Machuruku is an R package developed with Wilson X. Guillory for phylogenetic niche modeling and ancestral distribution estimation. Machuruku, named after the Quechua word for ‘ancient’, uses a modified Bioclim niche-modeling method and ancestral character estimation to reconstruct ancestral niches. Input data consists of present-day climate rasters, a time-calibrated phylogeny, and taxon occurrence data for all tips. Ancestral niche models can then be projected into paleoclimate data (a good sources is: www.paleoclim.org) to visualize the potential distributions of evolving lineages across time and space. The most update version of this is hosted on Wilson’s Github: https://github.com/wxguillo/machuruku. Please stay tunned for the assocaited paper coming soon in Systematic Biology!
To install Machuruku, simply run the following in R:
install.packages(c("BiocManager", "devtools")) BiocManager::install("ggtree") devtools::install_github("wxguillo/machuruku")
For both quick and detailed tutorials on how to use Machuruku, please visit the tutorial page in this repository.
Software citation and associated manuscript: Guillory WG, Brown JL. A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions. Systematic Biology - in press