#density, #centrality, #motifs, #node-level analysis, #network comparisons

Summary

This class introduces the fundamental concepts of network structure analysis with a focus on ecological networks. We will first learn how networks are defined mathematically. We will then explore key metrics of network structure at both the node and mesoscale scales, understanding how these structures correlate with biological processes and functions. We will cover different classes of measures, including density (connectance), degree distributions, and centrality. We will also discuss network comparisons to identify regularities that could indicate similar functionality or generative processes across different systems. Though the class is comprehensive, it covers merely the beginning of the tip of the iceberg… 😊

Goals

  1. Define networks mathenatically.
  2. Introduce basic metrics of structure, focusing on the node and meso-scale levels.
  3. Relate structure to ecological processes and functions.

Suggested Readings

Conceptual papers

Technical papers

  • Dale MRT, Fortin M-J. Quantitative analysis of ecological networks. Cambridge University Press; 2021. doi:10.1017/9781108649018

  1. Blüthgen N, Menzel F, Blüthgen N. Measuring specialization in species interaction networks. BMC Ecol. 2006;6: 9. doi:10.1186/1472-6785-6-9

  2. Delmas E, Besson M, Brice M-H, Burkle LA, Dalla Riva GV, Fortin M-J, et al. Analysing ecological networks of species interactions: Analyzing ecological networks. Biol Rev. 2019;94: 16–36. doi:10.1111/brv.12433

  3. Dormann CF, Fründ J, Blüthgen N, Gruber B. Indices, graphs and null models: analyzing bipartite ecological networks. The Open Ecology Journal. 2009;2: 7–24. doi:10.2174/1874213000902010007

  4. Costa A, Martín González AM, Guizien K, Doglioli AM, Gómez JM, Petrenko AA, et al. Ecological networks: Pursuing the shortest path, however narrow and crooked. Sci Rep. 2019;9: 17826. doi:10.1038/s41598-019-54206-x

  5. Simmons BI, Cirtwill AR, Baker NJ, Wauchope HS, Dicks LV, Stouffer DB, et al. Motifs in bipartite ecological networks: uncovering indirect interactions. Oikos. 2019;128: 154–170. doi:10.1111/oik.05670

Research papers

  1. Allesina S, Pascual M. Googling food webs: can an eigenvector measure species’ importance for coextinctions? PLoS Comput Biol. 2009;5: e1000494. doi:10.1371/journal.pcbi.1000494

  2. Bascompte J, Jordano P, Olesen JM. Asymmetric coevolutionary networks facilitate biodiversity maintenance. Science. 2006;312: 431–433. doi:10.1126/science.1123412

  3. Dunne JA, Williams RJ, Martinez ND. Food-web structure and network theory: The role of connectance and size. Proc Natl Acad Sci U S A. 2002;99: 12917–12922. doi:10.1073/pnas.192407699

  4. Gómez JM, Nunn CL, Verdú M. Centrality in primate-parasite networks reveals the potential for the transmission of emerging infectious diseases to humans. Proc Natl Acad Sci U S A. 2013;110: 7738–7741. doi:10.1073/pnas.1220716110

  5. Jordán F. Keystone species and food webs. Philos Trans R Soc Lond B Biol Sci. 2009;364: 1733–1741. doi:10.1098/rstb.2008.0335

  6. Jordano P, Bascompte J, Olesen JM. Invariant properties in coevolutionary networks of plant–animal interactions. Ecol Lett. 2003;6: 69–81. doi:10.1046/j.1461-0248.2003.00403.x

  7. Martín González AM, Dalsgaard B, Olesen JM. Centrality measures and the importance of generalist species in pollination networks. Ecol Complex. 2010;7: 36–43. doi:10.1016/j.ecocom.2009.03.008

  8. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002;298: 824–827. doi:10.1126/science.298.5594.824