Space, time, form: viewing the Tree of Life Roderic D.M. Page  Trends in Ecology & Evolution  Volume 27, Issue 2, Pages 113-120 (February 2012) DOI: 10.1016/j.tree.2011.12.002 Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Entries in the iEvoBio 2010 visualisation challenge. The five entries in the iEvoBio 2010 challenge were the interactive phylogeny viewers Phylobox (a) and jsPhyloSVG (b) [56], the GenGIS system for genomics data (c) [57], a treemap-based classification viewer from the Encyclopedia of Life (d) and the phylogeny and alignment viewer Nexplorer (e) [57]. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Tree visualisations. A selection of tree visualisations. The classical two-dimensional (2D) Euclidean drawing of a tree (a) is the most widely used, but other approaches are increasingly being explored, such as space-filling treemaps (b) and focus+context methods, such as hyperbolic viewers (c). Three-dimensional (3D) depictions include displaying a phylogeny on a 3D globe, such as Google Earth (d), and as a landscape the user can ‘fly through’ (e). 3D-stacked layouts can also be used to depict the relationship between multiple genes from the same species (f). Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Folding a tree. To save space, the subtree shaded in (a) is collapsed and drawn as a smaller triangle (b). The choice of which nodes to collapse can be automated, or left as a task for the user. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 Phylogenies in three dimensions. (a) Hyperbolic view of the National Center for Biotechnology Information taxonomy [58]. (b) Google Earth visualisation of the Hawaiian endemic katydid genus Banza based on the phylogeny from [58]. (c) Stacked representation of a gene tree with multiple gene duplications [32]. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 5 Reconciled trees and tanglegrams. (a) In a reconciled tree, one tree (such as a gene tree) is embedded inside another tree; for example, the phylogeny of the species from which the genes were obtained. (b) Trees for different, associated entities, such as genes and species, or hosts and parasites, can also be depicted using a tanglegram. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 6 Alternative visualisations of uncertainty in trees. (a) Two and a half dimensional visualisation of a series of trees where neighbouring trees show minor topological changes. (b) DensiTree visualisation of variation in estimates of branch length among a set of trees. (c) Phylogenetic network showing two conflicting signals for a set of four taxa. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 7 Interacting with phylogenies. (a) Displaying a phylogeny using multiple monitors. (b) Interacting with a visualisation using a touch screen. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure I Four representations of the same evolutionary tree that differ in ordering of the tips (a) or horizontal ordering of the internal nodes (b). Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure I Three different approaches to viewing very large objects on a computer screen. Trends in Ecology & Evolution 2012 27, 113-120DOI: (10.1016/j.tree.2011.12.002) Copyright © 2011 Elsevier Ltd Terms and Conditions