ToL History/Future

A Short History of the Tree of Life Project

Early history

The first glimmerings regarding the Tree of Life Project began sometime in the late '80's, when David was working on the computer program MacClade instead of working on his PhD thesis. MacClade is a phylogenetic analysis program for the Apple Macintosh that displays phylogenetic trees on the screen. Inspired by Hypercard, David planned to add a feature to MacClade that would allow the taxa at the tips of the branches of the tree on the screen to be hypertext links to MacClade files that showed trees for those taxa. The idea was that when the user touched on, say, the terminal taxon "mammal" in a tree of vertebrates, MacClade would close down the current file, and open the mammals file, and present the user with the stored tree for mammals. This seemed like enough of a pain to implement, and really, the thesis was waiting, that the idea was shelved until sometime around 1993, when the idea resurfaced.

The connection of phylogenetic trees with hypertext links is certainly not unique to the Tree of Life, and a number of other projects use the same format. Perhaps the two most well-known examples other than the Tree of Life project are LifeMap, an excellent CDROM produced in 1992 by the California Academy of Sciences, and University of California at Berkeley's Phylogeny of Life project. But there are others, and there are several WWW sites that contain classifications connected via hypertext links.

In 1993, David did some more thinking about this. The obvious medium in which to present these linked pages was no longer MacClade, but the World Wide Web. At first, the vision was to have the system just be a way to organize other web sites in a phylogenetic fashion. The vision grew, however, and the idea was formed of having the Tree itself distributed around the world, with different branches residing on different computers, and with a worldwide collection of experts authoring informative pages for their particular branches. David presented Wayne with the idea of having a global Tree of Life on the Web. It wasn't until the summer of 1994 that Wayne finally convinced David this was worth doing, and we got off our rears (the theses were long finished at that point, which was a shame, as theses are very productive for the displacement activities they inspire).

The real difficulty was that this would take a long time to do if specialized tools were not available to somewhat automate the process. David suggested adding features to MacClade that would produce formatted HTML pages containing trees. Wayne took the bull by the horns and added the first versions of these tools to MacClade. The first version of the Tree, put on line in prototype form on 16 November 1994, was written entirely using this version of MacClade. In late 1994, David took over the development of these tools, and rewrote much of them.

We sent out some notices on some relevant lists (e.g. entomo-l, TAXACOM, etc.) asking for suggestions and contributors, but we did not announce the project formally to the WWW community. Over the next few months the Tree went through some major appearance changes, in response in part to these suggestions.

Addition of remote branches and formal announcement of the Tree

In the early days, all pages on the Tree were on the home site in Tucson, Arizona. On 1 June 1995, the first remote branch of the Tree was added, the crayfish pages by Keith Crandall (U. Texas). These files resided on a computer in Austin, Texas. In the following years, a number of remote branches were added. The branches of the Tree that were authored by people other than the two of us, which were attached to the Tree when the Tree was first formally announced (5 January 1996), are as follows. (Some of these contain no more than a tree, others are fairly complete.)

Keith Crandall's crayfish pages.

First attached 1 June 1995; pages housed at the University of Texas, Austin.

Peter Beerli's Western Palearctic water frogs.

13 June 1995; University of Washington.

Scott Stockwell's scorpion pages.

16 June 1995; Smithsonian Institution.

John Lundberg's Chordata, Vertebrata, and fish pages.

4 July 1995; at the home site.

John Friel's banjo catfish pages.

5 July 1995; Florida State University.

James Albert and John Lundberg's electric fish.

2 August 1995; at the home site.

Jonathan Browne, Clarke Scholtz, et al.'s Scarabaeoidea pages.

24 August 1995; at the home site.

David Stern's pages on aphids and related insects

with contributions by Nancy Moran.

26 October 1995; Churchill College, Cambridge, England.

Tim Berra's salamanderfish page.

20 December 1995; at the home site.

W.E. Hall's featherwing beetles page .

2 January 1996; at the home site.

Mitch Sogin and David Patterson's basal eukaryote pages.

3 January 1996; at the home site.

David Cannatella, Lori Bockstanz, et al.'s frog pages.

3 January 1996; University of Texas at Austin. The addition of the branch turned Peter Beerli's pages into the first doubly-remote site (that is, a branch of the Tree on a computer other than the home computer that is connected not to the home site but to another remote site).

Allan Larson's salamander pages.

3 January 1996; at the home site.

Michel Laurin's Terrestrial Vertebrates and Amniotes pages.

4 January 1996; at the home site.

Rick McCourt et al.'s Green Plant pages

4 January 1996; at the home site.

Michael Donoghue's angiosperm pages

4 January 1996; at the home site.

Kenneth Sytsma and Jeffrey Hapeman's Myrtales pages

4 January 1996; at the home site.

On 5 January 1996, when the Tree of Life project was first formally announced, the Tree itself contained 948 pages, housed in seven computers on two continents.

Events since 1996

Since 1996, the Tree has more than doubled in size, through the efforts of more than 320 biologists from 21 countries. For information about growth of the Tree's branches and leaves since 1996, see the Growth Monitor page. David Maddison has continued to serve as coordinator and editor for the project.

Since the formal announcement, the following events are worthy of note:

• 12 July 1996. The first treehouse added to the Tree.
• January 1997. Katja Schulz joins the Tree of Life project as technical assistant. She becomes the managing editor.
• 11 September 1998. First peer-reviewed page added to the Tree, for the rove beetle subfamily Aleocharinae. Home pages associated with the Tree extensively revised.
• July 2000. The Tree of Life project receives funding from the National Science Foundation to aid in its conversion into a database-driven system. This is the first major funding for the project.
• October 2000. Travis Wheeler joins the project, as lead programmer in the rebuilding of the ToL. The reconstruction of the ToL begins.
• 18 April 2001. The first beta version of the new, database-driven Tree of Life website is released to a select group of beta testers.
• 25 October 2001. The beta 2 test version of the new Tree of Life website is released to the public.
• 12 February 2002. The database-driven version of the Tree of Life Project becomes the public version. The new project is now driven by a database, with web pages created dynamically. This new architecture allows the ToL to add many novel features that affect both the presentation of information and its use (for example, information sharing and analysis with other database systems and analytical tools).
• 23 April 2003. The first user customization features were added to the ToL site. Read more aboutl these features on the Customizing Your View of the Tree of Life page.
• 27 May 2003. Danny Mandel joins the ToL Home team as a programmer working on the development of the ToL data entry tools for contributors.

For a list of recent ToL events, please refer to the ToL News page.