Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees

Abstract

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user's taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

Keywords: Phylogeny; tree of life; web services.

Figure 1.

A simplified view of workflows supported by the Phylotastic portal (see text for explanation). A variety of methods are used to generate a list of taxa, which can be used to query for a tree topology. The topology can be scaled and decorated with images and links. The portal provides a built-in viewer for phylogenies, which may be downloaded as an image file or a Newick tree file.

Figure 2.

Dated phylogenetic tree of birds from Yellowstone National Park obtained as described in the text. Species from the user’s observation list are shown in red. Bird families are delimited by gray arcs. This figure was generated with functions from rphylotastic, DateLife, and ape R packages. The complete code for this vignette is in the rphylotastic package.

Figure 3.

Three separate groups of aquatic mammals (Cetacea, Pinnipedia, and Sirenia). This figure was generated using the Phylotastic portal, as described in the text.