codiv

Host-Microbe Codiversification Scans in R

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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.

The main function, codiv(), takes a host tree, a symbiont tree, and a data frame linking each symbiont to the host it was isolated from. For each qualifying node it runs one or more statistical methods (Hommola’s test, PACo, ParaFit, and an opt-in topology-only test) and reports a test statistic and a per-node permutation p-value. Helper functions cover scan-wide false-discovery control, leave-one-host-out analysis, parameter sensitivity sweeps, host-level summaries, molecular-clock regression, tanglegram plotting, and ground-truth simulation.

Installation

Install the development version from GitHub:

# install.packages("pak")
pak::pak("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
results <- codiv(sim$host_tree, sim$symbiont_tree, sim$links,
                 methods = "hommola", permutations = 99)

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

The package also ships the rodent gut-microbiome dataset from Sprockett et al. (2025) in inst/extdata, so you can run a real scan immediately — see vignette("codiv").

Citation

Daniel D. Sprockett, Brian A. Dillard, Abigail A. Landers, Jon G. Sanders, Andrew H. Moeller. (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