#structure, #multilplex, #interlayer

Figure from: Frydman et al., 2023 Methods Ecol Evol.

Summary

Ecological multilayer networks represent a sophisticated framework for analyzing complex ecological systems across multiple dimensions and scales. In tht class we will explore the history and development of multilayer networks in ecology, define multilayer networks and showcase research questions. We will emphasize the critical role of interlayer edges that connect different layers of interactions within the network. The accompanying exercise will cover various tools and methods for representing and analyzing multilayer networks, including matrix and tensor representations, centrality measures, and community detection techniques.

Goals

  1. Introduce the multilayer networks.
  2. Emphasize the role of interlayer edges.
  3. Provide examples for research questions.

References

Key papers

  • Kivelä M, Arenas A, Barthelemy M, Gleeson JP, Moreno Y, Porter MA. Multilayer networks. J Complex Networks. 2014;2: 203–271. doi:10.1093/comnet/cnu016

  • Pilosof S, Porter MA, Pascual M, Kéfi S. The multilayer nature of ecological networks. Nat Ecol Evol. 2017;1: 0101. doi:10.1038/s41559-017-0101

  • Frydman N, Freilikhman S, Talpaz I, Pilosof S. Practical guidelines and the EMLN R package for handling ecological multilayer networks. Methods Ecol Evol. 2023. doi:10.1111/2041-210x.14225

Research

  • Lafferty KD, Dobson AP, Kuris AM. Parasites dominate food web links. Proc Natl Acad Sci U S A. 2006;103: 11211–11216. doi:10.1073/pnas.0604755103

  • Rudolf VHW, Lafferty KD. Stage structure alters how complexity affects stability of ecological networks. Ecol Lett. 2011;14: 75–79. doi:10.1111/j.1461-0248.2010.01558.x

  • Fontaine C, Guimarães PR, Kéfi S, Loeuille N, Memmott J, van der Putten WH, et al. The ecological and evolutionary implications of merging different types of networks. Ecol Lett. 2011;14: 1170–1181. doi:10.1111/j.1461-0248.2011.01688.x

  • Poisot T, Canard E, Mouillot D, Mouquet N, Gravel D, Jordan F. The dissimilarity of species interaction networks. Ecol Lett. 2012;15: 1353–1361. doi:10.1111/ele.12002

  • Pocock MJO, Evans DM, Memmott J. The robustness and restoration of a network of ecological networks. Science. 2012;335: 973–977. doi:10.1126/science.1214915

  • 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. doi:10.1371/journal.pbio.1002527

  • 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

  • Timóteo S, Correia M, Rodríguez-Echeverría S, Freitas H, Heleno R. Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes. Nat Commun. 2018;9: 140. doi:10.1038/s41467-017-02658-y

  • Gosak M, Markovič R, Dolenšek J, Slak Rupnik M, Marhl M, Stožer A, et al. Network science of biological systems at different scales: A review. Phys Life Rev. 2018;24: 118–135. doi:10.1016/j.plrev.2017.11.003

  • Hutchinson MC, Bramon Mora B, Pilosof S, Barner AK, Kéfi S, Thébault E, et al. Seeing the forest for the trees: Putting multilayer networks to work for community ecology. Funct Ecol. 2019;33: 206–217. doi:10.1111/1365-2435.13237

  • Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum. PLoS Biol. 2019;17: e3000336. doi:10.1371/journal.pbio.3000336

  • Hervías-Parejo S, Tur C, Heleno R, Nogales M, Timóteo S, Traveset A. Species functional traits and abundance as drivers of multiplex ecological networks: first empirical quantification of inter-layer edge weights. Proc Biol Sci. 2020;287: 20202127. doi:10.1098/rspb.2020.2127

  • Galai G, He X, Rotblat B, Pilosof S. Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness. Nat Commun. 2023;14: 1–11. doi:10.1038/s41467-023-41906-2

  • Galai G, Arbel D, Klass K, Grinshpan I, Mizrahi I, Pilosof S. Scale-dependent signatures of microbial co-occurrence revealed via multilayer network analysis. EcoEvoRxiv. 2023. doi:10.32942/x2161c

  • Shapiro JT, Zorea A, Kav AB, Ontiveros VJ, Mizrahi I, Pilosof S. Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission. ISME J. 2023; 1–11. doi:10.1038/s41396-023-01373-5

Mathematics and network structure