Tree of Life Q + A

http://phylogeny.arizona.edu/tree/home.pages/questionsanswers.html (PC Press Internet CD, 03/1996)

Tree of Life Q + A

Questions and Answers about the Tree of Life

In addition to this document, a general introduction to the Tree is available, as is a Tree of Life Help document.

Table of Contents:

Using the Tree
Building the Tree
Miscellaneous
- How do faunal and floral treatments and collections data bases integrate into the system?
- Will there be a t-shirt?

Using the Tree

How do I find particular organisms in the Tree?

There are three methods to find pages on the Tree:

Wander up the branches of the Tree until you can find the group you are looking for. This is the scenic route. To aid you the authors of the pages are adding notes beside the taxa listed in the tree on each page, so that you know what you will find if you go up that branch. However, this can be tedious, and even still, you may not be able to find what you are looking for.
Check out the Sample Pages or Commonly Accessed Clades section of the Express Page; this will only be relevant, of course, if the group you are looking for is on one of the sample pages or is listed in the Commonly Accessed Clades.
Search for the group by using the form on the Search Page.

How is uncertainty in the phylogeny shown?

Many phylogenetic hypotheses, especially in poorly studied groups of organisms, are not well established. Uncertainty in the phylogeny can be expressed in the Tree in several ways.

The prefered method is for a Tree of Life page to show a single tree at the top of the page (for use in navigation through the Tree), and then to show, in the Discussion of Phylogenetic Relationships section, alternative trees, with a fair, open-minded, brief discussion of the evidence for and against the alternatives. The tree at the top of the page might, in this case, be a consensus view, showing only the well established branches, with regions of the tree poorly resolved (as shown by polytomous rather than dichotomous branching). On the other hand, the tree at the top might be the most well-supported tree according to the author of the page, with alternative and consensus tree shown below.

The Tree of Life project also allows the possibililty that there will be several competing pages for the same clade, although this is discouraged. If this approach were used, and if, for example, there were multiple trees for insects, then when one touched on the terminal taxon "Insecta" in the Hexapoda tree, instead of taking you to the insect tree it would take you to a note saying there are several alternative trees that might be followed at this point, and it would give the links to them. Alternatively, there may be a default link to one of the possible trees, but a footnote giving alternatives. Likewise, several alternatives may be presented going down the Tree when the containing clades have various alternative trees. Currently, no competing pages are present for any branch of the Tree.

Are the pages peer reviewed?

This will be an option in the future.

Are the pages considered publications?

We would hope that completed pages be considered publications, and would be considered as full publications if they are peer-reviewed. There are many issues to consider, including how one cites a page that is growing incrementally.

As the academic community increasingly considers the Internet an important means for disseminating information, academic administrations will need to adapt and create mechanisms to give credit appropriately for electronic works.

How should I cite the Tree of Life?

First, we repeat the warning from the Home Page of the Tree:

Warning! If you wish to cite a page in this project in a formal publication, you should not cite any page that contains the icon. In these instances you should cite the original publications. This system is still under construction, so in some cases the phylogenies and other information presented are not the most well-supported hypothesis available today; instead, they represent information that we had easy access to. If a page lacks a "Page Under Construction" icon, we suggest you contact the author or us regarding whether or how it might be cited in a publication.

However, once the Tree becomes more mature and peer-reviewed, it will be perfectly legitimate to cite material in the Tree. And even now, you may want to cite the Tree in a discussion of Internet resources. Here is a possibility:

Maddison, D.R. and W. P. Maddison. 1996. The Tree of Life: A distributed Internet project containing information about phylogeny and biodiversity. Internet address: http://phylogeny.arizona.edu/tree/phylogeny.html

Building the Tree

How does one build a Tree of Life page for a particular clade?

Our goal is to have the burden of maintaining different clades of the Tree of Life distributed throughout the world. We have built tools that facilitate creation of the HTML documents a site needs for its part of the Tree of Life. The main tool is a special version of MacClade (MacClade's WWW site contains information about the regular, release version of MacClade) that writes the tree in MacClade's tree window in HTML format and includes in the HTML file hypertext links and textual information based on information entered in special new editors within MacClade. With these tools it is fairly easy to create a clade page and link it into the Tree of Life. They will also encourage uniformity of appearance and behavior of the navigation through each page. Those interested in contributing some branches should contact us at tree@ag.arizona.edu.

Another document discusses how to contribute to the Tree of Life.

How is a new page linked in to the Tree?

Once the page is built, it needs to be linked in to the Tree of Life. The author of the page needs to contact the authors of the pages of the immediately containing clades so that pointers to the new page could be placed there.

Will there be complications in linking page to page?

Yes. Here are some of the ones that have occurred to us:

Sites will go off line temporarily (lightning storms, maintenance) or permanently (retirements, loss of funding). We will maintain a backup set of links to registered sites at the home server so that one can bypass the part of the Tree that is down. This backup system has not yet been built.

There will be on occasion alternative (competing?) pages for a given clade. This is to be dealt with as an issue of multiple trees (discussed in the section on uncertainty in the phylogeny); linking along the Tree of Life should fork to give the user choices for which of the alternative pages to enter.

Some difficult issues of linking occur when disagreement about phylogeny crosses levels of Tree of Life pages. For instance, suppose one phylogenetic hypothesis claims the Platyhelminthes is monophyletic and a page is established for that group. If there is a competing hypothesis that Platyhelminthes is polyphyletic, then a page for a containing clade (eg., animals) that follows the competing hypothesis may need to make multiple links into the Platyhelminthes page, one for each occurrence of a former platyhelminth on the tree of animals. This would also pose problems for the Platyhelminth page's linking back down the Tree into the containing page. Other disagreements between linking pages could be imagined that would require some patience and cooperation.

Pages may be developed which are beyond the reach of the finest level otherwise developed for the Tree of Life. A page may be developed, for instance, to a genus of rotifers before anyone has made an overall page for rotifers. In this case we may request the author of the page to provide a provisional set of trees of rotifers to help navigate up to that genus.

How is the system governed?

We are serving as Editors of the Tree, and are choosing people that will serve effectively as associate editors for particular parts of the Tree. Our current plan is to exercise more editorial control for the larger or more significant clades, with less and less control being exercised toward the tips of the Tree. For example, once a peer-review system is put into place, we will expect the more basal parts of the Tree to be peer-reviewed. Less importance will be placed on peer review for small clades at the tips of the Tree. Basal portions of the Tree will therefore evolve into something like a peer-reviewed journal, with the tips growing by more a form of cooperative anarchy. (Some small clades will be peer-reviewed, but some of them need not be.)

What if there are uncooperative authors?

One could imagine various ways an author of a page could fail to participate fairly. For instance, authors would be uncooperative if they fail to link descendent pages to their page. Controlling this would be difficult, and may require unlinking the pages of the uncooperative authors from the Tree.

How do faunas, floras and collections data bases integrate into the system?

Faunal and floral treatments deal with a limited geographic area, and as such may deal with only portions of the tree of any particular clade. These would not be considered portions of the Tree of Life itself, but could be easily built in parallel and well-linked to the Tree of Life. The tools for building Tree of Life pages can be used for building faunal and floral works; if you are interested in using these tools for this purpose, please contact us.

Will there be a t-shirt?

Maybe.