Tree of Life Help

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

Tree of Life Help

Tree of Life Help

The Tree of Life is a collection of WWW pages presenting information about the phylogenetic (or evolutionary) tree of organisms, and the properties of various groups. By following up the branches of the Tree, you can arrive at one of the many, many groups of organisms. There you may find information about the group, either contained in a page of the Tree of Life, or in Internet sites to which the page refers.

This help document contains information on the following topics:

The standard features of a page in the Tree of Life.
The function of the toolbar buttons.
Interpreting the tree or classification
How to navigate on the Tree of Life

Other documents that may be of interest are:

The home page of the Tree of Life
An introduction to phylogenetic biology, including a explanation of the nature of a phylogeny.
An introduction to the Tree of Life
Goals of the Tree of Life
Questions and answers about the Tree of Life.
A discussion of how to contribute to the Tree of Life.

A page in the Tree of Life

Each page concerns an evolutionary group of organisms, otherwise known as a clade. At the top of the page is a toolbar, consisting of several buttons for Tree navigation and several buttons that take you to various parts of the page. Below the toolbar is the introductory section of the page, followed by the phylogenetic tree or classification for the group of organisms. This phylogenetic tree contains your means of navigation through the Tree of Life: it has links to deeper parts of the Tree of Life (toward the root) and to finer parts of the Tree (toward the tips). Below the tree may be various topics, including an introduction to the group, characteristics of members of the group, a discussion of phylogenetic relationships, other sources of information about the group on the Internet, literature references, and so on. Finally, at the bottom of the page, is another toolbar with buttons that take you to various pages connected with the Tree of Life

Toolbar buttons

The buttons in the toolbars are as follows:

Buttons for navigating between taxa in the tree

The previous button or next button take you to the previous or next taxon as defined by the enclosing clade. For example, if your current page shows the tree or classification of the genus Sarimenia, and the enclosing clade's tree looks like this:
```
              ======================Neblumia
           ===|
           |  ======================Sarimenia
     ======|
           |              ==========Fubonidia 
           ==Fubonidiines=|
                          ==========Titanotilus
```
then the previous taxon button on Sarimenia's page will take you up to Neblumia (toward the top of the tree), and the next taxon button will take you down to Fubonidia. In general, the previous button takes you to the page for the terminal taxon that is closer to the top of the enclosing clade's page. If you were on the page for Sarimenia, and you pressed the next button several times, you would scroll from Sarimenia, to Fubonidia , and finally to Titanotilus. In general, the next button takes you down the list of terminal taxa, to the terminal taxon that is closer to the bottom of the page. The previous and next buttons allow you to quickly scroll through the pages for the terminal taxa of a clade.
Some sections of the tree violate this simple rule about the behavior of the next and previous buttons. One such section is the part of the tree showing hexapod orders. Consider the page showing the order Protura. Looking at the containing clade:
```
           ===Collembola
     ======|
     |     ===Protura
<<===|
     =========Diplura
     |
     =========Insecta
```
one would expect that the previous button would take one to the Collembola page, and the next button to the Diplura page. This is exactly what they do. However, on the Diplura page, while the previous button takes one to the Protura page, the next button does not take one to the Insecta page as one might expect, but instead takes one to the first order on the Insecta page, the Archaeognatha. Here is the tree on the Insecta page:
```
     =====================Archaeognatha
     |
     |  ==================Thysanura
     |  |
<<===|  |           ======Ephemeroptera
     ===|           |
        =Pterygota==|=====Odonata
                    |
                    ======Neoptera
```
On the page for each hexapod order then, the next and previous buttons take one to another hexapod order, so that repeated pressing of the next button would take you on a path from Collembola to Protura to Diplura to Archaeognatha to Thysanura to Ephemeroptera to Odonata and on through each of the Neopteran orders. If you wish to try this for yourself, you might go to the page for Collembola.
The enclosing clade button or down button takes you the enclosing clade, that is, the next larger clade that includes the current group.
The deep enclosing clade button allows you to quickly move down the Tree, by taking you down through several levels of enclosing clades. It is equivalent to pressing the enclosing clade button on several pages in succession.
The root button takes you to the root of the entire Tree of Life.

Buttons for moving to points on the current page

The go to tree button scrolls the current page so that the tree is at the top of the page.
The go to classification button scrolls the current page so that the classification for the group is at the top of the page.
The go to top button scrolls to the top of the page.
The go to bottom button scrolls to the bottom of the page.

Buttons to go to pages outside of the Tree itself

The tree help button takes you to this page.
The Tree of Life home page button takes you to the home page for the Tree of Life.
The Express page button takes you to the express page for the Tree of Life, from which you can jump to various branches in the Tree. The express page gives links to commonly accessed clades, and contains a search system so that you can ask for the page containing a particular group of organisms.

Interpreting the tree or classification

An example tree on the screen might look like this:

     ================== gut bacteria
     |
     |  =============== trees
     |  |
     |  |  ============ mushrooms
     |  |  |
     |  |  |     ====== fish
=====|  |  |     |
     ===|  |  ===|  === mammals
        ===|  |  ===|
           ===|     === birds
              |
              |  ====== dragonflies
              ===|
                 ====== beetles

This partial phylogeny shows only a few of the many millions of living species, and is therefore far from complete, but it is useful for this example. This phylogeny states that there was an ancestral species that split to give rise (billions of years later) on the one hand to gut bacteria, and on the other to multi-celled organisms we see today. The multi-celled lineage split again, and again, diversifying into numerous forms. The phylogeny states that there was an ancestral species that gave rise to mammals and birds, but not to the other species shown in the tree (that is, mammals and birds share a common ancestor that they do not share with other species on the tree), that all animals are descended from an ancestor not shared with fungi, plants, and bacteria, and so on.

The phylogeny shown above is dichotomous, in that at all branch points there are two immediate descendents. If there are more than two immediate descendents at a given branch, then the tree is polytomous. For example, in the following tree, there is a polytomy from which dragonflies, mayflies, and beetles arise, indicating that the relationships between these three lineages is not yet clear:

     ================== bacteria
     |
     |  =============== trees
     |  |
     |  |  ============ mushrooms
     |  |  |
     |  |  |     ====== fish
     |  |  |     |
=====|  |  |  ===|  === mammals
     ===|  |  |  ===|
        ===|  |     === birds
           ===|
              |  ====== mayflies
              |  |
              ===|===== dragonflies
                 |
                 ====== beetles

We don't know if dragonflies and mayflies are more closely related to each other than either is to beetles, or whether beetles are more closely related to mayflies, or beetles to dragonflies.

Branches that are shown as a series of vertical bars indicate that the group is not or is likely not monophyletic. In the following example, Group A is non-monophyletic, indicating that Group B's closest relative is actually a subgroup of Group A:

      |||||||||||||||||| Group A
======|
      |================= Group B

Navigating through the Tree of Life

To wander up the Tree, click on the taxa at the tips of the branches of each tree. That will take you to the page for that taxon. To go down the Tree, either click on the root of the tree on the page, or on the Down (for slowly going down the Tree) or Deep (for leapfrogging down the Tree) buttons.