1
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Giacomuzzo E, Jordán F. Food web aggregation: effects on key positions. OIKOS 2021. [DOI: 10.1111/oik.08541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emanuele Giacomuzzo
- Centre for Ecological Research Budapest Hungary
- Univ. of Zurich Zurich Switzerland
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology Dübendorf Switzerland
| | - Ferenc Jordán
- Democracy Inst., Central European Univ. Budapest Hungary
- Stazione Zoologica Anton Dohrn Napoli Italy
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2
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Farage C, Edler D, Eklöf A, Rosvall M, Pilosof S. Identifying flow modules in ecological networks using Infomap. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carmel Farage
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - Daniel Edler
- Integrated Science Lab Department of Physics Umeå University Umeå Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Anna Eklöf
- Division of Theoretical Biology Department of Physics, Chemistry and Biology Linköping University Linköping Sweden
| | - Martin Rosvall
- Integrated Science Lab Department of Physics Umeå University Umeå Sweden
| | - Shai Pilosof
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
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3
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Ohlsson M, Eklöf A. Spatial resolution and location impact group structure in a marine food web. Ecol Lett 2020; 23:1451-1459. [PMID: 32656918 DOI: 10.1111/ele.13567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/27/2019] [Accepted: 05/20/2020] [Indexed: 12/01/2022]
Abstract
Ecological processes in food webs depend on species interactions. By identifying broad-scaled interaction patterns, important information on species' ecological roles may be revealed. Here, we use the group model to examine how spatial resolution and proximity influence group structure. We examine a data set from the Barents Sea, with food webs described for both the whole region and 25 subregions. We test how the group structure in the networks differ comparing (1) the regional metaweb to subregions and (2) subregion to subregion. We find that more than half the species in the metaweb change groups when compared to subregions. Between subregions, networks with similar group structure are spatially related. Interestingly, although species overlap is important for similarity in group structure, there are notable exceptions. Our results highlight that species ecological roles vary depending on fine-scaled differences in the patterns of interactions, and that local network characteristics are important to consider.
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Affiliation(s)
- Mikael Ohlsson
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
| | - Anna Eklöf
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
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4
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Terry JCD, Lewis OT. Finding missing links in interaction networks. Ecology 2020; 101:e03047. [PMID: 32219855 DOI: 10.1002/ecy.3047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022]
Abstract
Documenting which species interact within ecological communities is challenging and labor intensive. As a result, many interactions remain unrecorded, potentially distorting our understanding of network structure and dynamics. We test the utility of four structural models and a new coverage-deficit model for predicting missing links in both simulated and empirical bipartite networks. We find they can perform well, although the predictive power of structural models varies with the underlying network structure. The accuracy of predictions can be improved by ensembling multiple models. Augmenting observed networks with most-likely missing links improves estimates of qualitative network metrics. Tools to identify likely missing links can be simple to implement, allowing the prioritization of research effort and more robust assessment of network properties.
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Affiliation(s)
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
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5
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Michalska-Smith MJ, Allesina S. Telling ecological networks apart by their structure: A computational challenge. PLoS Comput Biol 2019; 15:e1007076. [PMID: 31246974 PMCID: PMC6597030 DOI: 10.1371/journal.pcbi.1007076] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ecologists have been compiling ecological networks for over a century, detailing the interactions between species in a variety of ecosystems. To this end, they have built networks for mutualistic (e.g., pollination, seed dispersal) as well as antagonistic (e.g., herbivory, parasitism) interactions. The type of interaction being represented is believed to be reflected in the structure of the network, which would differ substantially between mutualistic and antagonistic networks. Here, we put this notion to the test by attempting to determine the type of interaction represented in a network based solely on its structure. We find that, although it is easy to separate different kinds of nonecological networks, ecological networks display much structural variation, making it difficult to distinguish between mutualistic and antagonistic interactions. We therefore frame the problem as a challenge for the community of scientists interested in computational biology and machine learning. We discuss the features a good solution to this problem should possess and the obstacles that need to be overcome to achieve this goal.
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Affiliation(s)
- Matthew J. Michalska-Smith
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Stefano Allesina
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
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6
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Farahpour F, Saeedghalati M, Brauer VS, Hoffmann D. Trade-off shapes diversity in eco-evolutionary dynamics. eLife 2018; 7:e36273. [PMID: 30117415 PMCID: PMC6126925 DOI: 10.7554/elife.36273] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
We introduce an Interaction- and Trade-off-based Eco-Evolutionary Model (ITEEM), in which species are competing in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the shape of the trade-off has a fundamental impact on eco-evolutionary dynamics, as it imposes four phases of diversity, including a sharp phase transition. Despite its minimalism, ITEEM produces a remarkable range of patterns of eco-evolutionary dynamics that are observed in experimental and natural systems. Most notably we find self-organization towards structured communities with high and sustained diversity, in which competing species form interaction cycles similar to rock-paper-scissors games.
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Affiliation(s)
- Farnoush Farahpour
- Bioinformatics and Computational BiophysicsUniversity of Duisburg-EssenEssenGermany
| | | | | | - Daniel Hoffmann
- Bioinformatics and Computational BiophysicsUniversity of Duisburg-EssenEssenGermany
- Center for Computational Sciences and SimulationUniversity of Duisburg-EssenEssenGermany
- Center for Medical BiotechnologyUniversity of Duisburg-EssenEssenGermany
- Center for Water and Environmental ResearchUniversity of Duisburg-EssenEssenGermany
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7
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Coexistence of many species in random ecosystems. Nat Ecol Evol 2018; 2:1237-1242. [PMID: 29988167 DOI: 10.1038/s41559-018-0603-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/08/2018] [Indexed: 11/08/2022]
Abstract
Rich ecosystems harbour thousands of species interacting in tangled networks encompassing predation, mutualism and competition. Such widespread biodiversity is puzzling, because in ecological models it is exceedingly improbable for large communities to stably coexist. One aspect rarely considered in these models, however, is that coexisting species in natural communities are a selected portion of a much larger pool, which has been pruned by population dynamics. Here we compute the distribution of the number of species that can coexist when we start from a pool of species interacting randomly, and show that even in this case we can observe rich, stable communities. Interestingly, our results show that, once stability conditions are met, network structure has very little influence on the level of biodiversity attained. Our results identify the main drivers responsible for widespread coexistence in natural communities, providing a baseline for determining which structural aspects of empirical communities promote or hinder coexistence.
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8
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Monteiro AB, Faria LDB. Matching consumer feeding behaviours and resource traits: a fourth-corner problem in food-web theory. Ecol Lett 2018; 21:1237-1243. [PMID: 29877014 DOI: 10.1111/ele.13096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/02/2018] [Accepted: 05/12/2018] [Indexed: 11/30/2022]
Abstract
For decades, food web theory has proposed phenomenological models for the underlying structure of ecological networks. Generally, these models rely on latent niche variables that match the feeding behaviour of consumers with their resource traits. In this paper, we used a comprehensive database to evaluate different hypotheses on the best dependency structure of trait-matching patterns between consumers and resource traits. We found that consumer feeding behaviours had complex interactions with resource traits; however, few dimensions (i.e. latent variables) could reproduce the trait-matching patterns. We discuss our findings in the light of three food web models designed to reproduce the multidimensionality of food web data; additionally, we discuss how using species traits clarify food webs beyond species pairwise interactions and enable studies to infer ecological generality at larger scales, despite potential taxonomic differences, variations in ecological conditions and differences in species abundance between communities.
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9
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Barner AK, Coblentz KE, Hacker SD, Menge BA. Fundamental contradictions among observational and experimental estimates of non-trophic species interactions. Ecology 2018; 99:557-566. [DOI: 10.1002/ecy.2133] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Allison K. Barner
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis Oregon 97331 USA
| | - Kyle E. Coblentz
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis Oregon 97331 USA
| | - Sally D. Hacker
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis Oregon 97331 USA
| | - Bruce A. Menge
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis Oregon 97331 USA
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10
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Michalska‐Smith MJ, Sander EL, Pascual M, Allesina S. Understanding the role of parasites in food webs using the group model. J Anim Ecol 2017; 87:790-800. [DOI: 10.1111/1365-2656.12782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/21/2017] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Mercedes Pascual
- Department of Ecology & Evolution University of Chicago Chicago IL USA
| | - Stefano Allesina
- Department of Ecology & Evolution University of Chicago Chicago IL USA
- Computation Institute University of Chicago Chicago IL USA
- Northwestern Institute on Complex Systems Northwestern University Evanston IL USA
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11
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Ilacqua N, Sánchez-Álvarez M, Bachmann M, Costiniti V, Del Pozo MA, Giacomello M. Protein Localization at Mitochondria-ER Contact Sites in Basal and Stress Conditions. Front Cell Dev Biol 2017; 5:107. [PMID: 29312934 PMCID: PMC5733094 DOI: 10.3389/fcell.2017.00107] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022] Open
Abstract
Mitochondria-endoplasmic reticulum (ER) contacts (MERCs) are sites at which the outer mitochondria membrane and the Endoplasmic Reticulum surface run in parallel at a constant distance. The juxtaposition between these organelles determines several intracellular processes such as to name a few, Ca2+ and lipid homeostasis or autophagy. These specific tasks can be exploited thanks to the enrichment (or re-localization) of dedicated proteins at these interfaces. Recent proteomic studies highlight the tissue specific composition of MERCs, but the overall mechanisms that control MERCs plasticity remains unclear. Understanding how proteins are targeted at these sites seems pivotal to clarify such contextual function of MERCs. This review aims to summarize the current knowledge on protein localization at MERCs and the possible contribution of the mislocalization of MERCs components to human disorders.
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Affiliation(s)
- Nicolò Ilacqua
- Department of Biology, University of Padova, Padova, Italy
| | - Miguel Sánchez-Álvarez
- Mechanoadaptation and Caveolae Biology Lab, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | | | | | - Miguel A Del Pozo
- Mechanoadaptation and Caveolae Biology Lab, Cell and Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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12
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Astegiano J, Altermatt F, Massol F. Disentangling the co-structure of multilayer interaction networks: degree distribution and module composition in two-layer bipartite networks. Sci Rep 2017; 7:15465. [PMID: 29133886 PMCID: PMC5684352 DOI: 10.1038/s41598-017-15811-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/02/2017] [Indexed: 11/29/2022] Open
Abstract
Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition. We focus on modular structure because of its high prevalence among ecological networks. We apply our method to two Lepidoptera-plant networks, one describing caterpillar-plant herbivory interactions and one representing adult Lepidoptera nectaring on flowers, thereby possibly pollinating them. More than 50% of the species established either herbivory or visitation interactions, but not both. These species were over-represented among plants and lepidopterans, and were present in most modules in both networks. Similarity in module composition between networks was high but not different from random expectations. Our method clearly delineates the importance of interpreting multilayer module composition similarity in the light of the constraints imposed by network structure to predict the potential indirect effects of species loss through interconnected modular networks.
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Affiliation(s)
- Julia Astegiano
- Instituto Multidisciplinario de Biología Vegetal, FCEFyN, Universidad Nacional de Córdoba, CONICET, Argentina.
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, 1919 route de Mende, F-34293, Montpellier, France.
| | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, CH-8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057, Zürich, Switzerland
| | - François Massol
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS - Université de Montpellier - Université Paul Valéry Montpellier - EPHE, 1919 route de Mende, F-34293, Montpellier, France
- CNRS, Université de Lille-Sciences et Technologies, UMR 8198 Evo-Eco-Paleo, SPICI group, F-59000, Lille, France
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13
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Giordano G, Altafini C. Qualitative and quantitative responses to press perturbations in ecological networks. Sci Rep 2017; 7:11378. [PMID: 28900208 PMCID: PMC5596000 DOI: 10.1038/s41598-017-11221-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/21/2017] [Indexed: 11/09/2022] Open
Abstract
Predicting the sign of press perturbation responses in ecological networks is challenging, due to the poor knowledge of the strength of the direct interactions among the species, and to the entangled coexistence of direct and indirect effects. We show in this paper that, for a class of networks that includes mutualistic and monotone networks, the sign of press perturbation responses can be qualitatively determined based only on the sign pattern of the community matrix, without any knowledge of parameter values. For other classes of networks, we show that a semi-qualitative approach yields sufficient conditions for community matrices with a given sign pattern to exhibit mutualistic responses to press perturbations; quantitative conditions can be provided as well for community matrices that are eventually nonnegative. We also present a computational test that can be applied to any class of networks so as to check whether the sign of the responses to press perturbations is constant in spite of parameter variations.
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Affiliation(s)
- Giulia Giordano
- Department of Automatic Control and LCCC Linnaeus Center, Lund University, Box 118, SE-221 00, Lund, Sweden
| | - Claudio Altafini
- Division of Automatic Control, Department of Electrical Engineering, Linköping University, SE-58183, Linköping, Sweden.
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14
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García-Callejas D, Molowny-Horas R, Araújo MB. Multiple interactions networks: towards more realistic descriptions of the web of life. OIKOS 2017. [DOI: 10.1111/oik.04428] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | - Miguel B. Araújo
- Depto de Biogeografía y Cambio Global; Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC); Madrid Spain
- InBio/Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Univ. de Évora, Largo dos Colegiais; Évora Portugal
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15
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Sander EL, Wootton JT, Allesina S. Ecological Network Inference From Long-Term Presence-Absence Data. Sci Rep 2017; 7:7154. [PMID: 28769079 PMCID: PMC5541006 DOI: 10.1038/s41598-017-07009-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/20/2017] [Indexed: 11/21/2022] Open
Abstract
Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son’s correlation coefficient, then comparing the model networks to empirical trophic and nontrophic webs in two ecological systems. We find that although each model significantly replicates the structure of at least one empirical network, no model significantly predicts network structure in both systems, and no model is clearly superior to the others. We also find that networks inferred for the Tatoosh intertidal match the nontrophic network much more closely than the trophic one, possibly due to the challenges of identifying trophic interactions from presence-absence data. Our findings suggest that although these methods hold some promise for ecological network inference, presence-absence data does not provide enough signal for models to consistently identify interactions, and networks inferred from these data should be interpreted with caution.
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Affiliation(s)
- Elizabeth L Sander
- University of Chicago, Department of Ecology and Evolution, Chicago, 60637, USA.
| | - J Timothy Wootton
- University of Chicago, Department of Ecology and Evolution, Chicago, 60637, USA
| | - Stefano Allesina
- University of Chicago, Department of Ecology and Evolution, Chicago, 60637, USA.,University of Chicago, Computation Institute, Chicago, 60637, USA
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16
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Dee LE, Allesina S, Bonn A, Eklöf A, Gaines SD, Hines J, Jacob U, McDonald-Madden E, Possingham H, Schröter M, Thompson RM. Operationalizing Network Theory for Ecosystem Service Assessments. Trends Ecol Evol 2017; 32:118-130. [DOI: 10.1016/j.tree.2016.10.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/23/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
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17
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Poisot T, Stouffer DB, Kéfi S. Describe, understand and predict: why do we need networks in ecology? Funct Ecol 2016. [DOI: 10.1111/1365-2435.12799] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Timothée Poisot
- Université de Montréal Département de Sciences Biologiques Montréal QC Canada
- Québec Centre for Biodiversity Sciences Montréal QC Canada
| | - Daniel B. Stouffer
- Centre for Integrative Ecology School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Sonia Kéfi
- Institut des Sciences de l’Évolution Université de Montpellier, CNRS, EPHE, IRD Montpellier France
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18
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Affiliation(s)
- J. A. Bissonette
- Department of Wildland Resources; Quinney College of Natural Resources; Utah State University; Logan UT 84322-5200 USA
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19
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Kéfi S, Miele V, Wieters EA, Navarrete SA, Berlow EL. How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience. PLoS Biol 2016; 14:e1002527. [PMID: 27487303 PMCID: PMC4972357 DOI: 10.1371/journal.pbio.1002527] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities' response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species (i.e., "multiplex networks"), as well as their consequences for community dynamics. Using network statistical modeling applied to a comprehensive ecological network, which includes trophic and diverse non-trophic links, we provide a first glimpse at what the full "entangled bank" of species looks like. The community exhibits clear multidimensional structure, which is taxonomically coherent and broadly predictable from species traits. Moreover, dynamic simulations suggest that this non-random patterning of how diverse non-trophic interactions map onto the food web could allow for higher species persistence and higher total biomass than expected by chance and tends to promote a higher robustness to extinctions.
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Affiliation(s)
- Sonia Kéfi
- Institut des Sciences de l’Evolution de Montpellier, BioDICée team, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Montpellier, France
| | - Vincent Miele
- Laboratoire Biométrie et Biologie Evolutive, CNRS, UMR5558, Université de Lyon, Villeurbanne, France
| | - Evie A. Wieters
- Estación Costera de Investigaciones Marinas (ECIM), Center for Marine Conservation, LINC-Global, Chile
| | - Sergio A. Navarrete
- Estación Costera de Investigaciones Marinas (ECIM), Center for Marine Conservation, LINC-Global, Chile
- Center for Applied Ecology and Sustainability (CAPES), Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric L. Berlow
- Vibrant Data Inc., San Francisco, California, United States of America
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20
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Golubski AJ, Westlund EE, Vandermeer J, Pascual M. Ecological Networks over the Edge: Hypergraph Trait-Mediated Indirect Interaction (TMII) Structure. Trends Ecol Evol 2016; 31:344-354. [DOI: 10.1016/j.tree.2016.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/01/2016] [Accepted: 02/06/2016] [Indexed: 10/22/2022]
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21
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Cardona C, Weisenhorn P, Henry C, Gilbert JA. Network-based metabolic analysis and microbial community modeling. Curr Opin Microbiol 2016; 31:124-131. [PMID: 27060776 DOI: 10.1016/j.mib.2016.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 03/17/2016] [Accepted: 03/20/2016] [Indexed: 01/08/2023]
Abstract
Network inference is being applied to studies of microbial ecology to visualize and characterize microbial communities. Network representations can allow examination of the underlying organizational structure of a microbial community, and identification of key players or environmental conditions that influence community assembly and stability. Microbial co-association networks provide information on the dynamics of community structure as a function of time or other external variables. Community metabolic networks can provide a mechanistic link between species through identification of metabolite exchanges and species specific resource requirements. When used together, co-association networks and metabolic networks can provide a more in-depth view of the hidden rules that govern the stability and dynamics of microbial communities.
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Affiliation(s)
- Cesar Cardona
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, United States; Department of Surgery, University of Chicago, Chicago, IL 60637, United States
| | - Pamela Weisenhorn
- Department of Surgery, University of Chicago, Chicago, IL 60637, United States; Division of Biosciences, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Chris Henry
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Jack A Gilbert
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, United States; Department of Surgery, University of Chicago, Chicago, IL 60637, United States; Division of Biosciences, Argonne National Laboratory, Lemont, IL 60439, United States.
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