The Tree of Life Web Project*

Abstract

The Tree of Life Web Project (ToL) provides information on the Internet about our current knowledge of the evolutionary tree of life and associated information about characteristics and diversity of life on Earth. Development of this open-access, database-driven system began in 1994; its official release was in 1996. Core scientific content in the project is compiled collaboratively by more than 540 biologists, all experts in particular groups of organisms, from over 35 countries. Additional learning materials are contributed by over 200 students, teachers, and amateur scientists, while images, movies, and sounds are contributed by both of these groups and over 200 media-only contributors. Administration of the project follows a hierarchical, community-based model, with authors for different parts of the ToL chosen by the scientists working in that particular field. The goals of the project are to document all species on Earth, as well as all significant clades; to provide basic information about the phylogeny of life; to share this information with other databases and analytical tools; and to encourage understanding and appreciation for biodiversity, evolution, and the interrelationships of Earth's wealth of species. Here we provide an outline of the goals and history of the project; the current content, administration, architecture, contributors, and audience, the challenges we have faced, and the future of the project.

Host Plant Utilization, Host Range Oscillations and Diversification in Nymphalid Butterflies: A Phylogenetic Investigation

“…Another way to show this is at the species level: there are about 6000 described species in the family (Maddison and Schulz 2007), but we found only 249 species with records of feeding on more than one plant order, and out of these only 79 have been indicated to feed on at least three orders (Table 1). For our purposes, furthermore, only the latter type of species can be seen as candidates for being "truly" polyphagous, that is opportunistic generalists, because it is a common pattern in Nymphalidae that a couple of ancestral clade-specific host orders are used in parallel-a pattern rather more indicative of conservative host use than opportunism.…”

Hybridisation is associated with increased fecundity and size in invasive taxa: meta‐analytic support for the hybridisation‐invasion hypothesis

“…We conducted phylogenetic meta-analyses using PhyloMeta version 1.3 (Lajeunesse 2011) to account for this non-independence. A phylogeny was constructed as follows: a base topology of plant taxa was derived from Phylomatic v.3 (Webb & Donoghue 2005) using tree R20120829; resolution within Asteraceae was added using topologies in Funk et al (2009); animal and fungal taxa were added based on Maddison & Schulz (2007). We aged internal nodes for the phylogeny of plant taxa based on Wikstr€ om et al (2001), using the bladj algorithm in Phylocom to interpolate ages of undated nodes (Webb et al 2008).…”

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta‐analysis

“…Plant-only phylogenies used the topology from the Davies et al (2004) supertree (through the Phylomatic web service; Webb & Donoghue 2005) and node age estimates from Wikström et al (2001). Topology and branch lengths for bird-only phylogenies were obtained from Hackett et al (2008), with additional taxa added using the online tree of life (Maddison et al 2007). For datasets including divergent animal taxa, we manually built phylogenies in MESQUITE v. 2.73 (Maddison & Maddison 2010) using information from multiple published phylogenies (see references in Figure 1 Bars show the number of published meta-analyses subject to potential phylogenetic non-independence (i.e.…”