Food web reconstruction through phylogenetic transfer of low‐rank network representation

Abstract Despite their importance in many ecological processes, collecting data and information on ecological interactions is an exceedingly challenging task. For this reason, large parts of the world have a data deficit when it comes to species interactions and how the resulting networks are structured. As data collection alone is unlikely to be sufficient, community ecologists must adopt predictive methods. We present a methodological framework that uses graph embedding and transfer learning to assemble a predicted list of trophic interactions of a species pool for which their interactions are unknown. Specifically, we ‘learn’ the information (latent traits) of species from a known interaction network and infer the latent traits of another species pool for which we have no a priori interaction data based on their phylogenetic relatedness to species from the known network. The latent traits can then be used to predict interactions and construct an interaction network. Here we assembled a metaweb for Canadian mammals derived from interactions in the European food web, despite only 4% of common species being shared between the two locations. The results of the predictive model are compared against databases of recorded pairwise interactions, showing that we correctly recover 91% of known interactions. The framework itself is robust even when the known network is incomplete or contains spurious interactions making it an ideal candidate as a tool for filling gaps when it comes to species interactions. We provide guidance on how this framework can be adapted by substituting some approaches or predictors in order to make it more generally applicable.