Motifs in the assembly of food web networks

Abstract

The assembly of local communities from regional pools is a multifaceted process that involves the confluence of interactions and environmental conditions at the local scale and biogeographic and evolutionary history at the regional scale. Understanding the relative influence of these factors on community structure has remained a challenge and mechanisms driving community assembly are often inferred from patterns of taxonomic, functional, and phylogenetic diversity. Moreover, community assembly is often viewed through the lens of competition and rarely includes trophic interactions or entire food webs. Here, we use motifs -subgraphs of nodes (e.g. species) and links (e.g. predation) whose abundance within a network deviates significantly as compared to a random network topology -to explore the assembly of food web networks found in the leaves of the northern pitcher plant Sarracenia purpurea. We compared counts of three-node motifs across a hierarchy of scales to a suite of null models to determine if motifs are over-, under-, or randomly represented. We then assessed if the pattern of representation of a motif in a given network matched that of the network it was assembled from. We found that motif representation in over 70% of site networks matched the continental network they were assembled from and over 75% of local networks matched the site networks they were assembled from for the majority of null models. This suggests that the same processes are shaping networks across scales. To generalize our results and effectively use a motif perspective to study community assembly, a theoretical framework detailing potential mechanisms for all possible combinations of motif representation is necessary.

The Interplay Between Landscape Structure and Biotic Interactions

“…A relatively new approach explores the network structure of multiple networks of the same type over large spatial extents (e.g., [166,172]). This approach has potential for identifying drivers of change in network structure, how species' roles change within networks over space and time [173], and the assembly of local networks from networks at continental and regional scales (a.k.a., metawebs; [174]). …”

Ecological network metrics: opportunities for synthesis

“…) to network assembly (Baiser et al. ), stability (Allesina and Pascual , Borrelli et al. ), and persistence in food‐webs (Stouffer and Bascompte ).…”

“…The ER model has been applied in ecology to address questions about the relationship between stability and complexity (May 1972) and the structure of genetic networks (Kauffman et al 2003). For example, randomized networks have been used to link motifs (Milo et al 2002) to network assembly (Baiser et al 2016), stability (Allesina and Pascual 2008, Borrelli et al 2015, and persistence in food-webs (Stouffer and Bascompte 2010).…”

Replication Timing Networks: a novel class of gene regulatory networks

“…We computed all possible network motifs composed by 2-4 nodes and identified the motifs with high enrichment in each RT network constructed per differentiation pathway (Supplemental Figures S3-S5). Statistical significance (pvalue <0.01) of each motif occurrence in the RT networks was calculated by comparing to the frequency of the same motif in randomized networks (Milo et al 2002;Baiser et al 2015;Elhesha 260 and Kahveci 2016). The most frequent motifs with 2, 3 and 4 nodes in each differentiation pathway are shown in Figure 4B.…”

“…The analysis was limited to motifs of ≤ 4 nodes. First, because it has been shown that the fundamental regulatory 555 sub-network patterns consist of a small number of nodes networks (Baiser et al, 2015;Elhesha and Kahveci, 2016;Milo et al, 2002;Yeger-Lotem et al, 2004). Second, because the number of possible motif topologies grow exponentially with number of nodes making it impossible to test larger motif sizes.…”