codiv

Performs Host-Microbe Codiversification Scans

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The codiv R package performs codiversification scans between pairs of host and symbiont phylogenetic trees. The main functions accepts a host tree, a symbiont tree, and a data.frame that links which symbionts were isolated from which hosts. It outputs a correlation coefficient for each node of the symbiont tree denoted how well it’s topology is correlated with the host tree. Nodes with a high degree of correlation are consistent with codiversification between hosts and those symbionts. Other helper functions are also included.

Installation

You can install the development version of codiv from GitHub with:

# install.packages("devtools")
devtools::install_github("DanielSprockett/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 Accepted.