Handling phylogeny data

This is a blog post on handling phylogeny data in R Statistical Software. The objective was to see how we map species on the phylogeny of the whole taxa. The main packages used were ape, and phytools to handle the phylogenetic analysis. This matters because studying closely related species often means studying animals that share similar behaviors, ecologies, and life histories. As a result, our understanding of animal movement may be much deeper for certain kinds of mammals than for mammals as a whole. The figure maps tracked species onto the evolutionary tree of mammals. Red branches represent lineages that have been studied using remote tracking technologies, while branch colors indicate different mammalian orders.

At first glance, the pattern is impossible to miss: rather than being spread evenly across the tree, tracked species cluster heavily within a handful of groups. Some mammalian orders contain dozens of the species from a particular set (red branches), while others have no tracked species at all. ——