavalli, and Stefano Allesina. “Cities as ecosystems.” Developments in environmental modelling 25 (2012): 297-318.
    [Bibtex]
    @article{citeulike:13364237,
    author = {Bodini, Antonio and Bondavalli, Cristina and Allesina, Stefano},
    citeulike-article-id = {13364237},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/b978-0-444-59396-2.00018-3},
    doi = {10.1016/b978-0-444-59396-2.00018-3},
    isbn = {9780444593962},
    journal = {Developments in Environmental Modelling},
    pages = {297--318},
    posted-at = {2014-09-16 02:36:44},
    priority = {2},
    publisher = {Elsevier},
    title = {Cities as Ecosystems},
    url = {http://dx.doi.org/10.1016/b978-0-444-59396-2.00018-3},
    volume = {25},
    year = {2012}
    }
  • [DOI] Martín González, Ana M., Stefano Allesina, Anselm Rodrigo, and Jordi Bosch. “Drivers of compartmentalization in a Mediterranean pollination network.” Oikos 121.12 (2012): 2001-2013.
    [Bibtex]
    @article{citeulike:13364232,
    author = {Mart\'{\i}n Gonz\'{a}lez, Ana M. and Allesina, Stefano and Rodrigo, Anselm and Bosch, Jordi},
    citeulike-article-id = {13364232},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1600-0706.2012.20279.x},
    doi = {10.1111/j.1600-0706.2012.20279.x},
    issn = {00301299},
    journal = {Oikos},
    month = dec,
    number = {12},
    pages = {2001--2013},
    posted-at = {2014-09-16 02:33:02},
    priority = {2},
    title = {Drivers of compartmentalization in a {M}editerranean pollination network},
    url = {http://dx.doi.org/10.1111/j.1600-0706.2012.20279.x},
    volume = {121},
    year = {2012}
    }

2011

  • [DOI] Zook, Alexander E., Anna Eklof, Ute Jacob, and Stefano Allesina. “Food webs: ordering species according to body size yields high degree of intervality.” Journal of theoretical biology 271.1 (2011): 106-113.
    [Bibtex]
    @article{citeulike:8417002,
    abstract = {Food webs, the networks describing ” who eats whom” in an ecosystem, are nearly interval, i.e. there is a way to order the species so that almost all the resources of each consumer are adjacent in the ordering. This feature has important consequences, as it means that the structure of food webs can be described using a single (or few) species' traits. Moreover, exploiting the quasi-intervality found in empirical webs can help build better models for food web structure. Here we investigate which species trait is a good proxy for ordering the species to produce quasi-interval orderings. We find that body size produces a significant degree of intervality in almost all food webs analyzed, although it does not match the maximum intervality for the networks. There is also a great variability between webs. Other orderings based on trophic levels produce a lower level of intervality. Finally, we extend the concept of intervality from predator-centered (in which resources are in intervals) to prey-centered (in which consumers are in intervals). In this case as well we find that body size yields a significant, but not maximal, level of intervality. These results show that body size is an important, although not perfect, trait that shapes species interactions in food webs. This has important implications for the formulation of simple models used to construct realistic representations of food webs.},
    author = {Zook, Alexander E. and Eklof, Anna and Jacob, Ute and Allesina, Stefano},
    citeulike-article-id = {8417002},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2010.11.045},
    day = {07},
    doi = {10.1016/j.jtbi.2010.11.045},
    issn = {00225193},
    journal = {Journal of Theoretical Biology},
    month = feb,
    number = {1},
    pages = {106--113},
    posted-at = {2014-09-16 02:59:08},
    priority = {2},
    title = {Food webs: Ordering species according to body size yields high degree of intervality},
    url = {http://dx.doi.org/10.1016/j.jtbi.2010.11.045},
    volume = {271},
    year = {2011}
    }
  • [DOI] Rojas-Echenique, José and Stefano Allesina. “Interaction rules affect species coexistence in intransitive networks.” Ecology 92.5 (2011): 1174-1180.
    [Bibtex]
    @article{citeulike:13364267,
    author = {Rojas-Echenique, Jos\'{e} and Allesina, Stefano},
    citeulike-article-id = {13364267},
    citeulike-linkout-0 = {http://dx.doi.org/10.1890/10-0953.1},
    doi = {10.1890/10-0953.1},
    issn = {0012-9658},
    journal = {Ecology},
    month = may,
    number = {5},
    pages = {1174--1180},
    posted-at = {2014-09-16 02:58:13},
    priority = {2},
    title = {Interaction rules affect species coexistence in intransitive networks},
    url = {http://dx.doi.org/10.1890/10-0953.1},
    volume = {92},
    year = {2011}
    }
  • [DOI] Allesina, Stefano. “Predicting trophic relations in ecological networks: a test of the Allometric Diet Breadth Model.” Journal of theoretical biology 279.1 (2011): 161-168.
    [Bibtex]
    @article{citeulike:7607292,
    abstract = {Few food web theory hypotheses/predictions can be readily tested using likelihoods of reproducing the data. Simple probabilistic models for food web structure, however, are an exception as their likelihoods were recently derived. Here I test the performance of a more complex model for food web structure that is grounded in the allometric scaling of interactions with body size and the theory of optimal foraging (Allometric Diet Breadth {Model—ADBM}). This deterministic model has been evaluated by measuring the fraction of trophic relations it correctly predicts. I contrasted this value with that produced by simpler models based on body sizes and found that the quantitative information on allometric scaling and optimal foraging does not significantly increase model fit. Also, I present a method to compute the p -value for the fraction of trophic interactions correctly predicted by the {ADBM}, or any other model, with respect to three probabilistic models. I find that the {ADBM} predicts significantly more links than random graphs, but other models can outperform it. Although optimal foraging and allometric scaling may improve our understanding of food webs, the {ADBM} needs to be modified or replaced to find support in the data.},
    author = {Allesina, Stefano},
    citeulike-article-id = {7607292},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2010.06.040},
    day = {13},
    doi = {10.1016/j.jtbi.2010.06.040},
    issn = {00225193},
    journal = {Journal of Theoretical Biology},
    month = jun,
    number = {1},
    pages = {161--168},
    posted-at = {2014-09-16 02:57:32},
    priority = {2},
    title = {Predicting trophic relations in ecological networks: A test of the {A}llometric {D}iet {B}readth {M}odel},
    url = {http://dx.doi.org/10.1016/j.jtbi.2010.06.040},
    volume = {279},
    year = {2011}
    }
  • [DOI] Allesina, Stefano and Jonathan M. Levine. “A competitive network theory of species diversity.” Proceedings of the national academy of sciences 108.14 (2011): 5638-5642.
    [Bibtex]
    @article{citeulike:9011646,
    abstract = {Nonhierarchical competition between species has been proposed as a potential mechanism for biodiversity maintenance, but theoretical and empirical research has thus far concentrated on systems composed of relatively few species. Here we develop a theory of biodiversity based on a network representation of competition for systems with large numbers of competitors. All species pairs are connected by an arrow from the inferior to the superior. Using game theory, we show how the equilibrium density of all species can be derived from the structure of the network. We show that when species are limited by multiple factors, the coexistence of a large number of species is the most probable outcome and that habitat heterogeneity interacts with network structure to favor diversity.},
    author = {Allesina, Stefano and Levine, Jonathan M.},
    citeulike-article-id = {9011646},
    citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1014428108},
    citeulike-linkout-1 = {http://www.pnas.org/content/early/2011/03/14/1014428108.abstract},
    citeulike-linkout-2 = {http://www.pnas.org/content/early/2011/03/14/1014428108.full.pdf},
    citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/108/14/5638},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/21415368},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=21415368},
    day = {05},
    doi = {10.1073/pnas.1014428108},
    issn = {1091-6490},
    journal = {Proceedings of the National Academy of Sciences},
    month = apr,
    number = {14},
    pages = {5638--5642},
    pmid = {21415368},
    posted-at = {2014-09-16 02:56:22},
    priority = {2},
    publisher = {National Academy of Sciences},
    title = {A competitive network theory of species diversity},
    url = {http://dx.doi.org/10.1073/pnas.1014428108},
    volume = {108},
    year = {2011}
    }
  • [DOI] Allesina, Stefano and Jonathan M. Levine. “Reply to Ferrarini: strengths and weaknesses of simple competition models.” Proceedings of the national academy of sciences 108.31 (2011): E346.
    [Bibtex]
    @article{citeulike:13364264,
    author = {Allesina, Stefano and Levine, Jonathan M.},
    citeulike-article-id = {13364264},
    citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.1108946108},
    citeulike-linkout-1 = {http://www.pnas.org/content/108/31/E346.full.abstract},
    citeulike-linkout-2 = {http://www.pnas.org/content/108/31/E346.full.full.pdf},
    day = {02},
    doi = {10.1073/pnas.1108946108},
    issn = {1091-6490},
    journal = {Proceedings of the National Academy of Sciences},
    month = aug,
    number = {31},
    pages = {E346},
    posted-at = {2014-09-16 02:55:46},
    priority = {2},
    publisher = {National Academy of Sciences},
    title = {Reply to {F}errarini: Strengths and weaknesses of simple competition models},
    url = {http://dx.doi.org/10.1073/pnas.1108946108},
    volume = {108},
    year = {2011}
    }
  • [DOI] Allesina, Stefano. “Measuring nepotism through shared last names: the case of Italian academia.” Plos one 6.8 (2011): e21160+.
    [Bibtex]
    @article{citeulike:9608197,
    abstract = {Nepotistic practices are detrimental for academia. Here I show how disciplines with a high likelihood of nepotism can be detected using standard statistical techniques based on shared last names among professors. As an example, I analyze the set of all 61,340 Italian academics. I find that nepotism is prominent in Italy, with particular disciplinary sectors being detected as especially problematic. Out of 28 disciplines, 9 – accounting for more than half of Italian professors – display a significant paucity of last names. Moreover, in most disciplines a clear north-south trend emerges, with likelihood of nepotism increasing with latitude. Even accounting for the geographic clustering of last names, I find that for many disciplines the probability of name-sharing is boosted when professors work in the same institution or sub-discipline. Using these techniques policy makers can target cuts and funding in order to promote fair practices.},
    author = {Allesina, Stefano},
    citeulike-article-id = {9608197},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0021160},
    citeulike-linkout-1 = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149595/},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21826195},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21826195},
    day = {3},
    doi = {10.1371/journal.pone.0021160},
    issn = {1932-6203},
    journal = {PLoS ONE},
    month = aug,
    number = {8},
    pages = {e21160+},
    pmcid = {PMC3149595},
    pmid = {21826195},
    posted-at = {2014-09-16 02:52:05},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Measuring Nepotism through Shared Last Names: The Case of {I}talian Academia},
    url = {http://dx.doi.org/10.1371/journal.pone.0021160},
    volume = {6},
    year = {2011}
    }
  • [DOI] Baskerville, Edward B., Andy P. Dobson, Trevor Bedford, Stefano Allesina, Michael T. Anderson, and Mercedes Pascual. “Spatial guilds in the Serengeti food web revealed by a Bayesian group model.” Plos comput biol 7.12 (2011): e1002321+.
    [Bibtex]
    @article{citeulike:13364254,
    abstract = {Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts. The relationships among organisms in an ecosystem can be described by a food web, a network representing who eats whom. Food web organization has important consequences for how populations change over time, how one species extinction can cause others, and how robustly ecosystems respond to disturbances. We present a computational method to analyze how species are organized into groups based on their interactions. We apply this method to the plant and mammal food web from the Serengeti savanna ecosystem in Tanzania, a pristine ecosystem increasingly threatened by human impacts. This web is unusually detailed, with plants identified down to individual species and corresponding habitats. Our analysis, which differs from the compartmental studies typically done in food webs, reveals that functionally distinct groups of carnivores, herbivores, and plants make up the Serengeti web, and that plant groups reflect distinct habitat types. Furthermore, since herbivore groups feed across multiple plant groups, and carnivore groups feed across multiple herbivore groups, energy represents a wider range of habitats as it flows up the web. This pattern may partly explain how the ecosystem remains in balance. Additionally, our method can be easily applied to other kinds of networks and modified to find other patterns.},
    author = {Baskerville, Edward B. and Dobson, Andy P. and Bedford, Trevor and Allesina, Stefano and Anderson, T. Michael and Pascual, Mercedes},
    citeulike-article-id = {13364254},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1002321},
    day = {29},
    doi = {10.1371/journal.pcbi.1002321},
    journal = {PLoS Comput Biol},
    month = dec,
    number = {12},
    pages = {e1002321+},
    posted-at = {2014-09-16 02:51:16},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Spatial Guilds in the {S}erengeti Food Web Revealed by a {B}ayesian Group Model},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1002321},
    volume = {7},
    year = {2011}
    }

2010

  • [DOI] Parker, JohnN, Christopher Lortie, and Stefano Allesina. “Characterizing a scientific elite: the social characteristics of the most highly cited scientists in environmental science and ecology.” Scientometrics 85.1 (2010): 129-143.
    [Bibtex]
    @article{citeulike:7162621,
    abstract = {In science, a relatively small pool of researchers garners a disproportionally large number of citations. Still, very little is known about the social characteristics of highly cited scientists. This is unfortunate as these researchers wield a disproportional impact on their fields, and the study of highly cited scientists can enhance our understanding of the conditions which foster highly cited work, the systematic social inequalities which exist in science, and scientific careers more generally. This study provides information on this understudied subject by examining the social characteristics and opinions of the 0.1\% most cited environmental scientists and ecologists. Overall, the social characteristics of these researchers tend to reflect broader patterns of inequality in the global scientific community. However, while the social characteristics of these researchers mirror those of other scientific elites in important ways, they differ in others, revealing findings which are both novel and surprising, perhaps indicating multiple pathways to becoming highly cited.},
    author = {Parker, JohnN and Lortie, Christopher and Allesina, Stefano},
    booktitle = {Scientometrics},
    citeulike-article-id = {7162621},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/s11192-010-0234-4},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/20927183},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=20927183},
    citeulike-linkout-3 = {http://www.springerlink.com/content/j5205442788316v6},
    citeulike-linkout-4 = {http://link.springer.com/article/10.1007/s11192-010-0234-4},
    day = {1},
    doi = {10.1007/s11192-010-0234-4},
    issn = {0138-9130},
    journal = {Scientometrics},
    month = oct,
    number = {1},
    pages = {129--143},
    pmid = {20927183},
    posted-at = {2014-09-16 03:00:49},
    priority = {2},
    publisher = {Springer Netherlands},
    title = {Characterizing a scientific elite: the social characteristics of the most highly cited scientists in environmental science and ecology},
    url = {http://dx.doi.org/10.1007/s11192-010-0234-4},
    volume = {85},
    year = {2010}
    }
  • [DOI] Melián, Carlos J., David Alonso, Diego P. Vázquez, James Regetz, and Stefano Allesina. “Frequency-Dependent selection predicts patterns of radiations and biodiversity.” Plos comput biol 6.8 (2010): e1000892+.
    [Bibtex]
    @article{citeulike:7719772,
    abstract = {Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and {DNA} sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches. Ecological opportunity, or filling a pre-existing unoccupied adaptive zone, is considered the dominant mechanism explaining the initial explosion of diversity. Although this type of niche filling can explain rates of diversification in some lineages, it is not sufficient for a radiation to occur. Instead of attributing the propensity to have an explosion of new species to external influences like niche availability, an alternative hypothesis can be based in frequency-dependent selection driven by the ecology in which organisms are embedded or endogenous sources mediated by gametes during fertilization. We show that genome diversification driven by higher reproductive probability of rare genotypes generates rapid initial speciation followed by a plateau with very low speciation rates, as shown by most empirical data. The absence of advantage of rare genotypes generates speciation events at constant rates. We predict decline over time and constant speciation rate in the cichlids and Darwin's finches, respectively, thus providing an alternative hypothesis for the origin of radiations and biodiversity in the absence of pre-existing niche filling. In addition to predicting observed temporal trends in diversification, our analysis also highlights new mechanistic models of evolutionary biodiversity dynamics that may become suitable to generate neutral models for testing observed patterns in speciation rates and species diversity.},
    author = {Meli\'{a}n, Carlos J. and Alonso, David and V\'{a}zquez, Diego P. and Regetz, James and Allesina, Stefano},
    citeulike-article-id = {7719772},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000892},
    day = {26},
    doi = {10.1371/journal.pcbi.1000892},
    journal = {PLoS Comput Biol},
    month = aug,
    number = {8},
    pages = {e1000892+},
    posted-at = {2014-09-16 02:59:50},
    priority = {2},
    publisher = {Public Library of Science},
    title = {{Frequency-Dependent} Selection Predicts Patterns of Radiations and Biodiversity},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000892},
    volume = {6},
    year = {2010}
    }

2009

  • [DOI] Allesina, Stefano. “Learning R the practical way — book review.” Ecology 90.8 (2009): 2333-2337.
    [Bibtex]
    @article{citeulike:13364268,
    author = {Allesina, Stefano},
    citeulike-article-id = {13364268},
    citeulike-linkout-0 = {http://dx.doi.org/10.1890/br09-36.1},
    doi = {10.1890/br09-36.1},
    issn = {0012-9658},
    journal = {Ecology},
    month = aug,
    number = {8},
    pages = {2333--2337},
    posted-at = {2014-09-16 03:08:09},
    priority = {2},
    title = {Learning {R} the Practical Way -- Book Review},
    url = {http://dx.doi.org/10.1890/br09-36.1},
    volume = {90},
    year = {2009}
    }
  • [DOI] Bodini, Antonio, Michele Bellingeri, Stefano Allesina, and Cristina Bondavalli. “Using food web dominator trees to catch secondary extinctions in action.” Philosophical transactions of the royal society b: biological sciences 364.1524 (2009): 1725-1731.
    [Bibtex]
    @article{citeulike:4537912,
    abstract = {In ecosystems, a single extinction event can give rise to multiple 'secondary' extinctions. Conservation effort would benefit from tools that help forecast the consequences of species removal. One such tool is the dominator tree, a graph-theoretic algorithm that when applied to food webs unfolds their complex architecture, yielding a simpler topology made of linear pathways that are essential for energy delivery. Each species along these chains is responsible for passing energy to the taxa that follow it and, as such, it is indispensable for their survival. To assess the predictive potential of the dominator tree, we compare its predictions with the effects that followed the collapse of the capelin (Mallotus villosus) in the Barents Sea ecosystem. To this end, we first compiled a food web for this ecosystem, then we built the corresponding dominator tree and, finally, we observed whether model predictions matched the empirical observations. This analysis shows the potential and the drawbacks of the dominator trees as a tool for understanding the causes and consequences of extinctions in food webs.},
    author = {Bodini, Antonio and Bellingeri, Michele and Allesina, Stefano and Bondavalli, Cristina},
    citeulike-article-id = {4537912},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rstb.2008.0278},
    citeulike-linkout-1 = {http://rstb.royalsocietypublishing.org/content/364/1524/1725?rss=1.abstract},
    citeulike-linkout-2 = {http://rstb.royalsocietypublishing.org/content/364/1524/1725?rss=1.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19451123},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19451123},
    day = {27},
    doi = {10.1098/rstb.2008.0278},
    issn = {1471-2970},
    journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
    month = jun,
    number = {1524},
    pages = {1725--1731},
    pmid = {19451123},
    posted-at = {2014-09-16 03:05:35},
    priority = {2},
    publisher = {The Royal Society},
    title = {Using food web dominator trees to catch secondary extinctions in action},
    url = {http://dx.doi.org/10.1098/rstb.2008.0278},
    volume = {364},
    year = {2009}
    }
  • [DOI] Dobson, Andy, Stefano Allesina, Kevin Lafferty, and Mercedes Pascual. “The assembly, collapse and restoration of food webs.” Philosophical transactions of the royal society b: biological sciences 364.1524 (2009): 1803-1806.
    [Bibtex]
    @article{citeulike:4537904,
    abstract = {10.1098/rstb.2009.0002},
    author = {Dobson, Andy and Allesina, Stefano and Lafferty, Kevin and Pascual, Mercedes},
    citeulike-article-id = {4537904},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rstb.2009.0002},
    citeulike-linkout-1 = {http://rstb.royalsocietypublishing.org/content/364/1524/1803?rss=1.abstract},
    citeulike-linkout-2 = {http://rstb.royalsocietypublishing.org/content/364/1524/1803?rss=1.full.pdf},
    citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19451129},
    citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19451129},
    day = {27},
    doi = {10.1098/rstb.2009.0002},
    issn = {1471-2970},
    journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
    month = jun,
    number = {1524},
    pages = {1803--1806},
    pmid = {19451129},
    posted-at = {2014-09-16 03:04:33},
    priority = {2},
    publisher = {The Royal Society},
    title = {The assembly, collapse and restoration of food webs},
    url = {http://dx.doi.org/10.1098/rstb.2009.0002},
    volume = {364},
    year = {2009}
    }
  • [DOI] Allesina, Stefano, Antonio Bodini, and Mercedes Pascual. “Functional links and robustness in food webs.” Philosophical transactions of the royal society b: biological sciences 364.1524 (2009): 1701-1709.
    [Bibtex]
    @article{citeulike:4537915,
    abstract = {The robustness of ecosystems to species losses is a central question in ecology, given the current pace of extinctions and the many species threatened by human impacts, including habitat destruction and climate change. Robustness from the perspective of secondary extinctions has been addressed in the context of food webs to consider the complex network of species interactions that underlie responses to perturbations. In-silico removal experiments have examined the structural properties of food webs that enhance or hamper the robustness of ecosystems to species losses, with a focus on the role of hubs, the most connected species. Here we take a different approach and focus on the role of the connections themselves. We show that trophic links can be divided into functional and redundant based on their contribution to robustness. The analysis of empirical webs shows that hubs are not necessarily the most important species as they may hold many redundant links. Furthermore, the fraction of functional connections is high and constant across systems regardless of size and interconnectedness. The main consequence of this scaling pattern is that ecosystem robustness can be considerably reduced by species extinctions even when these do not result in any secondary extinctions. This introduces the possibility of tipping points in the collapse of ecosystems.},
    author = {Allesina, Stefano and Bodini, Antonio and Pascual, Mercedes},
    citeulike-article-id = {4537915},
    citeulike-linkout-0 = {http://dx.doi.org/10.1098/rstb.2008.0214},
    citeulike-linkout-1 = {http://rstb.royalsocietypublishing.org/content/364/1524/1701?rss=1.abstract},
    citeulike-linkout-2 = {http://rstb.royalsocietypublishing.org/content/364/1524/1701?rss=1.full.pdf},
    citeulike-linkout-3 = {http://rstb.royalsocietypublishing.org/cgi/content/abstract/364/1524/1701},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19451121},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19451121},
    day = {27},
    doi = {10.1098/rstb.2008.0214},
    issn = {1471-2970},
    journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
    month = jun,
    number = {1524},
    pages = {1701--1709},
    pmid = {19451121},
    posted-at = {2014-09-16 03:03:45},
    priority = {2},
    publisher = {The Royal Society},
    title = {Functional links and robustness in food webs},
    url = {http://dx.doi.org/10.1098/rstb.2008.0214},
    volume = {364},
    year = {2009}
    }
  • [DOI] Allesina, Stefano and Mercedes Pascual. “Food web models: a plea for groups.” Ecology letters 12.7 (2009): 652-662.
    [Bibtex]
    @article{citeulike:4472117,
    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.},
    address = {National Center for Ecological Analysis and Synthesis, 735 State St., Suite 300. Santa Barbara, CA 93101, USA; Department of Ecology and Evolutionary Biology, and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 481091048, USA},
    author = {Allesina, Stefano and Pascual, Mercedes},
    citeulike-article-id = {4472117},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1461-0248.2009.01321.x},
    citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122374239/ABSTRACT},
    doi = {10.1111/j.1461-0248.2009.01321.x},
    issn = {1461023X},
    journal = {Ecology Letters},
    month = jul,
    number = {7},
    pages = {652--662},
    posted-at = {2014-09-16 03:03:02},
    priority = {2},
    publisher = {Blackwell Publishing Ltd},
    title = {Food web models: a plea for groups},
    url = {http://dx.doi.org/10.1111/j.1461-0248.2009.01321.x},
    volume = {12},
    year = {2009}
    }
  • [DOI] Allesina, Stefano and Mercedes Pascual. “Googling food webs: can an eigenvector measure species’ importance for coextinctions?.” Plos comput biol 5.9 (2009): e1000494+.
    [Bibtex]
    @article{citeulike:5725961,
    abstract = {A major challenge in ecology is forecasting the effects of species' extinctions, a pressing problem given current human impacts on the planet. Consequences of species losses such as secondary extinctions are difficult to forecast because species are not isolated, but interact instead in a complex network of ecological relationships. Because of their mutual dependence, the loss of a single species can cascade in multiple coextinctions. Here we show that an algorithm adapted from the one Google uses to rank web-pages can order species according to their importance for coextinctions, providing the sequence of losses that results in the fastest collapse of the network. Moreover, we use the algorithm to bridge the gap between qualitative (who eats whom) and quantitative (at what rate) descriptions of food webs. We show that our simple algorithm finds the best possible solution for the problem of assigning importance from the perspective of secondary extinctions in all analyzed networks. Our approach relies on network structure, but applies regardless of the specific dynamical model of species' interactions, because it identifies the subset of coextinctions common to all possible models, those that will happen with certainty given the complete loss of prey of a given predator. Results show that previous measures of importance based on the concept of ” hubs” or number of connections, as well as centrality measures, do not identify the most effective extinction sequence. The proposed algorithm provides a basis for further developments in the analysis of extinction risk in ecosystems. Predicting the consequences of species' extinction is a crucial problem in ecology. Species are not isolated, but connected to each others in tangled networks of relationships known as food webs. In this work we want to determine which species are critical as they support many other species. The fact that species are not independent, however, makes the problem difficult to solve. Moreover, the number of possible ” importance'” rankings for species is too high to allow a solution by enumeration. Here we take a ” reverse engineering” approach: we study how we can make biodiversity collapse in the most efficient way in order to investigate which species cause the most damage if removed. We show that adapting the algorithm Google uses for ranking web pages always solves this seemingly intractable problem, finding the most efficient route to collapse. The algorithm works in this sense better than all the others previously proposed and lays the foundation for a complete analysis of extinction risk in ecosystems.},
    author = {Allesina, Stefano and Pascual, Mercedes},
    citeulike-article-id = {5725961},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000494},
    day = {4},
    doi = {10.1371/journal.pcbi.1000494},
    journal = {PLoS Comput Biol},
    month = sep,
    number = {9},
    pages = {e1000494+},
    posted-at = {2014-09-16 03:02:40},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?},
    url = {http://dx.doi.org/10.1371/journal.pcbi.1000494},
    volume = {5},
    year = {2009}
    }
  • [DOI] Scotti, Marco, Cristina Bondavalli, Antonio Bodini, and Stefano Allesina. “Using trophic hierarchy to understand food web structure.” Oikos 118.11 (2009): 1695-1702.
    [Bibtex]
    @article{citeulike:6038618,
    author = {Scotti, Marco and Bondavalli, Cristina and Bodini, Antonio and Allesina, Stefano},
    citeulike-article-id = {6038618},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1600-0706.2009.17073.x},
    citeulike-linkout-1 = {http://www.ingentaconnect.com/content/mksg/oki/2009/00000118/00000011/art00011},
    doi = {10.1111/j.1600-0706.2009.17073.x},
    issn = {00301299},
    journal = {Oikos},
    month = nov,
    number = {11},
    pages = {1695--1702},
    posted-at = {2014-09-16 03:02:00},
    priority = {2},
    publisher = {Blackwell Publishing},
    title = {Using trophic hierarchy to understand food web structure},
    url = {http://dx.doi.org/10.1111/j.1600-0706.2009.17073.x},
    volume = {118},
    year = {2009}
    }
  • [DOI] Allesina, S., A. Azzi, D. Battini, and A. Regattieri. “Performance measurement in supply chains: new network analysis and entropic indexes.” International journal of production research 48.8 (2009): 2297-2321.
    [Bibtex]
    @article{citeulike:6569142,
    abstract = {Industrial organisations must supply a variety of products and services, meet the needs of fragmented customer expectations, and cope with the consequences of the globalisation of world markets, all of which are producing significant levels of complexity. This study develops a new quantitative measurement of complexity for a supply network based on network analysis, which is often used to study natural ecosystems, focusing in particular on the concept of entropy of information. The research reports advances in both theory on the supply network analysis problem and on its application to industrial contexts. Eight indexes based on entropy are presented. These measures provide a meaningful analysis of the level of complexity in the whole supply network mapping the exchanges of goods between the different actors in the network. The impact of possible modifications of the structure can simply be evaluated using these tools, providing a simple evaluation of the different scenarios. The proposed method takes a holistic point of view to tackle the problem of supply network optimisation. A real world application of the developed new methodology is presented.},
    author = {Allesina, S. and Azzi, A. and Battini, D. and Regattieri, A.},
    citeulike-article-id = {6569142},
    citeulike-linkout-0 = {http://dx.doi.org/10.1080/00207540802647327},
    citeulike-linkout-1 = {http://www.tandfonline.com/doi/abs/10.1080/00207540802647327},
    day = {22},
    doi = {10.1080/00207540802647327},
    journal = {International Journal of Production Research},
    month = apr,
    number = {8},
    pages = {2297--2321},
    posted-at = {2014-09-16 03:01:23},
    priority = {2},
    publisher = {Taylor \& Francis},
    title = {Performance measurement in supply chains: new network analysis and entropic indexes},
    url = {http://dx.doi.org/10.1080/00207540802647327},
    volume = {48},
    year = {2009}
    }

2008

  • [DOI] Allesina, Stefano and Mercedes Pascual. “Network structure, predator–prey modules, and stability in large food webs.” Theoretical ecology 1.1 (2008): 55-64.
    [Bibtex]
    @article{citeulike:2638499,
    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.},
    author = {Allesina, Stefano and Pascual, Mercedes},
    booktitle = {Theoretical Ecology},
    citeulike-article-id = {2638499},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/s12080-007-0007-8},
    citeulike-linkout-1 = {http://www.springerlink.com/content/h356l05184436095},
    citeulike-linkout-2 = {http://link.springer.com/article/10.1007/s12080-007-0007-8},
    day = {1},
    doi = {10.1007/s12080-007-0007-8},
    issn = {1874-1738},
    journal = {Theoretical Ecology},
    month = mar,
    number = {1},
    pages = {55--64},
    posted-at = {2014-09-16 03:11:17},
    priority = {2},
    publisher = {Springer Netherlands},
    title = {Network structure, predator–prey modules, and stability in large food webs},
    url = {http://dx.doi.org/10.1007/s12080-007-0007-8},
    volume = {1},
    year = {2008}
    }
  • [DOI] Allesina, Stefano, David Alonso, and Mercedes Pascual. “A general model for food web structure.” Science 320.5876 (2008): 658-661.
    [Bibtex]
    @article{citeulike:2746787,
    abstract = {A central problem in ecology is determining the processes that shape the complex networks known as food webs formed by species and their feeding relationships. The topology of these networks is a major determinant of ecosystems' dynamics and is ultimately responsible for their responses to human impacts. Several simple models have been proposed for the intricate food webs observed in nature. We show that the three main models proposed so far fail to fully replicate the empirical data, and we develop a likelihood-based approach for the direct comparison of alternative models based on the full structure of the network. Results drive a new model that is able to generate all the empirical data sets and to do so with the highest likelihood.},
    author = {Allesina, Stefano and Alonso, David and Pascual, Mercedes},
    citeulike-article-id = {2746787},
    citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1156269},
    citeulike-linkout-1 = {http://www.sciencemag.org/content/320/5876/658.abstract},
    citeulike-linkout-2 = {http://www.sciencemag.org/content/320/5876/658.full.pdf},
    citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/320/5876/658},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18451301},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18451301},
    day = {02},
    doi = {10.1126/science.1156269},
    issn = {1095-9203},
    journal = {Science},
    month = may,
    number = {5876},
    pages = {658--661},
    pmid = {18451301},
    posted-at = {2014-09-16 03:10:27},
    priority = {2},
    publisher = {American Association for the Advancement of Science},
    title = {A General Model for Food Web Structure},
    url = {http://dx.doi.org/10.1126/science.1156269},
    volume = {320},
    year = {2008}
    }
  • [DOI] Lafferty, Kevin D., Stefano Allesina, Matias Arim, Cherie J. Briggs, Giulio De Leo, Andrew P. Dobson, Jennifer A. Dunne, Pieter T. J. Johnson, Armand M. Kuris, David J. Marcogliese, Neo D. Martinez, Jane Memmott, Pablo A. Marquet, John P. McLaughlin, Erin A. Mordecai, Mercedes Pascual, Robert Poulin, and David W. Thieltges. “Parasites in food webs: the ultimate missing links.” Ecology letters 11.6 (2008): 533-546.
    [Bibtex]
    @article{citeulike:2769066,
    author = {Lafferty, Kevin D. and Allesina, Stefano and Arim, Matias and Briggs, Cherie J. and De Leo, Giulio and Dobson, Andrew P. and Dunne, Jennifer A. and Johnson, Pieter T. J. and Kuris, Armand M. and Marcogliese, David J. and Martinez, Neo D. and Memmott, Jane and Marquet, Pablo A. and McLaughlin, John P. and Mordecai, Erin A. and Pascual, Mercedes and Poulin, Robert and Thieltges, David W.},
    citeulike-article-id = {2769066},
    citeulike-linkout-0 = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1461-0248.2008.01174.x},
    citeulike-linkout-1 = {http://dx.doi.org/10.1111/j.1461-0248.2008.01174.x},
    citeulike-linkout-2 = {http://www.ingentaconnect.com/content/bsc/ele/2008/00000011/00000006/art00001},
    doi = {10.1111/j.1461-0248.2008.01174.x},
    issn = {1461023X},
    journal = {Ecology Letters},
    month = jun,
    number = {6},
    pages = {533--546},
    posted-at = {2014-09-16 03:09:40},
    priority = {2},
    publisher = {Blackwell Publishing},
    title = {Parasites in food webs: the ultimate missing links},
    url = {http://dx.doi.org/10.1111/j.1461-0248.2008.01174.x},
    volume = {11},
    year = {2008}
    }

2007

  • [DOI] Peacor, Scott D., Stefano Allesina, Rick L. Riolo, and Tim S. Hunter. “A new computational system, DOVE (Digital Organisms in a Virtual Ecosystem), to study phenotypic plasticity and its effects in food webs.” Ecological modelling 205.1-2 (2007): 13-28.
    [Bibtex]
    @article{citeulike:2810301,
    abstract = {Food webs are abstract models that represent who eats whom relationships in ecosystems. Classical food web representations do not typically include phenotypic plasticity, in which one species responds to changes in density of other species by modifying traits such as behavior and morphology. Such changes, which are presumably adaptive, will affect the magnitude of both direct and indirect effects on species fitness. Empirical evidence suggests that phenotypic plasticity is likely to have large impacts on the structure and dynamics of ecological communities. Whereas theoretical studies support this, there is much that we do not understand that may require new theoretical approaches. We have constructed a computational system, Digital Organisms in a Virtual Ecosystem ({DOVE}), to address this problem. Its features include an individual-based approach, in which a type of genetic algorithm is used to evolve animal behavior in a dynamic environment. Here we present an overview of the ecological problems motivating the creation of {DOVE} and its basic structure and operation. We also discuss the kinds of decisions and tradeoffs that were considered to make {DOVE} as simple as possible but still rich enough to allow us to address our fundamental questions. We then use {DOVE} to examine optimal foraging strategies of prey in the presence of fluctuating predator risk, and show that activity levels are highly dependent on competitor density in a manner that would be difficult or impossible to explore with traditional techniques. This, and other pilot studies of {DOVE}, suggests that it can be used to gain insight into the origin and consequences of phenotypic plasticity and other properties of ecological communities.},
    author = {Peacor, Scott D. and Allesina, Stefano and Riolo, Rick L. and Hunter, Tim S.},
    citeulike-article-id = {2810301},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2007.01.026},
    citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6VBS-4NK47C0-1/1/d9cc2363037af254cafc3799e93108fd},
    day = {10},
    doi = {10.1016/j.ecolmodel.2007.01.026},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = jul,
    number = {1-2},
    pages = {13--28},
    posted-at = {2014-09-16 03:12:09},
    priority = {2},
    title = {A new computational system, {DOVE} ({D}igital {O}rganisms in a {V}irtual {E}cosystem), to study phenotypic plasticity and its effects in food webs},
    url = {http://dx.doi.org/10.1016/j.ecolmodel.2007.01.026},
    volume = {205},
    year = {2007}
    }

2006

  • [DOI] Allesina, Stefano, Antonio Bodini, and Cristina Bondavalli. “Secondary extinctions in ecological networks: bottlenecks unveiled.” Ecological modelling 194.1-3 (2006): 150-161.
    [Bibtex]
    @article{citeulike:530910,
    abstract = {In ecosystems, a single extinction event could eventually precipitate in a mass extinction, involving species that may be several connections away from the target of the perturbation. This topic has been illuminated by recent studies on network mechanics, thanks to the concepts of hub, error and targeted removal, attack sensitivity, small world, and so forth. To forecast the effects of a species removal one can use an algorithm that unfolds a complex food web into a topologically simpler scheme, called its dominator tree. This structure is simple, elegant, and highly informative; all the bottlenecks and the effects of species removal are clearly {traceable.While} food web studies are mostly qualitative, in this paper the use of the dominator tree is extended to weighted food webs, in which link magnitude is specified. These structures were obtained from ecological flow networks. In eight of these food webs, the analysis consisted in removing links that were weaker than a threshold of magnitude and building the dominator tree associated to the remaining structure. By progressively increasing the threshold up to the value that would make the graph disconnected, we had the opportunity to investigate patterns of dominance as a function of link magnitude.},
    author = {Allesina, Stefano and Bodini, Antonio and Bondavalli, Cristina},
    booktitle = {Special Issue on the Fourth European Conference on Ecological Modelling - Selected Papers from the Fourth European Conference on Ecological Modelling, September 27 - October 1, 2004, Bled, Slovenia},
    citeulike-article-id = {530910},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2005.10.016},
    citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6VBS-4HNYMSD-6/2/bf3388a52e4e889fcbc8df9375c5a3e7},
    day = {25},
    doi = {10.1016/j.ecolmodel.2005.10.016},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = mar,
    number = {1-3},
    pages = {150--161},
    posted-at = {2014-09-16 03:15:31},
    priority = {2},
    title = {Secondary extinctions in ecological networks: Bottlenecks unveiled},
    url = {http://dx.doi.org/10.1016/j.ecolmodel.2005.10.016},
    volume = {194},
    year = {2006}
    }
  • [DOI] Bondavalli, Cristina, Antonio Bodini, Giampaolo Rossetti, and Stefano Allesina. “Detecting stress at the whole-ecosystem level: the case of a mountain lake (Lake Santo, Italy).” Ecosystems 9.5 (2006): 768-787.
    [Bibtex]
    @article{citeulike:898326,
    abstract = {Detecting the early signs of stress is imperative for the conservation of natural ecosystems. They may, however, go unrecognized because ecosystems, when disturbed, may act as sinks that absorb the external impact without showing any evident changes. This seems to be the case for Lake Santo, a small water body located in a mountainous area of northern Italy. Tourism activity in this area began to develop in the early 1970s and grew continuously over the following 20 years. This activity caused a continually increasing nutrient load into the waters, but surprisingly the lake has remained oligo-mesotrophic, as it was before human pressure became a stressor to the lake. To anticipate possible severe damage to the ecosystem, we searched for early signs of stress by carrying out a retrospective analysis based on a whole-ecosystem approach using trophic flow networks. Ecosystem properties of the lake as calculated from network analysis for the disturbed (year 1991) and unimpacted (year 1973) configurations were compared, with the support of sensitivity analysis and statistical tests. We found evidence that in the period 1970–90 nutrient enrichment did change the course of normal development as the observed increase in system throughput was accompanied by a drop in the level of mutual organization of flows, which instead would be expected to increase during the natural progression of the ecosystem. The scenario that emerged from the comparison of system-level indices, cycling activity, trophic structure, and trophic efficiency indicates that the ecosystem has been subjected to stress. In particular, the type of disturbance corresponds to a quantitative definition of eutrophication.},
    author = {Bondavalli, Cristina and Bodini, Antonio and Rossetti, Giampaolo and Allesina, Stefano},
    booktitle = {Ecosystems},
    citeulike-article-id = {898326},
    citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10021-005-0065-y},
    citeulike-linkout-1 = {http://link.springer.com/article/10.1007/s10021-005-0065-y},
    day = {28},
    doi = {10.1007/s10021-005-0065-y},
    journal = {Ecosystems},
    number = {5},
    pages = {768--787},
    posted-at = {2014-09-16 03:14:36},
    priority = {2},
    publisher = {Springer-Verlag},
    title = {Detecting Stress at the Whole-Ecosystem Level: The Case of a Mountain Lake ({L}ake {S}anto, {I}taly)},
    url = {http://dx.doi.org/10.1007/s10021-005-0065-y},
    volume = {9},
    year = {2006}
    }
  • [DOI] Scotti, Marco, Stefano Allesina, Cristina Bondavalli, Antonio Bodini, and Luis G. Abarca-Arenas. “Effective trophic positions in ecological acyclic networks.” Ecological modelling 198.3-4 (2006): 495-505.
    [Bibtex]
    @article{citeulike:13364269,
    author = {Scotti, Marco and Allesina, Stefano and Bondavalli, Cristina and Bodini, Antonio and Abarca-Arenas, Luis G.},
    citeulike-article-id = {13364269},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2006.06.005},
    doi = {10.1016/j.ecolmodel.2006.06.005},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = oct,
    number = {3-4},
    pages = {495--505},
    posted-at = {2014-09-16 03:14:06},
    priority = {2},
    title = {Effective trophic positions in ecological acyclic networks},
    url = {http://dx.doi.org/10.1016/j.ecolmodel.2006.06.005},
    volume = {198},
    year = {2006}
    }
  • [DOI] Peacor, Scott D., Stefano Allesina, Rick L. Riolo, and Mercedes Pascual. “Phenotypic plasticity opposes species invasions by altering fitness surface.” Plos biol 4.11 (2006): e372+.
    [Bibtex]
    @article{citeulike:2807829,
    abstract = {Understanding species invasion is a central problem in ecology because invasions of exotic species severely impact ecosystems, and because invasions underlie fundamental ecological processes. However, the influence on invasions of phenotypic plasticity, a key component of many species interactions, is unknown. We present a model in which phenotypic plasticity of a resident species increases its ability to oppose invaders, and plasticity of an invader increases its ability to displace residents. Whereas these effects are expected due to increased fitness associated with phenotypic plasticity, the model additionally reveals a new and unforeseen mechanism by which plasticity affects invasions: phenotypic plasticity increases the steepness of the fitness surface, thereby making invasion more difficult, even by phenotypically plastic invaders. Our results should apply to phenotypically plastic responses to any fluctuating environmental factors including predation risk, and to other factors that affect the fitness surface such as the generalism of predators. We extend the results to competition, and argue that phenotypic plasticity's effect on the fitness surface will destabilize coexistence at local scales, but stabilize coexistence at regional scales. Our study emphasizes the need to incorporate variable interaction strengths due to phenotypic plasticity into invasion biology and ecological theory on competition and coexistence in fragmented landscapes.},
    author = {Peacor, Scott D. and Allesina, Stefano and Riolo, Rick L. and Pascual, Mercedes},
    citeulike-article-id = {2807829},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0040372},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17076585},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17076585},
    day = {31},
    doi = {10.1371/journal.pbio.0040372},
    journal = {PLoS Biol},
    month = oct,
    number = {11},
    pages = {e372+},
    pmid = {17076585},
    posted-at = {2014-09-16 03:13:17},
    priority = {2},
    publisher = {Public Library of Science},
    title = {Phenotypic Plasticity Opposes Species Invasions by Altering Fitness Surface},
    url = {http://dx.doi.org/10.1371/journal.pbio.0040372},
    volume = {4},
    year = {2006}
    }

2005

  • [DOI] Allesina, Stefano, Antonio Bodini, and Cristina Bondavalli. “Ecological subsystems via graph theory: the role of Strongly Connected Components.” Oikos 110.1 (2005): 164-176.
    [Bibtex]
    @article{citeulike:13364271,
    author = {Allesina, Stefano and Bodini, Antonio and Bondavalli, Cristina},
    citeulike-article-id = {13364271},
    citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.0030-1299.2005.13082.x},
    doi = {10.1111/j.0030-1299.2005.13082.x},
    issn = {00301299},
    journal = {Oikos},
    month = jul,
    number = {1},
    pages = {164--176},
    posted-at = {2014-09-16 03:18:02},
    priority = {2},
    title = {Ecological subsystems via graph theory: the role of {S}trongly {C}onnected {C}omponents},
    url = {http://dx.doi.org/10.1111/j.0030-1299.2005.13082.x},
    volume = {110},
    year = {2005}
    }
  • [DOI] Allesina, Stefano, Cristina Bondavalli, and Ursula M. Scharler. “The consequences of the aggregation of detritus pools in ecological networks.” Ecological modelling 189.1-2 (2005): 221-232.
    [Bibtex]
    @article{citeulike:375432,
    abstract = {Ecological networks are quantitative, graph-based descriptions of ecosystems, consisting of compartments (trophospecies and nutrient pools) that exchange fluxes of nutrients or energy. Previous research pointed out how the model's design is a crucial task that can heavily influence analyses results, and how merging compartments for the purpose of comparing two or more different ecosystems can significantly alter the indices on which the comparison is based. All these works have been focused on the aggregation of trophospecies, whereas networks may comprise several nutrient compartments that may be lumped as well, either for lack of information or for comparison {constraints.We} show how the aggregation of these non-living compartments can have a greater influence on network analysis results than trophospecies clustering. This problem should on the one hand encourage modelers to make an effort to test the possible effects of aggregations, and on the other show how the role of non-living compartments could be very important in determining network dynamics.},
    author = {Allesina, Stefano and Bondavalli, Cristina and Scharler, Ursula M.},
    citeulike-article-id = {375432},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecolmodel.2005.04.002},
    citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6VBS-4G9R2F2-1/2/e494a6ca507acd86ed4ead9c7f9c42d7},
    day = {25},
    doi = {10.1016/j.ecolmodel.2005.04.002},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = nov,
    number = {1-2},
    pages = {221--232},
    posted-at = {2014-09-16 03:17:06},
    priority = {2},
    title = {The consequences of the aggregation of detritus pools in ecological networks},
    url = {http://dx.doi.org/10.1016/j.ecolmodel.2005.04.002},
    volume = {189},
    year = {2005}
    }
  • [DOI] Allesina, Stefano and Antonio Bodini. “Food web networks: scaling relation revisited.” Ecological complexity 2.4 (2005): 323-338.
    [Bibtex]
    @article{citeulike:12157015,
    abstract = {Food webs seem to possess scale invariant attributes among which efficiency has been recently included. Considering food webs as transportation networks it has been shown that minimum spanning trees, topologies that minimize cost for delivering medium, satisfy a universal scaling relation. It is not clear, however, whether resource distribution follows the criterion of minimum cost, because longer, less efficient routes are used as well. Because of this, instead of focusing on minimum length spanning trees ({MLST}) we consider directed acyclic graphs ({DAGs}) as better descriptors of food web hierarchies. Twenty well known empirical food webs have been transformed into {DAGs} and a scaling relation has been observed between number of nodes and their level of effective connectivity. Although we derived the scaling relation for {DAGs} using topological arguments, the exponent of the equation C ∝ A\^{I}· shows same mathematical properties than its functional counterpart computed through flow analysis. This suggests that \^{I}· can be used as a proxy for efficiency in food webs. The values of this coefficient for {DAGs} are lower than the ones obtained for minimum spanning trees, suggesting that food webs lie in the range of medium-to-low efficiency networks. This challenges the idea that these systems would be more efficient than other types of networks.},
    author = {Allesina, Stefano and Bodini, Antonio},
    citeulike-article-id = {12157015},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ecocom.2005.05.001},
    doi = {10.1016/j.ecocom.2005.05.001},
    issn = {1476945X},
    journal = {Ecological Complexity},
    month = dec,
    number = {4},
    pages = {323--338},
    posted-at = {2014-09-16 03:16:21},
    priority = {2},
    title = {Food web networks: Scaling relation revisited},
    url = {http://dx.doi.org/10.1016/j.ecocom.2005.05.001},
    volume = {2},
    year = {2005}
    }

2004

  • [DOI] Allesina, Stefano and Cristina Bondavalli. “WAND: an ecological network analysis user-friendly tool.” Environmental modelling & software 19.4 (2004): 337-340.
    [Bibtex]
    @article{citeulike:13364273,
    author = {Allesina, Stefano and Bondavalli, Cristina},
    citeulike-article-id = {13364273},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.envsoft.2003.10.002},
    doi = {10.1016/j.envsoft.2003.10.002},
    issn = {13648152},
    journal = {Environmental Modelling \& Software},
    month = apr,
    number = {4},
    pages = {337--340},
    posted-at = {2014-09-16 03:20:49},
    priority = {2},
    title = {{WAND}: an ecological network analysis user-friendly tool},
    url = {http://dx.doi.org/10.1016/j.envsoft.2003.10.002},
    volume = {19},
    year = {2004}
    }
  • [DOI] Allesina, Stefano and Robert E. Ulanowicz. “Cycling in ecological networks: Finn’s index revisited.” Computational biology and chemistry 28.3 (2004): 227-233.
    [Bibtex]
    @article{citeulike:13364272,
    author = {Allesina, Stefano and Ulanowicz, Robert E.},
    citeulike-article-id = {13364272},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.compbiolchem.2004.04.002},
    doi = {10.1016/j.compbiolchem.2004.04.002},
    issn = {14769271},
    journal = {Computational Biology and Chemistry},
    month = jul,
    number = {3},
    pages = {227--233},
    posted-at = {2014-09-16 03:19:57},
    priority = {2},
    title = {Cycling in ecological networks: {F}inn's index revisited},
    url = {http://dx.doi.org/10.1016/j.compbiolchem.2004.04.002},
    volume = {28},
    year = {2004}
    }
  • [DOI] Allesina, Stefano and Antonio Bodini. “Who dominates whom in the ecosystem? energy flow bottlenecks and cascading extinctions.” Journal of theoretical biology 230.3 (2004): 351-358.
    [Bibtex]
    @article{citeulike:2291070,
    abstract = {In this paper, we investigate the problem of secondary extinction in food webs through the use of dominator trees, network topological structures that reduce food webs to linear pathways that are essential for energy delivery. Each species along these chains is responsible for passing energy to the taxa that follow it, and, as such, it is indispensable for their survival; because of this it is said to dominate them. The higher the number of species a node dominates, the greater the impact resulting from its removal. By computing dominator trees for 13 well-studied food webs we obtained for each of them the number of nodes dominated by a single species and the number of nodes that dominate each species. We illustrate the procedure for the Grassland Ecosystem showing the potential of this method for identifying species that play a major role in energy delivery and are likely to cause the greatest damage if removed. Finally, by means of two indices that measure error and attack sensitivity, we confirm a previous hypothesis that food webs are very robust to random loss of species but very fragile to the selective loss of the hubs.},
    author = {Allesina, Stefano and Bodini, Antonio},
    citeulike-article-id = {2291070},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jtbi.2004.05.009},
    citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6WMD-4CVV71S-3/2/321abad625ebf365324651cd5dcf4435},
    day = {7},
    doi = {10.1016/j.jtbi.2004.05.009},
    issn = {00225193},
    journal = {Journal of Theoretical Biology},
    month = oct,
    number = {3},
    pages = {351--358},
    posted-at = {2014-09-16 03:19:04},
    priority = {2},
    title = {Who dominates whom in the ecosystem? Energy flow bottlenecks and cascading extinctions},
    url = {http://dx.doi.org/10.1016/j.jtbi.2004.05.009},
    volume = {230},
    year = {2004}
    }

2003

  • [DOI] Allesina, Stefano and Cristina Bondavalli. “Steady state of ecosystem flow networks: a comparison between balancing procedures.” Ecological modelling 165.2-3 (2003): 221-229.
    [Bibtex]
    @article{citeulike:1212061,
    abstract = {When modelling real ecosystems, a number of techniques need steady state condition to proceed in their analysis. In ecosystem network models this means that energy entering the system exactly balances the output. Steady state, however, is not a straightforward outcome of network construction and, to have this condition satisfied, network analysis uses balancing procedure. This operation leads to restructuring the weighted network, changing the values of some network flows; this can affect drastically the results of the analysis. Presently, two algorithms are used for balancing ecosystem networks: input-based approach and output-based approach. In the former input flows are kept constant while outputs and transfer coefficients are manipulated; the latter requires that inputs and intercompartmental flows are modified. This paper discusses the effects of these algorithms on some products of network analysis, in particular system level indices such as total system throughput ({TST}) and ascendency. Also it suggests four new procedures that, while balancing the networks, can minimise changes on measured flows and distortion on results of the analysis.},
    author = {Allesina, Stefano and Bondavalli, Cristina},
    citeulike-article-id = {1212061},
    citeulike-linkout-0 = {http://dx.doi.org/10.1016/s0304-3800(03)00075-9},
    citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6VBS-48GP66V-1/2/41295d1b481add548866f717e1730558},
    day = {15},
    doi = {10.1016/s0304-3800(03)00075-9},
    issn = {03043800},
    journal = {Ecological Modelling},
    month = jul,
    number = {2-3},
    pages = {221--229},
    posted-at = {2014-09-16 03:21:19},
    priority = {2},
    title = {Steady state of ecosystem flow networks: a comparison between balancing procedures},
    url = {http://dx.doi.org/10.1016/s0304-3800(03)00075-9},
    volume = {165},
    year = {2003}
    }