Trophic groups and modules: two levels of group detection in food webs

Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups (TGs), which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group concepts remains unknown in empirical food webs. While recent developments in network theory have led to efficient methods for detecting modules in food webs, the determination of TGs (groups of species that are functionally similar) is largely based on subjective expert knowledge. We develop a novel algorithm for TG detection. We apply this method to empirical food webs and show that aggregation into TGs allows for the simplification of food webs while preserving their information content. Furthermore, we reveal a two-level hierarchical structure where modules partition food webs into large bottom–top trophic pathways, whereas TGs further partition these pathways into groups of species with similar trophic connections. This provides new perspectives for the study of dynamical and functional consequences of food-web structure, bridging topological and dynamical analysis. TGs have a clear ecological meaning and are found to provide a trade-off between network complexity and information loss.

[1]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[2]  R. Ulanowicz,et al.  The Seasonal Dynamics of The Chesapeake Bay Ecosystem , 1989 .

[3]  Guy Woodward,et al.  Quantification and Resolution of a Complex, Size-Structured Food Web , 2005 .

[4]  R. Guimerà,et al.  Functional cartography of complex metabolic networks , 2005, Nature.

[5]  Hod Lipson,et al.  Networks, dynamics, and modularity. , 2004, Physical review letters.

[6]  C. Townsend,et al.  Is resolution the solution?: the effect of taxonomic resolution on the calculated properties of three stream food webs , 2000 .

[7]  Owen T Lewis,et al.  Structural dynamics and robustness of food webs. , 2010, Ecology letters.

[8]  Stefano Allesina,et al.  Relevance of evolutionary history for food web structure , 2012, Proceedings of the Royal Society B: Biological Sciences.

[9]  Stefano Allesina,et al.  Who dominates whom in the ecosystem? Energy flow bottlenecks and cascading extinctions. , 2004, Journal of theoretical biology.

[10]  Neo D. Martinez,et al.  Effect of scale on food web structure. , 1993, Science.

[11]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W. Zachary,et al.  An Information Flow Model for Conflict and Fission in Small Groups , 1977, Journal of Anthropological Research.

[13]  Owyn E. Snodgrass,et al.  Stable Isotope Analysis Challenges Wasp-Waist Food Web Assumptions in an Upwelling Pelagic Ecosystem , 2012, Scientific Reports.

[14]  S. Hall,et al.  Food-web patterns : lessons from a species-rich web , 1991 .

[15]  Jennifer A. Dunne,et al.  Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity , 2013, PLoS biology.

[16]  S. Opitz,et al.  Trophic interactions in Caribbean coral reefs , 1996 .

[17]  Jean-Jacques Daudin,et al.  Detection of structurally homogeneous subsets in graphs , 2013, Statistics and Computing.

[18]  Neil Rooney,et al.  Integrating food web diversity, structure and stability. , 2012, Trends in ecology & evolution.

[19]  P. Yodzis,et al.  In search of operational trophospecies in a tropical aquatic food web , 1999 .

[20]  T. Vicsek,et al.  Uncovering the overlapping community structure of complex networks in nature and society , 2005, Nature.

[21]  Owen L Petchey,et al.  Size, foraging, and food web structure , 2008, Proceedings of the National Academy of Sciences.

[22]  Benjamin Wright,et al.  Direct Factor Analysis in Sociometry , 1961 .

[23]  H. White,et al.  “Structural Equivalence of Individuals in Social Networks” , 2022, The SAGE Encyclopedia of Research Design.

[24]  Stefano Allesina,et al.  Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions? , 2009, PLoS Comput. Biol..

[25]  E A Leicht,et al.  Mixture models and exploratory analysis in networks , 2006, Proceedings of the National Academy of Sciences.

[26]  Edward B. Baskerville,et al.  Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model , 2010, PLoS Comput. Biol..

[27]  Colin Fontaine,et al.  Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks , 2010, Science.

[28]  Daniel B. Stouffer,et al.  Origin of compartmentalization in food webs. , 2010, Ecology.

[29]  Stéphane Legendre,et al.  Food-web aggregation, methodological and functional issues , 2013 .

[30]  Raj Kumar Pan,et al.  Modularity produces small-world networks with dynamical time-scale separation , 2008, 0802.3671.

[31]  G. Sugihara,et al.  Effects of taxonomic and trophic aggregation on food web properties , 1997, Oecologia.

[32]  J. Bascompte,et al.  Compartmentalization increases food-web persistence , 2011, Proceedings of the National Academy of Sciences.

[33]  Neo D. Martinez Artifacts or Attributes? Effects of Resolution on the Little Rock Lake Food Web , 1991 .

[34]  K. Reitz,et al.  Graph and Semigroup Homomorphisms on Networks of Relations , 1983 .

[35]  Stefano Allesina,et al.  Food web models: a plea for groups. , 2009, Ecology letters.

[36]  Raymond L. Lindeman The trophic-dynamic aspect of ecology , 1942 .

[37]  Charles C. Elton Animal Ecology , 1927, Nature.

[38]  R. Carter 11 – IT and society , 1991 .

[39]  J. Bascompte,et al.  The modularity of pollination networks , 2007, Proceedings of the National Academy of Sciences.

[40]  Jordi Bascompte,et al.  Compartments in a marine food web associated with phylogeny, body mass, and habitat structure. , 2009, Ecology letters.

[41]  Salvador Balle,et al.  Thermo-optical "canard orbits" and excitable limit cycles. , 2004, Physical review letters.

[42]  F. Q. Ribeiro The meta-analysis , 2017, Brazilian journal of otorhinolaryngology.

[43]  Michel Loreau,et al.  Functional diversity governs ecosystem response to nutrient enrichment , 2000, Nature.

[44]  Neo D. Martinez,et al.  Mechanistic theory and modelling of complex food-web dynamics in Lake Constance. , 2012, Ecology letters.

[45]  M. Loreau,et al.  Differential responses of size‐based functional groups to bottom–up and top–down perturbations in pelagic food webs: a meta‐analysis , 2014 .

[46]  R. May,et al.  Stability and Complexity in Model Ecosystems , 1976, IEEE Transactions on Systems, Man, and Cybernetics.

[47]  K. Havens,et al.  Scale and Structure in Natural Food Webs , 1992, Science.

[48]  S. Borgatti,et al.  Defining and measuring trophic role similarity in food webs using regular equivalence. , 2003, Journal of theoretical biology.

[49]  Ferenc Jordán,et al.  The sensitivity of food web topology to temporal data aggregation , 2009 .

[50]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[51]  P. Yodzis,et al.  Local trophodynamics and the interaction of marine mammals and fisheries in the Benguela ecosystem , 1998 .

[52]  Ana L. N. Fred,et al.  Robust data clustering , 2003, 2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2003. Proceedings..

[53]  Zongfu Yu,et al.  Measurement of time-dependent CP asymmetries in Bjavax.xml.bind.JAXBElement@6d610b0 → D(*)±π± decays and constraints on sin(2β + γ) , 2004 .

[54]  Ferenc Jordán,et al.  Identifying important species: Linking structure and function in ecological networks , 2008 .

[55]  Mark Novak,et al.  Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters. , 2012, Ecology letters.

[56]  A. Dobson,et al.  Parasites dominate food web links. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Andrea Lancichinetti,et al.  Detecting the overlapping and hierarchical community structure in complex networks , 2008, 0802.1218.

[58]  S. Carpenter,et al.  Food Webs, Body Size, and Species Abundance in Ecological Community Description , 2005 .

[59]  Roger Guimerà,et al.  Module identification in bipartite and directed networks. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[60]  Santo Fortunato,et al.  Community detection in graphs , 2009, ArXiv.