Performs Host-Microbe Codiversification Scans
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.
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.