Lifemap: Exploring the Entire Tree of Life

Abstract

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Fig 1. Three successive zoom levels in Lifemap illustrating the half-circle representation employed.

Each clade is represented by a half-circle whose size depends on the relative number of species in the clade as compared to its sister clades at a given level. Note that these proportions are not respected at the tree root where the three superkingdoms are arbitrarily given the same size. Computation of the size of each half-circle is based on the angle they are associated with (α and β on the first panel): if n_A and n_B are the number of species in clades A and B, respectively, the angles in degrees are computed as follows: $\alpha =180\times \sqrt{n_A}/\left(\sqrt{n_A}+\sqrt{n_B}\right)$ and $\beta =180\times \sqrt{n_B}/\left(\sqrt{n_A}+\sqrt{n_B}\right)$. The square root reduces the difference in half-circle sizes between very small and very large groups. At every level, the half-circles (clades) are randomly distributed within their parental half-circle.

Fig 2. Screenshots of the Lifemap tool.

(A) Example of the appearance of Lifemap when zooming to the primates order. (B) Example of information displayed in the general public version when clicking on a node. (C) Visualization of the path between two taxa. Lemur image credit: Mathias Appel, Flickr (https://flic.kr/p/FKtBbU).

Fig 3. Screenshots of the Lifemap server.

Visualizing a tree with the Lifemap server is a three-step process that is performed from the dedicated web page (top screen). Once the tree file has been uploaded and the computations have been performed, the tree can be explored (bottom screen). This last screenshot shows the appearance of Lifemap for a fully bifurcating tree with nodes automatically named (see text).

Fig 4. Principle of the tiling system used in Lifemap.

Like in OSM, the image displayed at a given zoom level is composed of paving (or tiling) of small square images. To each of these square images at a given zoom level corresponds four images of the same size at the next level.