  Identifying undocumented or potential future interactions among species is a
challenge facing modern ecologists. Recent link prediction methods rely on
trait data, however large species interaction databases are typically sparse
and covariates are limited to only a fraction of species. On the other hand,
evolutionary relationships, encoded as phylogenetic trees, can act as proxies
for underlying traits and historical patterns of parasite sharing among hosts.
We show that using a network-based conditional model, phylogenetic information
provides strong predictive power in a recently published global database of
host-parasite interactions. By scaling the phylogeny using an evolutionary
model, our method allows for biological interpretation often missing from
latent variable models. To further improve on the phylogeny-only model, we
combine a hierarchical Bayesian latent score framework for bipartite graphs
that accounts for the number of interactions per species with the host
dependence informed by phylogeny. Combining the two information sources yields
significant improvement in predictive accuracy over each of the submodels
alone. As many interaction networks are constructed from presence-only data, we
extend the model by integrating a correction mechanism for missing
interactions, which proves valuable in reducing uncertainty in unobserved
interactions.
