codiv

Host–microbe codiversification analysis in R.

codiv scans pairs of phylogenetic trees — a host tree and a symbiont tree — and asks, at every internal node of the symbiont tree, whether the symbionts’ branching pattern mirrors their hosts’. Nodes where symbiont topology tracks host topology are evidence of codiversification: hosts and their microbes diversifying together.

What it does

• Multi-method node scan (codiv()) — runs multiple statistical methods (Hommola’s test, PACo, ParaFit, and a topology-only test) at every qualifying node to quantify the similarity between the host and symbiont trees, with per-node permutation p-values.
• Rigorous scan-wide significance (codiv_null_scans()) — a second-order permutation test that accounts for the phylogenetic non-independence of nested clades.
• Interpretation & robustness — leave-one-host-out analysis, parameter sensitivity sweeps, host-level summaries, a molecular-clock regression, and ggplot2 tanglegrams.
• Ground-truth simulation (simulate_codiv_data()) — generate host/symbiont datasets with known codiversification to validate and calibrate.

Installation

# install.packages("devtools")
devtools::install_github("SprockettLab/codiv")

Quick example

library(codiv)

# simulate a small dataset with known co-diversification
sim <- simulate_codiv_data(n_hosts = 12, n_clades = 20, seed = 1)

# scan every qualifying node of the symbiont tree
codiv_results <- codiv(sim$host_tree, sim$symbiont_tree, sim$links,
                       methods = "hommola", permutations = 99)

codiv_results            # compact overview: settings + significant nodes per method
summary(codiv_results)   # per-method statistic ranges and significant-node counts

The package ships the full rodent dataset from Sprockett et al. (2025) in inst/extdata, so you can run a real scan immediately.

Where to go next

• Getting Started — the main tutorial.
• Simulation & validation — ground truth and false-discovery control.
• Secondary analyses — robustness, dating, and visualization.
• Reference — every user-facing function.

Citation

If you use codiv, please cite:

Sprockett, D. D., Dillard, B. A., Landers, A. A., Sanders, J. G., & Moeller, A. H. (2025). Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice. Nature Communications. https://doi.org/10.1038/s41467-025-57435-z