Predicting Species Interactions from Phylogenetic Distance

Tools to model and predict host-parasite (and other pairwise species) interactions from phylogenetic distance under presence-only data. Provides pairwise host-sharing logistic models with cluster-aware bootstrap and slope comparison between clades, presence-only performance metrics (a threshold efficiency metric and a phylogenetic partial receiver operating characteristic (ROC) adapted from Peterson, Papes and Soberon (2008) ), positive-unlabeled host prediction, and leave-hosts-out validation. Methods build on Robles-Fernandez and Lira-Noriega (2017) .

phylopred

Predicting species interactions from phylogenetic distance under presence-only data.

phylopred models the probability that two species share a parasite (or other interaction) as a function of their phylogenetic distance, and predicts new hosts for a parasite from its known hosts:

• Pairwise host-sharing logistic models, parasite-cluster bootstrap, and formal slope comparison between clades (generalist vs specialist).
• Presence-only performance metrics: threshold efficiency f_gamma = a / (gamma * b + c) and a phylogenetic partial ROC (sensitivity vs fraction of the phylogeny predicted suitable).
• Positive-unlabeled (PU) host prediction with xplus on phylogenetic features.
• Leave-hosts-out validation of predictive performance.

Installation

remotes::install_github("alrobles/phylopred")

Documentation site: https://alrobles.github.io/phylopred/

Example

library(phylopred)

pairs <- prepare_pair_data(beetleTreeInteractions, phy_dist)
fit <- fit_phylopred_model(pairs)
summary(fit)

parasite <- names(sort(table(pairs$parasite), decreasing = TRUE))[1]
one <- pairs[pairs$parasite == parasite, ]
one$pred <- predict(fit$fit, newdata = one, type = "response")
m <- host_threshold_metric(one$pred, one$suscept)
plot(m)
roc <- phylo_partial_roc(one$pred, one$suscept, error_rate = 0.95)
plot(roc)

See the vignette caligus-vs-lepeophtheirus for a complete real-data case study with the cofid copepod-fish interaction database and the Fish Tree of Life.

Manuscript

The manuscript, supplementary material, and archived analysis results are maintained separately in the phylopred-paper repository.

References

• Robles-Fernandez, A. L. & Lira-Noriega, A. (2017). Combining phylogenetic and occurrence information for risk assessment of pest and pathogen interactions with host plants. Frontiers in Applied Mathematics and Statistics, 3:17. doi:10.3389/fams.2017.00017
• Peterson, A. T., Papes, M. & Soberon, J. (2008). Rethinking receiver operating characteristic analysis applications in ecological niche modeling. Ecological Modelling, 213, 63-72.
• Rabosky, D. L. and colleagues (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559, 392-395.
• Morales-Serna, F. N. (2025). Global patterns of modularity and narrow host use in fish-parasitic copepods (Crustacea). Biodiversity Data Journal, 13, e163693. https://doi.org/10.3897/BDJ.13.e163693 — basis of the cofid database (https://github.com/alrobles/cofid)