Taxa, Trees, Characters ˇ


Publication Quality Trees

Mesquite is not designed for rigorous tree-estimation procedures, such a Maximum Parsimony, Maximum Likelihood, or Bayesian tree estimation. However, trees generated from programs such as PAUP, PHYLIP, and MrBayes can be read into and manipulated in Mesquite. This guide will help you perform these manipulations to create a tree usable for scientific publication. Users should begin by familiarizing themselves with the Mesquite file structure. There is also a Youtube video showing you how to make publication quality trees.

Step 1: Get a tree

Step 2: Choose Tree Form

Some examples of Tree Forms:
external image diagonalTree.gif
external image squareTree.gif
external image curvogramTree.gif
external image ballsNSticksTree.gif
Balls N Sticks
Most trees are published as "Square Trees", which you can select from the Display menu in the Tree Window. There are a variety of other formats available, which we encourage you to explore, but some of the following instructions will only apply to square trees (this is noted where it applies).

Step 3: Branch Lengths

To show branch lengths of a tree, select Display > Branches Proportional to Lengths. The branches will now reflect lengths, and a scale is shown. You can toggle the scale off/on from the Display menu (Display > Show Scale). Note: if the branch lengths for a tree are unassigned, and Branches Proportional to Lengths is selected, the tree will be drawn with arbitrary branch lengths (usually so that each branch has a length of 1.0) and the scale shown. If you don't know if the tree has branch lengths assigned, see the instructions for viewing the tree in newick format, below. Alternatively, you can check branch lengths by using the "Adjust Branch Length" tool (external image adjustBranchLength.gif); if a branch does not have a branch length assigned, the box that opens when you use the Adjust Branch Length tool will show a "?".

Step 4: Branch Colors

There are two approaches to coloring branches, the first colors all branches of the tree, and the second applies different colors to different branches (there is a third means of coloring branches, according to Character Reconstructions, but for this step, we only discuss the first two). To color all the branches of a tree, select Display > Branch Color and choose from the list of available colors.
To color individual branches, you can use the Branch Coloring tool (external image color.gif) from the Tree Window tool palette on the left-hand side of the Tree Window. This tool can be used to add colors for cosmetic effect to a tree (these colors play no role in analyses, and are not dictated by character states per se. See "Character Reconstructions" under step 6 below for branch coloring that based on character reconstructions). To set the color, right/control-click on the Branch Coloring tool icon, select Branch Paint Color, and choose from the list of available colors. Clicking on a branch with this tool will color that branch, control-clicking on a branch will color that branch, and all the descendant branches.
You can remove colors from branches by right/control-clicking on the Branch Coloring tool icon, and selecting Remove Color. The Remove Color tool works the same way as the branch coloring tool on single branches (click) and entire clades (control-click). You can also remove all colors from a tree by selecting Remove All Color from the Branch Coloring Tool icon options. It is important to note that colors added with the Branch Coloring tool will always be on top - any color changes applied from the Display > Branch Colors will not be visible on branches that have been colored using the Branch Coloring tool.

Step 5: Taxon Name Colors and Size

To color taxon names, you can partition the taxa into groups (groups are not the same as associations. To set a group, first go to the Taxa window for the Taxon block that contains the Taxon names you'd like to color (this will be the taxon block that corresponds to the tree window you are looking at). There should be a "Group" column on the list. If not, you can show the column by selecting Columns > Group Membership (taxa). First, select all the taxa in your first group. Using the small black triangle at the top of the column, select New group... (clicking once on the black triangle will bring up the Group menu). In the New Taxon Group dialog, type a name for this Group, and select a color. From the Group menu (accessible from the top of the Group column), you can create additional new Groups, edit current Groups, and set Group membership. For the latter, select the taxa you wish to place in the group, and selectSet Group > from the Group menu (the list of groups is shown). Each taxon can only be assigned to a single Group. The taxon names in the Tree Window should be the same color as assigned to the Group. If they are not, you can color them so by selecting, in the Tree Window, Display > Color and Style of Taxon Names > Color by Taxon Group. Alternatively, you can color the background of the taxon text by taxon group by selecting Display > Names > Background Color by Taxon Group. Of course, you'll likely want to turn off Color by Taxon Group, or the names will be the same color as the background, and thus won't be visible! Because taxa can only be assigned membership to one Group, if you would like to draw more than one tree, which differ only in Taxon Name coloration (topology and branch lengths being the same), it would be easiest to draw the tree first with one set of Group memberships, then save the file under a different name, and in the new file, change the Group memberships. This will make it easier to assign different Group memberships without overwriting other desired memberships.

You can make some taxa have larger taxon names (e.g. for the ingroup) by choosing Display>Highlight of Selected Taxa, and selecting one of the enlarging options. Then, if you select taxa, their names will be larger than the unselected taxa.

Step 6: Extras

external image abcTree.GIF

Step 7: Exporting the Tree

When you're satisfied with the tree in the Tree Window, select File > Save Tree as PDF... (you can add the extension ".pdf" when you save the tree. Mesquite will not do this automatically, but applications capable of reading pdf files will still be able to open it without the extension).