Workflow diagram of the network and cluster analyses.

For each of the 10 nested river basins included in the study, a species’ presence-absence matrix was first compiled then converted to a species’ edge list or a species × species Jaccard dissimilarity matrix. Edge lists were used to build unipartite networks, followed by modularity analysis through simulated annealing. (Pairwise effect sizes from cooccurrence analyses were estimated for use in subsequent tests of nest associate species and are not utilized within the workflow diagram.) Dissimilarity matrices were used in PAM cluster analyses. Comparisons of network modules and PAM clusters included congruence (C) analysis and ratios of mean distances within and among groups (MDwithin:among) when the number of PAM clusters (k) was equal to the number of modules (k = no. modules). However, network and cluster comparisons were limited to MDwithin:among when an optimal number of PAM clusters was independently identified with the gap statistic (k = optimal no.). R packages used in each step of the workflow are shown in curly brackets within gray bubbles (e.g., ‘igraph’).