Accessing the Open Tree of Life

Bobcat (Lynx rufus)

Bobcat (Lynx rufus) by dkeeffe via iNaturalist. Photo licensed under CC BY-NC 4.0.

Phylogenetic trees can be tricky to assemble, but advances in genetic sequencing and informatics has made the process significantly easier. Still, published phylogenies are often only available as image files with no standard for storage and representation. The Open Tree of Life (OTL) project aims to change this, allowing researchers to assemble and maintain phylogenies in standardized environment. Using a new software package, rotl, researchers can now use the popular data processing suite, R, to directly interact programmatically with the OTL data. The present paper describes how researchers can extract relationships between taxa, but also access phylogenies from specific studies of interest. Species data accessed via rotl can easily be integrated with GBIF-mediated occurrences to visualize occurrences associated with a specific study. The rotl package fits well into the range of R tools available to biodiversity researchers.

Citation information 

Michonneau F, Brown JW and Winter DJ (2016) rotl : an R package to interact with the Open Tree of Life data. Methods in Ecology and Evolution. Wiley-Blackwell 7(12): 1476–1481. Available at doi:10.1111/2041-210X.12593.