Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty

Abstract

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H2′]) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co‐occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host–parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%–10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

A waterfowl seed‐dispersal network from the Neotropical region is nested and modular

“…For the same reason, at the species level, only the results for the coscoroba swan may be taken with caution, while those for the remaining species will likely be robust. The effect of sample size for bipartite networks has recently been evaluated by Llopis-Belenguer et al (2022), finding that the categorical (but not the quantitative) classification of networks in nestedness and modularity is robust to a reduced sample size.…”

Do macroinvertebrate abundance and community structure depend on the quality of ponds located in peri-urban areas?

“…In this sense, questions of determination level are less important, since the same precision has been maintained for all samples. Furthermore, studies on interaction networks have shown that the level of determination of specimens has little effect on network characteristics, provided that this level of determination does not fall below too high a threshold (Llopis-Belenguer et al 2023; Renaud et al 2020).…”